-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of FSL automatic digest system
Sent: Tuesday, April 16, 2013 2:10 PM
To: [log in to unmask]
Subject: FSL Digest - 15 Apr 2013 to 16 Apr 2013 - Special issue (#2013-117)
There are 22 messages totaling 10028 lines in this issue.
Topics in this special issue:
1. fslroi
2. about BET (6)
3. What should a ts_dir directory of nets_example.m script making use of
FSLNets contain? (4)
4. fsl_regfilt design
5. Problem Sienax (2)
6. Missing DTI tracts info.
7. Max Voxel Intensity discrepancy (2)
8. First level analysis - stats not completing (2)
9. higher-feat 3 sessions (bl, placebo, treatment), 2 groups
10. Contrast Masking problem
11. registration templates comparison
----------------------------------------------------------------------
Date: Tue, 16 Apr 2013 01:32:35 +0200
From: wolf zinke <[log in to unmask]>
Subject: Re: fslroi
Hi,
fslroi uses voxel, but would not be the right tool for your purpose
anyway, since it changes the image size, cropping it to the defined region.
If you want to create a cubic mask you can use the -roi option of
fslmaths. This option uses voxel coordinates, so you have to adjust the
values according to your voxel dimension.
If you want to create a more sphere-like ROI you can do follow this
description in a recent post:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;6ce4bff3.1301
I hope this helps,
wolf
On 04/16/2013 12:52 AM, Nucleos P wrote:
> Hello Experts -
>
> When using fslroi it is unclear if the x size, y size, and z size
> refer to mm or # of voxels around the coordinates?
>
> For instance, if I wanted to create a mask at ROI 125, 97, 107 MNI 152
> voxel coordinates and then extend to points outside (e.g. 8mm) how
> would I set this up?
>
> Thank you,
> Cat
------------------------------
Date: Tue, 16 Apr 2013 11:34:39 +0800
From: Wei-Ta Chen <[log in to unmask]>
Subject: about BET
Dear FSL experts:
I used BET with the flag -F to strip skulls of my resting-state fMRI
recording. However, there remains some skull layer outside the brain. When
I used BET with the flags -F and -R, the results was much better
without remaining unwanted skull layers.
However, I found the brain extracted skull by the former method (using
single flag -F) looked "brighter" under fslview compared to that extracted
skull by the latter method (using flags -R and -F), although the
voxel-specific intensity value read the same by both methods.
Will this difference influence my later processing of resting-state data?
Any suggestion? Thanks.
Best,
Edward Chen
Taipei Veterans General Hospital
------------------------------
Date: Tue, 16 Apr 2013 04:46:20 +0100
From: Stephen Smith <[log in to unmask]>
Subject: Re: about BET
Hi - no, presumably all that has changed is the auto-setting of the
intensity display range in FSLView - this is fine.
Cheers.
On 16 Apr 2013, at 04:34, Wei-Ta Chen <[log in to unmask]> wrote:
> Dear FSL experts:
>
> I used BET with the flag -F to strip skulls of my resting-state fMRI
recording. However, there remains some skull layer outside the brain. When I
used BET with the flags -F and -R, the results was much better without
remaining unwanted skull layers.
> However, I found the brain extracted skull by the former method (using
single flag -F) looked "brighter" under fslview compared to that extracted
skull by the latter method (using flags -R and -F), although the
voxel-specific intensity value read the same by both methods.
>
> Will this difference influence my later processing of resting-state data?
Any suggestion? Thanks.
>
> Best,
>
> Edward Chen
> Taipei Veterans General Hospital
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
------------------------------
Date: Tue, 16 Apr 2013 05:21:37 +0000
From: "Watson, Christopher" <[log in to unmask]>
Subject: Re: What should a ts_dir directory of nets_example.m script making
use of FSLNets contain?
Well, can you locate the "slices_summary" script?
If you can, then make sure you make it executable; i.e. chmod 755
slices_summary
If you cannot, then you will have to find/download the script, add it to
your path, and make it executable
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
Himanshu Joshi [[log in to unmask]]
Sent: Monday, April 15, 2013 5:45 AM
To: [log in to unmask]
Subject: Re: [FSL] What should a ts_dir directory of nets_example.m script
making use of FSLNets contain?
After using the suggested script, the time-series plot for all components
is plotted mentioning the error
/bin/bash: slices_summary: command not found
Error using imread (line 369)
File "grot.png" does not exist.
Error in nets_pics (line 4)
picgood=imread('grot.png'); figure; imagesc(picgood); axis off; title('good
components');
Error in myfslnets (line 33)
nets_pics(ts,group_maps); % quick views of the good and bad
components
On Mon, Apr 15, 2013 at 12:51 PM, Stephen Smith
<[log in to unmask]<mailto:[log in to unmask]>> wrote:
On 15 Apr 2013, at 08:17, Himanshu Joshi
<[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hello lovely people,
I am using FSLNets for finding correlations among the spatial maps using
nets_examples.m. I had copied it to another file named myfslnets.m, but
while using the script I have a confusion that What should we provide at
ts_dir=GroupICA.dr ?
I am unable to find .dr file in my dual regression output directory.
I had a dual regression output directory containing all subjects time-series
named
dr_stage1_subject00000.txt...dr_stage1_subject0001.txt..........till 20
subjects
I suppose I have to provide the address of this dualregression output
folder like
ts_dir= '/home/mv/Desktop/Test/dualreg_output';
yes
I am not sure about this sign- ' is required or not in the script
Thanking you in anticipation
--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Ph.D Scholar
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore
http://mbial.weebly.com/himanshu-joshi.html
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717) 2176
[log in to unmask]<mailto:[log in to unmask]>
http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore
http://mbial.weebly.com/himanshu-joshi.html
------------------------------
Date: Tue, 16 Apr 2013 11:10:05 +0530
From: Himanshu Joshi <[log in to unmask]>
Subject: Re: What should a ts_dir directory of nets_example.m script making
use of FSLNets contain?
I have FSL 4.1 installed
and $FSLDIR is set as
FSL_DIR /usr/share/fsl/4.1
shall I set it as /usr/share/fsl/4.1/bin
On Mon, Apr 15, 2013 at 4:39 PM, Stephen Smith <[log in to unmask]> wrote:
> This means you either don't have the most recent FSL or $FSLDIR/bin isn't
> in your path.
>
>
>
> On 15 Apr 2013, at 10:45, Himanshu Joshi <[log in to unmask]> wrote:
>
> After using the suggested script, the time-series plot for all
> components is plotted mentioning the error
>
>
>
> /bin/bash: slices_summary: command not found
> Error using imread (line 369)
> File "grot.png" does not exist.
>
> Error in nets_pics (line 4)
> picgood=imread('grot.png'); figure; imagesc(picgood); axis off;
> title('good components');
>
> Error in myfslnets (line 33)
> nets_pics(ts,group_maps); % quick views of the good and bad
> components
>
>
> On Mon, Apr 15, 2013 at 12:51 PM, Stephen Smith
<[log in to unmask]>wrote:
>
>>
>> On 15 Apr 2013, at 08:17, Himanshu Joshi <[log in to unmask]> wrote:
>>
>> Hello lovely people,
>>
>> I am using FSLNets for finding correlations among the spatial maps using
>> nets_examples.m. I had copied it to another file named myfslnets.m, but
>> while using the script I have a confusion that What should we provide at
>> ts_dir=GroupICA.dr ?
>>
>> I am unable to find .dr file in my dual regression output directory.
>>
>> I had a dual regression output directory containing all subjects
>> time-series named
>> dr_stage1_subject00000.txt...dr_stage1_subject0001.txt..........till 20
>> subjects
>>
>> I suppose I have to provide the address of this dualregression output
>> folder like
>> ts_dir= '/home/mv/Desktop/Test/dualreg_output';
>>
>>
>> yes
>>
>> I am not sure about this sign- *'* is required or not in the script
>>
>> Thanking you in anticipation
>>
>> --
>> *Himanshu Joshi*
>> M.Tech. Cognitive & Neuroscience.
>> Ph.D Scholar
>> Senior Research Fellow
>> Department of Psychiatry
>> NIMHANS, Bangalore
>>
>> http://mbial.weebly.com/himanshu-joshi.html
>>
>>
>>
>>
>>
---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717) 2176
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>
>>
---------------------------------------------------------------------------
>>
>>
>>
>>
>
>
> --
> *Himanshu Joshi*
> M.Tech. Cognitive & Neuroscience.
> Senior Research Fellow
> Department of Psychiatry
> NIMHANS, Bangalore
>
> http://mbial.weebly.com/himanshu-joshi.html
>
>
>
>
---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717) 2176
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
---------------------------------------------------------------------------
>
>
>
>
--
*Himanshu Joshi*
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore
http://mbial.weebly.com/himanshu-joshi.html
------------------------------
Date: Tue, 16 Apr 2013 05:42:53 +0000
From: "Watson, Christopher" <[log in to unmask]>
Subject: Re: What should a ts_dir directory of nets_example.m script making
use of FSLNets contain?
Hi Himanshu,
I think the #1 suggestion will be to upgrade to the latest version of FSL,
and then see if you have any problems.
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
Himanshu Joshi [[log in to unmask]]
Sent: Tuesday, April 16, 2013 1:40 AM
To: [log in to unmask]
Subject: Re: [FSL] What should a ts_dir directory of nets_example.m script
making use of FSLNets contain?
I have FSL 4.1 installed
and $FSLDIR is set as
FSL_DIR /usr/share/fsl/4.1
shall I set it as /usr/share/fsl/4.1/bin
On Mon, Apr 15, 2013 at 4:39 PM, Stephen Smith
<[log in to unmask]<mailto:[log in to unmask]>> wrote:
This means you either don't have the most recent FSL or $FSLDIR/bin isn't in
your path.
On 15 Apr 2013, at 10:45, Himanshu Joshi
<[log in to unmask]<mailto:[log in to unmask]>> wrote:
After using the suggested script, the time-series plot for all components
is plotted mentioning the error
/bin/bash: slices_summary: command not found
Error using imread (line 369)
File "grot.png" does not exist.
Error in nets_pics (line 4)
picgood=imread('grot.png'); figure; imagesc(picgood); axis off; title('good
components');
Error in myfslnets (line 33)
nets_pics(ts,group_maps); % quick views of the good and bad
components
On Mon, Apr 15, 2013 at 12:51 PM, Stephen Smith
<[log in to unmask]<mailto:[log in to unmask]>> wrote:
On 15 Apr 2013, at 08:17, Himanshu Joshi
<[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hello lovely people,
I am using FSLNets for finding correlations among the spatial maps using
nets_examples.m. I had copied it to another file named myfslnets.m, but
while using the script I have a confusion that What should we provide at
ts_dir=GroupICA.dr ?
I am unable to find .dr file in my dual regression output directory.
I had a dual regression output directory containing all subjects time-series
named
dr_stage1_subject00000.txt...dr_stage1_subject0001.txt..........till 20
subjects
I suppose I have to provide the address of this dualregression output
folder like
ts_dir= '/home/mv/Desktop/Test/dualreg_output';
yes
I am not sure about this sign- ' is required or not in the script
Thanking you in anticipation
--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Ph.D Scholar
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore
http://mbial.weebly.com/himanshu-joshi.html
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717) 2176
[log in to unmask]<mailto:[log in to unmask]>
http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore
http://mbial.weebly.com/himanshu-joshi.html
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717) 2176
[log in to unmask]<mailto:[log in to unmask]>
http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore
http://mbial.weebly.com/himanshu-joshi.html
------------------------------
Date: Tue, 16 Apr 2013 09:06:07 +0300
From: Helen Sawaya <[log in to unmask]>
Subject: fsl_regfilt design
Dear experts
I am running fsl_regfilt on individual preprocessed functional images to
regress motion spikes and white matter signal. I want to use this output in
group ICA and then dual regression. I was wondering if the design matrix in
fsl_regfilt should include a column of 1s before the columns representing
the confounds and then use -f " " to regress the confounds. (example column
of 1s, column of motion spikes, column of white matter signal, then use -f
"2,3")
1 0 10050.9
1 0 10037.6
1 0 10025.1
1 0 10037.8
1 0 10049
1 1 10051
1 0 10051.4
1 0 10053.7
I created a design without the column of ones and had a great deal of white
matter signal in my melodic components so I'm wondering if I did not
properly regress out the white matter signal from the filtered functional
image.
Thank you!!!
Helen
------------------------------
Date: Tue, 16 Apr 2013 11:52:32 +0200
From: Patricia Pires <[log in to unmask]>
Subject: Problem Sienax
Dear all,
I wrote this a few days ago, unfortunately I still have not solved the
problem. Any help would be appreciated.
Yours sincerely,
Patricia
---------- Forwarded message ----------
From: SUBSCRIBE FSL Patricia Pires <[log in to unmask]>
Date: 2013/4/12
Subject: [FSL] Sienax
To: [log in to unmask]
Dear FSLexperts,
i am using Sienax for a cross-sectional volume comparison (GM and WM)
between two groups.
I am using crop T13D NIfTI images and run sienax:
sienax co_image.nii -B "-f 0.22" -d
I've noticed that some images are well segmented or it is easy to modify
them just moving "-f" option, however other images are very bad segmented
because it was used a quite strange image. I attach both examples,
respectively.
How is it possible if i proceed equally for all the analyses?
Any help would be very appreciated.
------------------------------
Date: Tue, 16 Apr 2013 11:03:54 +0100
From: Saad Jbabdi <[log in to unmask]>
Subject: Re: Missing DTI tracts info.
Hi
The best way to troubleshoot the subjects where tractography has failed is
to relax the prior constraints (i.e. no exclusion/inclusion masks) and look
at the results of the tractography to see why you don't get those
connections.
Cheers
Saad
On 15 Apr 2013, at 18:57, Erica Tatham wrote:
> Hey Saad,
>
> Thanks for the quick reply. I agree I havn't given you much information.
> But because the script that I am using is so long, I'm not sure where
things may have gone wrong. I have been checking the data along the way- but
I'll definitaly have to comb through it again.
> I put this post up to get some feedback on common errors that happen to
others that may result in missing data. Do you have any further suggestions
on common error prone sections of the analysis? Having a few starting points
may assist me in combing through my data.
> Just to give you more info on my seeds/target. I am using a surface map
produced by freesurfer to define the different gray/white matter regions.
The tracts are based on connections between these gray/white matter regions.
Do you believe that my lack of directions would affect the efficiency of
this type of analysis?
>
> thanks again
>
>
> On Sat, Apr 13, 2013 at 8:56 AM, Saad Jbabdi <[log in to unmask]> wrote:
> Hi Erica
>
> I am afraid it is difficult for us to diagnose your problem given the
information that you gave us.
>
> I am assuming that you are running tractography in a bunch of subjects
using some sort of automated script. And for each pathway, the script uses
different sets of inclusion/exclusion masks to isolate the pathway. Right?
And you are saying that tractography fails to recover some pathways for some
subjects (i.e. the corresponding fdt_paths is zero). In this case, you are
going to have to examine those cases individually to figure out what has
happened.
> For example, the bvecs may be wrong for a subset of your subjects. Or the
inclusion/exclusion masks may not be appropriate for those
subjects/pathways, etc. etc.
>
> Hope this helps a bit
> Saad
>
>
>
> On 12 Apr 2013, at 21:17, Erica Tatham wrote:
>
>> Hi FSL experts.
>>
>> I have run my tractography analysis on the majority of my participants
and I noticed that I am missing DTI data (FA, RD, MD) for many of my
participant's tracts or I am only getting DTI information for ~40% of the
tracts (note: the tracts with DTI information are not consistent across all
participants).
>>
>> I have maintained the standard protocol for all analysis and was
wondering if anyone had any insight into why I may be loosing data. I think
the problem is that the tracts are not being located, and therefore DTI
information can not be calculated for those tracts. Does anyone have any
suggestions on the most standard way to change my analysis so that I obtain
more information - or should I just work with that I have?
>>
>> Below is some info on my analysis......
>>
>> I have 12 directions in my data
>>
>> The tracts I am looking at:
>> Superior Longitudinal Fasciculus
>> Inferior Longitudinal Fasciculus
>> Cingulum Bundle
>> Cortico-spinal tract
>> Inferior Frontal-occipital fasciculus
>> Uncinate Fasciculus
>>
>> Thank you, thank you, thank you for any help :)
>> I really appreciate that there is a wonderful forum like this, and
hopefully when I know enough about FSL I can help other people out.
>>
>> Cheers
>> Erica
>>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Erica Tatham, B.Sc
> M.Sc. Candidate
> McMaster Integrative Neuroscience Discovery & Study
> McMaster University
> 1280 Main St W., Hamilton On
> Email: [log in to unmask]
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
------------------------------
Date: Tue, 16 Apr 2013 12:12:58 +0100
From: Stephen Smith <[log in to unmask]>
Subject: Re: Problem Sienax
Hi - the SIENA/X web-page reporting gives you images showing the various
stages of the processing - you need to look carefully through this to find
out at what stage the registration has not worked. To increase the
robustness of such analyses it is always wise/safe to make sure the input
data is oriented as with the MNI152, and also potentially use fslroi to
remove large amounts of unnecessary neck slices.
Steve.
On 16 Apr 2013, at 10:52, Patricia Pires <[log in to unmask]> wrote:
> Dear all,
>
> I wrote this a few days ago, unfortunately I still have not solved the
problem. Any help would be appreciated.
>
> Yours sincerely,
>
> Patricia
>
>
> ---------- Forwarded message ----------
> From: SUBSCRIBE FSL Patricia Pires <[log in to unmask]>
> Date: 2013/4/12
> Subject: [FSL] Sienax
> To: [log in to unmask]
>
>
> Dear FSLexperts,
>
> i am using Sienax for a cross-sectional volume comparison (GM and WM)
between two groups.
> I am using crop T13D NIfTI images and run sienax:
>
> sienax co_image.nii -B "-f 0.22" -d
>
> I've noticed that some images are well segmented or it is easy to modify
them just moving "-f" option, however other images are very bad segmented
because it was used a quite strange image. I attach both examples,
respectively.
>
> How is it possible if i proceed equally for all the analyses?
>
> Any help would be very appreciated.
>
>
> <I2std.png><I2std.png>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717) 2176
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
------------------------------
Date: Tue, 16 Apr 2013 17:17:52 +0530
From: Himanshu Joshi <[log in to unmask]>
Subject: Re: What should a ts_dir directory of nets_example.m script making
use of FSLNets contain?
I will consider your sugesstion and upgrade my fsl to 5.0
but for the time being I had downloaded the slices_summary script and made
it executable
now error 1 regarding slices_summary is not there now the problem is
Cannot open
/home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC.sum/0000.png for
reading
Segmentation fault (core dumped)
slices_summary
/home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC.sum grot.png 0
1 2 3 4 5 6 8 10 13 14 16 17: Segmentation fault
Error using imread (line 369)
File "grot.png" does not exist.
Error in nets_pics (line 4)
picgood=imread('grot.png'); figure; imagesc(picgood); axis off; title('good
components');
Error in myfslnets (line 33)
nets_pics(ts,group_maps);
I am providing group_maps as
group_maps='/home/mv/Desktop/Test/all.gica/groupmelodic.ica/melodic_IC
yes there is no such file exists like melodic_IC.sum/ 0000.png
I dont know I suppose myfslnets.m will create this
any comments
On Tue, Apr 16, 2013 at 11:12 AM, Watson, Christopher <
[log in to unmask]> wrote:
> Hi Himanshu,
> I think the #1 suggestion will be to upgrade to the latest version of FSL,
> and then see if you have any problems.
>
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
> Himanshu Joshi [[log in to unmask]]
> Sent: Tuesday, April 16, 2013 1:40 AM
> To: [log in to unmask]
> Subject: Re: [FSL] What should a ts_dir directory of nets_example.m script
> making use of FSLNets contain?
>
> I have FSL 4.1 installed
> and $FSLDIR is set as
> FSL_DIR /usr/share/fsl/4.1
>
> shall I set it as /usr/share/fsl/4.1/bin
>
>
>
> On Mon, Apr 15, 2013 at 4:39 PM, Stephen Smith <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
> This means you either don't have the most recent FSL or $FSLDIR/bin isn't
> in your path.
>
>
>
> On 15 Apr 2013, at 10:45, Himanshu Joshi <[log in to unmask]<mailto:
> [log in to unmask]>> wrote:
>
> After using the suggested script, the time-series plot for all
> components is plotted mentioning the error
>
>
>
> /bin/bash: slices_summary: command not found
> Error using imread (line 369)
> File "grot.png" does not exist.
>
> Error in nets_pics (line 4)
> picgood=imread('grot.png'); figure; imagesc(picgood); axis off;
> title('good components');
>
> Error in myfslnets (line 33)
> nets_pics(ts,group_maps); % quick views of the good and bad
> components
>
>
> On Mon, Apr 15, 2013 at 12:51 PM, Stephen Smith <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> On 15 Apr 2013, at 08:17, Himanshu Joshi <[log in to unmask]<mailto:
> [log in to unmask]>> wrote:
>
> Hello lovely people,
>
> I am using FSLNets for finding correlations among the spatial maps using
> nets_examples.m. I had copied it to another file named myfslnets.m, but
> while using the script I have a confusion that What should we provide at
> ts_dir=GroupICA.dr ?
>
> I am unable to find .dr file in my dual regression output directory.
>
> I had a dual regression output directory containing all subjects
> time-series named
> dr_stage1_subject00000.txt...dr_stage1_subject0001.txt..........till 20
> subjects
>
> I suppose I have to provide the address of this dualregression output
> folder like
> ts_dir= '/home/mv/Desktop/Test/dualreg_output';
>
> yes
>
> I am not sure about this sign- ' is required or not in the script
>
> Thanking you in anticipation
>
> --
> Himanshu Joshi
> M.Tech. Cognitive & Neuroscience.
> Ph.D Scholar
> Senior Research Fellow
> Department of Psychiatry
> NIMHANS, Bangalore
>
> http://mbial.weebly.com/himanshu-joshi.html
>
>
>
---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717) 2176
> [log in to unmask]<mailto:[log in to unmask]>
> http://www.fmrib.ox.ac.uk/~steve
>
---------------------------------------------------------------------------
>
>
>
>
>
>
> --
> Himanshu Joshi
> M.Tech. Cognitive & Neuroscience.
> Senior Research Fellow
> Department of Psychiatry
> NIMHANS, Bangalore
>
> http://mbial.weebly.com/himanshu-joshi.html
>
>
>
---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717) 2176
> [log in to unmask]<mailto:[log in to unmask]>
> http://www.fmrib.ox.ac.uk/~steve
>
---------------------------------------------------------------------------
>
>
>
>
>
>
> --
> Himanshu Joshi
> M.Tech. Cognitive & Neuroscience.
> Senior Research Fellow
> Department of Psychiatry
> NIMHANS, Bangalore
>
> http://mbial.weebly.com/himanshu-joshi.html
>
--
*Himanshu Joshi*
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore
http://mbial.weebly.com/himanshu-joshi.html
------------------------------
Date: Tue, 16 Apr 2013 14:40:02 +0100
From: William Pettersson-Yeo <[log in to unmask]>
Subject: Max Voxel Intensity discrepancy
Dear FSL experts,
I have an image in which i'm trying to find the voxels with the minimum, and
maximum, signal intensities respectively.
The command, 'fslstats input_file -R' shows the min/max intensities in the
image to be -0.0181 and 0.0178.
However, the same image set at a 70% threshold of these minimum/maximum
values (i.e. only showing the either the top, or bottom, 30% of voxel
intensities) is completely blank.
Furthermore, the coordinates of the maximum voxel returned by the command
'fslstats input_image -x', refer to a voxel of intensity 0.0076.
Lastly, using the 'cluster' command, no voxels of any value are found when
the threshold (-t) is set to 0.01205 and above. This also corresponds with a
manual search through the image, combined with gradually increasing the
lower threshold until no voxels are visible.
If anyone could help me understand the discrepancy between the outputs of
the different commands, it would be much appreciated. Should I simply use
the maximum/minimum signal intensity suggested by the cluster command?
Many thanks,
William
------------------------------
Date: Tue, 16 Apr 2013 22:18:10 +0800
From: Wei-Ta Chen <[log in to unmask]>
Subject: Re: about BET
Dear Stephen:
One more question. After skull stripping by BET, I usually extract the 7th
volume of my resting-state recordings (200 time points in total) by fslroi
for further linear and nonlinear registration. However, using both flags
(-R and -F) of BET, I cannot extract one specific volume by fslroi.
Previously I used only -F flag of BET and fslroi worked. Why?
It seemed "bet <input data> -F -R" yielded a "concatenated" single volume
rather than a time series with separate volumes, as I checked the BET
results by fslview. Should I use the flag -f instead and find tune the f
value to get the best BET results (for the sake of fslroi use) ?
Best,
Edward
2013/4/16 Stephen Smith <[log in to unmask]>
> Hi - no, presumably all that has changed is the auto-setting of the
> intensity display range in FSLView - this is fine.
> Cheers.
>
>
> On 16 Apr 2013, at 04:34, Wei-Ta Chen <[log in to unmask]> wrote:
>
> Dear FSL experts:
>
> I used BET with the flag -F to strip skulls of my resting-state fMRI
> recording. However, there remains some skull layer outside the brain. When
> I used BET with the flags -F and -R, the results was much better
> without remaining unwanted skull layers.
> However, I found the brain extracted skull by the former method (using
> single flag -F) looked "brighter" under fslview compared to that extracted
> skull by the latter method (using flags -R and -F), although the
> voxel-specific intensity value read the same by both methods.
>
> Will this difference influence my later processing of resting-state data?
> Any suggestion? Thanks.
>
> Best,
>
> Edward Chen
> Taipei Veterans General Hospital
>
>
>
>
---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
---------------------------------------------------------------------------
>
>
>
>
------------------------------
Date: Tue, 16 Apr 2013 14:24:13 +0000
From: Mark Jenkinson <[log in to unmask]>
Subject: Re: Max Voxel Intensity discrepancy
Hi,
This sounds very odd and not anything like I've seen before.
Is your image a 3D or a 4D image.
I can imagine that with a 4D image you could get strange things apparently
happening if you did not look at all timepoints.
If you still cannot figure out what is going on, please upload the image to:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
All the best,
Mark
On 16 Apr 2013, at 14:40, William Pettersson-Yeo
<[log in to unmask]> wrote:
> Dear FSL experts,
>
> I have an image in which i'm trying to find the voxels with the minimum,
and maximum, signal intensities respectively.
>
> The command, 'fslstats input_file -R' shows the min/max intensities in the
image to be -0.0181 and 0.0178.
>
> However, the same image set at a 70% threshold of these minimum/maximum
values (i.e. only showing the either the top, or bottom, 30% of voxel
intensities) is completely blank.
>
> Furthermore, the coordinates of the maximum voxel returned by the command
'fslstats input_image -x', refer to a voxel of intensity 0.0076.
>
> Lastly, using the 'cluster' command, no voxels of any value are found when
the threshold (-t) is set to 0.01205 and above. This also corresponds with a
manual search through the image, combined with gradually increasing the
lower threshold until no voxels are visible.
>
> If anyone could help me understand the discrepancy between the outputs of
the different commands, it would be much appreciated. Should I simply use
the maximum/minimum signal intensity suggested by the cluster command?
>
> Many thanks,
> William
------------------------------
Date: Tue, 16 Apr 2013 15:25:01 +0100
From: Stephen Smith <[log in to unmask]>
Subject: Re: about BET
Hi - get a 3D bet brain mask that you like and then mask the 4D data with it
using fslmaths
fslmaths my4d -mas my3d_bet_mask my4d_masked
Steve.
On 16 Apr 2013, at 15:18, Wei-Ta Chen <[log in to unmask]> wrote:
> Dear Stephen:
>
> One more question. After skull stripping by BET, I usually extract the 7th
volume of my resting-state recordings (200 time points in total) by fslroi
for further linear and nonlinear registration. However, using both flags (-R
and -F) of BET, I cannot extract one specific volume by fslroi. Previously I
used only -F flag of BET and fslroi worked. Why?
>
> It seemed "bet <input data> -F -R" yielded a "concatenated" single volume
rather than a time series with separate volumes, as I checked the BET
results by fslview. Should I use the flag -f instead and find tune the f
value to get the best BET results (for the sake of fslroi use) ?
>
> Best,
>
> Edward
>
>
>
>
>
> 2013/4/16 Stephen Smith <[log in to unmask]>
> Hi - no, presumably all that has changed is the auto-setting of the
intensity display range in FSLView - this is fine.
> Cheers.
>
>
> On 16 Apr 2013, at 04:34, Wei-Ta Chen <[log in to unmask]> wrote:
>
>> Dear FSL experts:
>>
>> I used BET with the flag -F to strip skulls of my resting-state fMRI
recording. However, there remains some skull layer outside the brain. When I
used BET with the flags -F and -R, the results was much better without
remaining unwanted skull layers.
>> However, I found the brain extracted skull by the former method (using
single flag -F) looked "brighter" under fslview compared to that extracted
skull by the latter method (using flags -R and -F), although the
voxel-specific intensity value read the same by both methods.
>>
>> Will this difference influence my later processing of resting-state data?
Any suggestion? Thanks.
>>
>> Best,
>>
>> Edward Chen
>> Taipei Veterans General Hospital
>
>
>
---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
---------------------------------------------------------------------------
>
>
>
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
------------------------------
Date: Wed, 17 Apr 2013 00:16:37 +0800
From: Wei-Ta Chen <[log in to unmask]>
Subject: Re: about BET
Dear Stephen:
Let me confirm. If the BET results with -R option is good for me, do you
mean to add an extra flag -m to transform the BET result into a mask which
can be used further to mask my 4D data?
Great thanks to your time.
Best,
Wei-Ta
2013/4/16 Stephen Smith <[log in to unmask]>
> Hi - get a 3D bet brain mask that you like and then mask the 4D data with
> it using fslmaths
> fslmaths my4d -mas my3d_bet_mask my4d_masked
> Steve.
>
>
>
> On 16 Apr 2013, at 15:18, Wei-Ta Chen <[log in to unmask]> wrote:
>
> Dear Stephen:
>
> One more question. After skull stripping by BET, I usually extract the 7th
> volume of my resting-state recordings (200 time points in total) by fslroi
> for further linear and nonlinear registration. However, using both flags
> (-R and -F) of BET, I cannot extract one specific volume by fslroi.
> Previously I used only -F flag of BET and fslroi worked. Why?
>
> It seemed "bet <input data> -F -R" yielded a "concatenated" single volume
> rather than a time series with separate volumes, as I checked the BET
> results by fslview. Should I use the flag -f instead and find tune the f
> value to get the best BET results (for the sake of fslroi use) ?
>
> Best,
>
> Edward
>
>
>
>
>
> 2013/4/16 Stephen Smith <[log in to unmask]>
>
>> Hi - no, presumably all that has changed is the auto-setting of the
>> intensity display range in FSLView - this is fine.
>> Cheers.
>>
>>
>> On 16 Apr 2013, at 04:34, Wei-Ta Chen <[log in to unmask]> wrote:
>>
>> Dear FSL experts:
>>
>> I used BET with the flag -F to strip skulls of my resting-state fMRI
>> recording. However, there remains some skull layer outside the brain.
When
>> I used BET with the flags -F and -R, the results was much better
>> without remaining unwanted skull layers.
>> However, I found the brain extracted skull by the former method (using
>> single flag -F) looked "brighter" under fslview compared to that
extracted
>> skull by the latter method (using flags -R and -F), although the
>> voxel-specific intensity value read the same by both methods.
>>
>> Will this difference influence my later processing of resting-state data?
>> Any suggestion? Thanks.
>>
>> Best,
>>
>> Edward Chen
>> Taipei Veterans General Hospital
>>
>>
>>
>>
>>
---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>
>>
---------------------------------------------------------------------------
>>
>>
>>
>>
>
>
>
---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
---------------------------------------------------------------------------
>
>
>
>
------------------------------
Date: Tue, 16 Apr 2013 16:35:45 +0000
From: Mark Jenkinson <[log in to unmask]>
Subject: Re: First level analysis - stats not completing
Dear Mary,
It is hard to know exactly what went wrong from just this info. Can you send
the whole contents of your log file?
All the best,
Mark
Mary Elizabeth Sutherland <[log in to unmask]> wrote:
Dear Jake,
The log file seems to show that the initialisation, prestats, stats, and
registration run (the last lines are in the registration:
/usr/local/fsl/bin/imcp ../example_func ../example_func_distorted
/usr/local/fsl/bin/imcp example_func ../example_func
However, in the stats directory in the output I only have
Corrections.nii.gz
dof
logfile
pe1.nii.gz
pe2.nii.gz
res4d.nii.gz
sigmasquareds.nii.gz
smoothness
threshac1.nii.gz
Thank you so much for your help!
~ mary
------------------------------
Date: Tue, 16 Apr 2013 16:49:22 +0000
From: Mark Jenkinson <[log in to unmask]>
Subject: Re: higher-feat 3 sessions (bl, placebo, treatment), 2 groups
Dear Thomas,
The answer here is simple - just do the triple t-test as this is already
accounting for any offset within each individual subject and so the age and
sex covariates are completely redundant (since these are fixed values for
each subject).
If you want to look at differences between groups then just have separate
versions of EV1 and EV2 for each group and then construct the appropriate
differences in the contrasts.
All the best,
Mark
"Goldschmidt, Thomas" <[log in to unmask]> wrote:
Dear fsl-experts,
I have some questions regarding the higher-feat analysis of an experiment
(n-back-task) with 3 different sessions (BL, placebo, treatment) and two
groups (15patients, 10HC). I am interested if there is a treatment effect on
brain activation during task performance in patients and/or controls. Thus,
I want to know if there is a difference in brain activation after treatment
(compared to baseline) and if this differs to placebo. Later, I would also
be interested in a difference between patients and controls.
Based on the Feat-practical and earlier questions in this list: I made up
the following design:
1. Individual Feat-analysis (activation during n1n2n3>n0)
2. 2nd-level Feat: Mixed Effect analysis (Flame 1 with automated outlier
de-weighting)
Matrix (here only 5patients and 5 HC for the sake of simplicity):
Group
BL
placebo
treatment
demeaned age
demeaned sex
1
1
0
0
-9.62
0.41
1
1
0
0
2.12
0.41
1
1
0
0
6.74
0.41
1
1
0
0
-22.75
0.41
1
1
0
0
14.84
-0.59
2
1
0
0
2.24
0.41
2
1
0
0
2.91
-0.59
2
1
0
0
-2.38
0.41
2
1
0
0
-1.91
-0.59
2
1
0
0
-2.01
0.41
1
0
1
0
-9.62
0.41
1
0
1
0
2.12
0.41
1
0
1
0
6.74
0.41
1
0
1
0
-22.75
0.41
1
0
1
0
14.84
-0.59
2
0
1
0
2.24
0.41
2
0
1
0
2.91
-0.59
2
0
1
0
-2.38
0.41
2
0
1
0
-1.91
-0.59
2
0
1
0
-2.01
0.41
1
0
0
1
-9.62
0.41
1
0
0
1
2.12
0.41
1
0
0
1
6.74
0.41
1
0
0
1
-22.75
0.41
1
0
0
1
14.84
-0.59
2
0
0
1
2.24
0.41
2
0
0
1
2.91
-0.59
2
0
0
1
-2.38
0.41
2
0
0
1
-1.91
-0.59
2
0
0
1
-2.01
0.41
Contrasts:
EV1
EV2
EV3
EV4
EV5
BL:
1
0
0
0
0
Placebo:
0
1
0
0
0
Treatment:
0
0
1
0
0
This matrix doesn't work because of the different groups (what would I need
to change?). It does work however, if I do the analysis separately for
patients and controls.
3. 3rd level feat (mixed effect, flame1 without outlier de-weighting) with
the 3 3D copes from the 2nd level, done as a triple t-test
Matrix (only for patients)
group
EV1
EV2
1
1
1
1
-1
0
1
0
-1
Contrasts:
EV1
EV2
placebo - baseline
-2
-1
treatment - baseline
-1
-2
treatment - placebo
1
-1
placebo - treatment
-1
1
QUESTION: Is this design ok or should I try to incorporate 2nd and 3rd level
feat in one higher-feat-analysis such as in a triple t-test (mixed effect,
flame1 with outlier de-weighting):
This matrix only works without the EVs for age and sex (otherways it states
that at least 1 EV is (close to) a linear combination of the others).
EV1
EV2
EV3
...
...
..
...
age
sex
1
1
1
0
0
0
0
-2.435
0.41
1
1
0
1
0
0
0
-1.965
-0.59
1
1
0
0
1
0
0
2.065
0.41
1
1
0
0
0
1
0
-2.775
-0.59
1
1
0
0
0
0
1
-9.67039
0.41
-1
0
1
0
0
0
0
-2.435
0.41
-1
0
0
1
0
0
0
-1.965
-0.59
-1
0
0
0
1
0
0
2.065
0.41
-1
0
0
0
0
1
0
-2.775
-0.59
-1
0
0
0
0
0
1
-9.67039
0.41
0
-1
1
0
0
0
0
-2.435
0.41
0
-1
0
1
0
0
0
-1.965
-0.59
0
-1
0
0
1
0
0
2.065
0.41
0
-1
0
0
0
1
0
-2.775
-0.59
0
-1
0
0
0
0
1
-9.67039
0.41
With contrasts:
EV1
EV2
...
...
...
...
...
...
...
placebo - baseline
-2
-1
0
0
0
0
0
0
0
treatment - baseline
-1
-2
0
0
0
0
0
0
0
treatment - placebo
1
-1
0
0
0
0
0
0
0
placebo - treatment
-1
1
0
0
0
0
0
0
0
Which design is better (and did I choose the right higher level-modelling?)
and in case it's the first (multi-level) how could I incorporate the
different groups and in case it's the second (only two levels) how could I
incorporate different groups and add age and sex as EVs?
I would be very pleased to get some help with these questions!
Best,
Thomas
------------------------------
Date: Tue, 16 Apr 2013 17:56:51 +0100
From: Gail Musen <[log in to unmask]>
Subject: Re: Contrast Masking problem
Hi Matthew,
I have tarred and uploaded the example directories. Thanks so much.
Best,
Musen Lab
------------------------------
Date: Tue, 16 Apr 2013 18:13:46 +0100
From: Rali Dimitrova <[log in to unmask]>
Subject: registration templates comparison
Hi
Apologies for this question in advance but what is the best way to compare
the registration quality (or to quantify the degree of deformation applied
to the FA maps) to standard space obtained using two different registration
templates? Could the FA_to_target.* files be used to compute or extract the
amount of warping required for each target across the FA data ?
Thank you.
Best wishes,
Rali
------------------------------
Date: Tue, 16 Apr 2013 18:28:05 +0100
From: Stephen Smith <[log in to unmask]>
Subject: Re: about BET
Yes
On 16 Apr 2013, at 17:16, Wei-Ta Chen <[log in to unmask]> wrote:
> Dear Stephen:
>
> Let me confirm. If the BET results with -R option is good for me, do you
mean to add an extra flag -m to transform the BET result into a mask which
can be used further to mask my 4D data?
>
> Great thanks to your time.
>
> Best,
>
> Wei-Ta
>
>
> 2013/4/16 Stephen Smith <[log in to unmask]>
> Hi - get a 3D bet brain mask that you like and then mask the 4D data with
it using fslmaths
> fslmaths my4d -mas my3d_bet_mask my4d_masked
> Steve.
>
>
>
> On 16 Apr 2013, at 15:18, Wei-Ta Chen <[log in to unmask]> wrote:
>
>> Dear Stephen:
>>
>> One more question. After skull stripping by BET, I usually extract the
7th volume of my resting-state recordings (200 time points in total) by
fslroi for further linear and nonlinear registration. However, using both
flags (-R and -F) of BET, I cannot extract one specific volume by fslroi.
Previously I used only -F flag of BET and fslroi worked. Why?
>>
>> It seemed "bet <input data> -F -R" yielded a "concatenated" single volume
rather than a time series with separate volumes, as I checked the BET
results by fslview. Should I use the flag -f instead and find tune the f
value to get the best BET results (for the sake of fslroi use) ?
>>
>> Best,
>>
>> Edward
>>
>>
>>
>>
>>
>> 2013/4/16 Stephen Smith <[log in to unmask]>
>> Hi - no, presumably all that has changed is the auto-setting of the
intensity display range in FSLView - this is fine.
>> Cheers.
>>
>>
>> On 16 Apr 2013, at 04:34, Wei-Ta Chen <[log in to unmask]> wrote:
>>
>>> Dear FSL experts:
>>>
>>> I used BET with the flag -F to strip skulls of my resting-state fMRI
recording. However, there remains some skull layer outside the brain. When I
used BET with the flags -F and -R, the results was much better without
remaining unwanted skull layers.
>>> However, I found the brain extracted skull by the former method (using
single flag -F) looked "brighter" under fslview compared to that extracted
skull by the latter method (using flags -R and -F), although the
voxel-specific intensity value read the same by both methods.
>>>
>>> Will this difference influence my later processing of resting-state
data? Any suggestion? Thanks.
>>>
>>> Best,
>>>
>>> Edward Chen
>>> Taipei Veterans General Hospital
>>
>>
>>
---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>
---------------------------------------------------------------------------
>>
>>
>>
>>
>
>
>
---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
---------------------------------------------------------------------------
>
>
>
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
------------------------------
Date: Tue, 16 Apr 2013 15:00:09 -0300
From: Mary Elizabeth Sutherland <[log in to unmask]>
Subject: Re: First level analysis - stats not completing
Dear Mark,
Thank you! I have copied and pasted the logfile into this email. Let me know
if you need any additional information!
~ mary e.
Progress Report / Log
Started at Fri Apr 12 19:58:26 ART 2013
Feat main script
/bin/cp /tmp/feat_FtJgqd.fsf design.fsf
/usr/local/fsl/bin/feat_model design
mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;ln -s
/usr/local/fsl/doc/images .files/images
/usr/local/fsl/bin/fsl_sub -T 10 -l logs -N feat0_init
/usr/local/fsl/bin/feat
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/design.fsf -D
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat -I 1 -init
26585
/usr/local/fsl/bin/fsl_sub -T 60 -l logs -N feat1b_reg -j 26585
/usr/local/fsl/bin/feat
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/design.fsf -D
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat -I 1 -reg
26657
/usr/local/fsl/bin/fsl_sub -T 12 -l logs -N feat2_pre -j 26657,26585
/usr/local/fsl/bin/feat
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/design.fsf -D
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat -I 1 -prestats
29608
/usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat3_film -j 29608
/usr/local/fsl/bin/feat
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/design.fsf -D
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat -I 1 -film
30211
/usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 29608,30211,26657
/usr/local/fsl/bin/feat
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/design.fsf -D
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat -stop
/usr/local/fsl/bin/mainfeatreg -d
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat -l
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/logs/feat5_reg -R
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/report_unwarp.html -r
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/report_reg.html -i
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/example_func.nii.gz -n 10 -h
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_anat_brain -w BBR -x 90 -s
/Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm_brain -y
12 -z 90 -a
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/fi
eldmap -b
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/ma
g1_brain -e 30.0 -f 10 -g 0.58 -p y- -w BBR
Option -d ( output directory ) selected with argument
"/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/S
ubject01_run1_trial_types+.feat"
Option -l ( logfile )input with argument
"/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/S
ubject01_run1_trial_types+.feat/logs/feat5_reg"
Option -R ( html unwarping report ) selected with argument
"/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/S
ubject01_run1_trial_types+.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument
"/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/S
ubject01_run1_trial_types+.feat/report_reg.html"
Option -i ( main input ) input with argument
"/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/S
ubject01_run1_trial_types+.feat/example_func.nii.gz"
Option -n ( use nonlinear reg ) input with argument "10"
Option -h ( high-res structural image ) selected with argument
"/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/S
ubject01_anat_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument
"/Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm_brain"
Option -y ( standard dof ) selected with argument "12"
Option -z ( standard search ) selected with argument "90"
Option -a ( fieldmap image ) selected with argument
"/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/f
ieldmap"
Option -b ( field ) selected with argument
"/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/m
ag1_brain"
Option -e ( echo time ) selected with argument "30.0"
Option -f ( signal loss Threshold ) selected with argument "10"
Option -g ( echo spacing ) selected with argument "0.58"
Option -p ( phase encoding direction ) selected with argument "y-"
Option -w ( highres dof ) selected with argument "BBR"
whirlgif Rev 3.04 (c) 1997-1999 by Hans Dinsen-Hansen
(c) 1995-1996 by Kevin Kadow
(c) 1990-1993 by Mark Podlipec
Processed 2 files.
Initialisation
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/20
121106_08201300060001t2starepi2Dstandard12ch1441213s006a001
prefiltered_func_data -odt float
Total original volumes = 38
/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 19 1
Prestats
/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out
prefiltered_func_data_mcf -mats -plots -reffile reg/unwarp/EF_D_example_func
-rmsrel -rmsabs
/bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat
prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms
prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms
prefiltered_func_data_mcf_rel_mean.rms mc
/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT
estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h
144 -o rot.png
/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT
estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h
144 -o trans.png
/usr/local/fsl/bin/fsl_tsplot -i
prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t
'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a
absolute,relative -o disp.png
/usr/local/fsl/bin/applywarp -i reg/unwarp/FM_UD_fmap_mag_brain_mask -r
example_func --abs --premat=reg/unwarp/FM_UD_fmap_mag_brain2str.mat
--postmat=reg/highres2example_func.mat -o
reg/unwarp/EF_UD_fmap_mag_brain_mask
/usr/local/fsl/bin/fslsplit prefiltered_func_data grot
/usr/local/fsl/bin/applywarp -i grot0000 -o grot0000
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0000 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0001 -o grot0001
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0001 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0002 -o grot0002
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0002 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0003 -o grot0003
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0003 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0004 -o grot0004
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0004 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0005 -o grot0005
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0005 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0006 -o grot0006
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0006 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0007 -o grot0007
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0007 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0008 -o grot0008
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0008 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0009 -o grot0009
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0009 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0010 -o grot0010
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0010 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0011 -o grot0011
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0011 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0012 -o grot0012
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0012 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0013 -o grot0013
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0013 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0014 -o grot0014
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0014 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0015 -o grot0015
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0015 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0016 -o grot0016
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0016 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0017 -o grot0017
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0017 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0018 -o grot0018
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0018 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0019 -o grot0019
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0019 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0020 -o grot0020
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0020 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0021 -o grot0021
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0021 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0022 -o grot0022
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0022 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0023 -o grot0023
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0023 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0024 -o grot0024
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0024 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0025 -o grot0025
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0025 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0026 -o grot0026
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0026 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0027 -o grot0027
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0027 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0028 -o grot0028
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0028 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0029 -o grot0029
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0029 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0030 -o grot0030
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0030 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0031 -o grot0031
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0031 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0032 -o grot0032
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0032 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0033 -o grot0033
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0033 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0034 -o grot0034
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0034 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0035 -o grot0035
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0035 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0036 -o grot0036
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0036 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/applywarp -i grot0037 -o grot0037
--premat=mc/prefiltered_func_data_mcf.mat/MAT_0037 -w
reg/example_func2highres_warp.nii.gz -r example_func --abs
--postmat=reg/highres2example_func.mat
/usr/local/fsl/bin/fslmerge -t prefiltered_func_data_unwarp grot0000
grot0001 grot0002 grot0003 grot0004 grot0005 grot0006 grot0007
grot0008 grot0009 grot0010 grot0011 grot0012 grot0013 grot0014
grot0015 grot0016 grot0017 grot0018 grot0019 grot0020 grot0021
grot0022 grot0023 grot0024 grot0025 grot0026 grot0027 grot0028
grot0029 grot0030 grot0031 grot0032 grot0033 grot0034 grot0035
grot0036 grot0037
/bin/rm -f grot*
/usr/local/fsl/bin/slicetimer -i prefiltered_func_data_unwarp
--out=prefiltered_func_data_st -r 11.5000000000 --odd
/usr/local/fsl/bin/fslmaths prefiltered_func_data_st -Tmean mean_func
/usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv
mask_mask mask
/usr/local/fsl/bin/fslmaths prefiltered_func_data_st -mas mask
prefiltered_func_data_bet
/usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 1794.082764
/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 179.4082764 -Tmin
-bin mask -odt char
/usr/local/fsl/bin/fslstats prefiltered_func_data_st -k mask -p 50
1169.191895
/usr/local/fsl/bin/fslmaths mask -dilF mask
/usr/local/fsl/bin/fslmaths prefiltered_func_data_st -mas mask
prefiltered_func_data_thresh
/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
/usr/local/fsl/bin/susan prefiltered_func_data_thresh 876.89392125
3.39702760085 3 1 1 mean_func 876.89392125 prefiltered_func_data_smooth
/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask
prefiltered_func_data_smooth
/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 8.55291594371
prefiltered_func_data_intnorm
/usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf
5.21739130435 -1 prefiltered_func_data_tempfilt
/usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt
filtered_func_data
/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func
/bin/rm -rf prefiltered_func_data*
Stats
mkdir -p custom_timing_files ; /bin/cp
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/EventFiles/S
ameTempo/Subject1_run1_DiffCorrect.txt custom_timing_files/ev1.txt
mkdir -p custom_timing_files ; /bin/cp
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/EventFiles/S
ameTempo/Subject1_run1_SameCorrect.txt custom_timing_files/ev2.txt
paste -d ' '
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/logfiles/Sub
ject01fonc1incorrect.dat > confoundevs.txt
/usr/local/fsl/bin/feat_model design confoundevs.txt
/usr/local/fsl/bin/film_gls -rn stats -sa -ms 5 filtered_func_data
design.mat 1000.0
Log directory is: stats
paradigm.getDesignMatrix().Nrows()=38
paradigm.getDesignMatrix().Ncols()=3
sizeTS=38
numTS=54842
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
mode = 10074.2
sig = 1820
Spatially smoothing auto corr estimates
.....
Completed
Tukey M = 6
Tukey estimates... Completed
Completed
Prewhitening and Computing PEs...
Percentage done:
1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,2
9,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54
,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,
80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
Saving results...
Completed
/usr/local/fsl/bin/smoothest -d 35 -m mask -r stats/res4d >
stats/smoothness
Registration
/bin/mkdir -p
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_run1_trial_types+.feat/reg
/usr/local/fsl/bin/fslmaths ../example_func EF_D_example_func
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/fi
eldmap FM_UD_fmap
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/ma
g1_brain FM_UD_fmap_mag
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/ma
g1_brain FM_UD_fmap_mag_brain
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/ma
g1 FM_UD_fmap_mag
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -V | awk '{ print $1 }'
38663
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -v | awk '{ print $1 }'
122880
0.31464
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -bin
FM_UD_fmap_mag_brain_mask -odt short
/usr/local/fsl/bin/fslmaths FM_UD_fmap -abs -bin -mas
FM_UD_fmap_mag_brain_mask -mul -1 -add 1 -bin FM_UD_fmap_mag_brain_mask_inv
/usr/local/fsl/bin/cluster -i FM_UD_fmap_mag_brain_mask_inv -t 0.5
--no_table -o FM_UD_fmap_mag_brain_mask_idx
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain_mask_idx -R | awk '{ print
$2 }'
79.000000
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask_idx -thr 79.000000
-bin -mul -1 -add 1 -bin -mas FM_UD_fmap_mag_brain_mask
FM_UD_fmap_mag_brain_mask
/usr/local/fsl/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
-6.238736
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -6.238736 -mas
FM_UD_fmap_mag_brain_mask FM_UD_fmap
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -P 98
1651.000000
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -thr 825.5 -bin
FM_UD_fmap_mag_brain_mask50
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero
FM_UD_fmap_mag_brain_mask_ero
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask_ero -add
FM_UD_fmap_mag_brain_mask50 -thr 0.5 -bin FM_UD_fmap_mag_brain_mask
/usr/local/fsl/bin/fslmaths FM_UD_fmap -mas FM_UD_fmap_mag_brain_mask
FM_UD_fmap
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -mas
FM_UD_fmap_mag_brain_mask FM_UD_fmap_mag_brain
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero
FM_UD_fmap_mag_brain_mask_ero
/usr/local/fsl/bin/fugue --loadfmap=FM_UD_fmap
--savefmap=FM_UD_fmap_tmp_fmapfilt --mask=FM_UD_fmap_mag_brain_mask
--despike --despikethreshold=2.1
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub FM_UD_fmap_tmp_fmapfilt -mas
FM_UD_fmap_mag_brain_mask_ero -add FM_UD_fmap_tmp_fmapfilt FM_UD_fmap
/bin/rm -f FM_UD_fmap_tmp_fmapfilt* FM_UD_fmap_mag_brain_mask_ero*
FM_UD_fmap_mag_brain_mask50* FM_UD_fmap_mag_brain_i*
/usr/local/fsl/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
1.871621
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub 1.871621 -mas
FM_UD_fmap_mag_brain_mask FM_UD_fmap
/usr/local/fsl/bin/fslstats FM_UD_fmap -R | awk '{ print $1 }'
-1267.710815
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -1267.710815 -add 10 -mas
FM_UD_fmap_mag_brain_mask grot
/usr/local/fsl/bin/fslstats grot -l 1 -p 0.1 -p 95
603.927368 1470.487793
/usr/local/fsl/bin/overlay 0 0 FM_UD_fmap_mag -a grot 603.927368 1470.487793
fmap+mag
/usr/local/fsl/bin/slicer fmap+mag -s 3 -x 0.35 sla.png -x 0.45 slb.png -x
0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png
-y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65
sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png
+ sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png +
sll.png fmap+mag.png; rm sl?.png
/usr/local/fsl/bin/sigloss -i FM_UD_fmap --te=0.03 -m
FM_UD_fmap_mag_brain_mask -s FM_UD_fmap_sigloss
/usr/local/fsl/bin/fslmaths FM_UD_fmap_sigloss -mul FM_UD_fmap_mag_brain
FM_UD_fmap_mag_brain_siglossed -odt float
/usr/local/fsl/bin/fslmaths FM_UD_fmap_sigloss -thr 0.9 FM_UD_fmap_sigloss
-odt float
/usr/local/fsl/bin/overlay 1 0 FM_UD_fmap_mag_brain -a FM_UD_fmap_sigloss 0
1 FM_UD_sigloss+mag
/usr/local/fsl/bin/slicer FM_UD_sigloss+mag -s 3 -x 0.35 sla.png -x 0.45
slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y
0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png
-z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png +
sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png +
slk.png + sll.png FM_UD_sigloss+mag.png; rm sl?.png
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_anat_brain highres
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Su
bject01_anat highres_head
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm_brain
standard
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm
standard_head
/usr/local/fsl/bin/fslmaths
/Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm_brain_mask
_dil standard_mask
did not find file: example_func2highres.mat. Generating transform.
/usr/local/fsl/bin/epi_reg --epi=example_func --t1=highres_head
--t1brain=highres --out=example_func2highres --fmap=unwarp/FM_UD_fmap
--fmapmag=unwarp/FM_UD_fmap_mag --fmapmagbrain=unwarp/FM_UD_fmap_mag_brain
--echospacing=0.00058 --pedir=y-
Running FAST segmentation FLIRT pre-alignment Registering fieldmap to
structural Running BBR with fieldmap 0.343783 0.998858 0.042228 -0.022346
0.000000 -0.041668 0.998820 0.024966 0.000000 0.023374 -0.024006 0.999438
0.000000 -0.347484 0.804341 2.909863 1.000000 Making warp fields and
applying registration to EPI series
mv example_func2highres_fieldmap2str.mat unwarp/FM_UD_fmap_mag_brain2str.mat
mv example_func2highres_fieldmaprads2epi.mat unwarp/FM_UD_fmap2epi.mat
/usr/local/fsl/bin/immv example_func2highres_fieldmaprads2epi_shift
unwarp/FM_UD_fmap2epi_shift
/usr/local/fsl/bin/immv example_func2highres_fieldmap2str
unwarp/FM_UD_fmap_mag_brain2str
/usr/local/fsl/bin/fslstats FM_UD_fmap2epi_shift -R -P 1 -P 99
-6.134327 7.225882 -1.369861 2.736245
/usr/local/fsl/bin/flirt -ref ../example_func -in FM_UD_fmap_mag_brain
-applyxfm -init FM_UD_fmap2epi.mat -out EF_UD_fmap_mag_brain
/usr/local/fsl/bin/fslmaths FM_UD_fmap2epi_shift -mul -1 grot
/usr/local/fsl/bin/overlay 1 0 EF_UD_fmap_mag_brain -a FM_UD_fmap2epi_shift
0.0001 2.736245 grot 0.0001 1.36986 EF_UD_shift+mag
/usr/local/fsl/bin/slicer EF_UD_shift+mag -s 3 -x 0.35 sla.png -x 0.45
slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y
0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png
-z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png +
sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png +
slk.png + sll.png EF_UD_shift+mag.png; rm sl?.png
/bin/cp /usr/local/fsl/etc/luts/ramp.gif .ramp.gif
/bin/cp /usr/local/fsl/etc/luts/ramp2.gif .ramp2.gif
overlay 0 0 FM_UD_fmap_mag_brain2str -a ../example_func2highres_fast_wmedge
0.001 5 fieldmap2edges
/usr/local/fsl/bin/slicer fieldmap2edges -s 3 -x 0.35 sla.png -x 0.45
slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y
0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png
-z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png +
sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png +
slk.png + sll.png fieldmap2edges.png; rm sl?.png
/usr/local/fsl/bin/slicer FM_UD_fmap_mag_brain2str ../highres -s 2 -x 0.35
sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y
0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png
-z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png FM_UD_fmap_mag_brain2str1.png ;
/usr/local/fsl/bin/slicer ../highres FM_UD_fmap_mag_brain2str -s 2 -x 0.35
sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y
0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png
-z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png FM_UD_fmap_mag_brain2str2.png ;
/usr/local/fsl/bin/pngappend FM_UD_fmap_mag_brain2str1.png -
FM_UD_fmap_mag_brain2str2.png FM_UD_fmap_mag_brain2str.png; /bin/rm -f
sl?.png FM_UD_fmap_mag_brain2str2.png
/bin/rm FM_UD_fmap_mag_brain2str1.png
/usr/local/fsl/bin/flirt -ref ../highres -in ../example_func -out
example_func_distorted2highres -applyxfm -init ../example_func2highres.mat
-interp trilinear
/usr/local/fsl/bin/slicer example_func_distorted2highres ../highres -s 2 -x
0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png
-y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45
slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend
sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png +
slh.png + sli.png + slj.png + slk.png + sll.png
example_func_distorted2highres1.png ; /usr/local/fsl/bin/slicer ../highres
example_func_distorted2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55
slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y
0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png
; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png +
sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png +
sll.png example_func_distorted2highres2.png ; /usr/local/fsl/bin/pngappend
example_func_distorted2highres1.png - example_func_distorted2highres2.png
example_func_distorted2highres.png; /bin/rm -f sl?.png
example_func_distorted2highres2.png
/bin/rm example_func_distorted2highres1.png
/usr/local/fsl/bin/slicer ../example_func2highres ../highres -s 2 -x 0.35
sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y
0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png
-z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png ../example_func2highres1.png ;
/usr/local/fsl/bin/slicer ../highres ../example_func2highres -s 2 -x 0.35
sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y
0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png
-z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png ../example_func2highres2.png ;
/usr/local/fsl/bin/pngappend ../example_func2highres1.png -
../example_func2highres2.png ../example_func2highres.png; /bin/rm -f sl?.png
../example_func2highres2.png
/bin/rm ../example_func2highres1.png
/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat
../example_func2highres.mat
/usr/local/fsl/bin/applywarp -i ../example_func2highres -r ../example_func
--premat=highres2example_func.mat -o example_func_undistorted
/usr/local/fsl/bin/overlay 0 0 example_func_distorted2highres -a
../example_func2highres_fast_wmedge 0.001 10 grot
/usr/local/fsl/bin/slicer grot -s 3 -x 0.35 sla.png -x 0.45 slb.png -x
0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png
-y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65
sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png
+ sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png +
sll.png EF_D_edges.gif
/usr/local/fsl/bin/overlay 0 0 ../example_func2highres -a
../example_func2highres_fast_wmedge 0.001 10 grot
/usr/local/fsl/bin/slicer grot -s 3 -x 0.35 sla.png -x 0.45 slb.png -x
0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png
-y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65
sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png
+ sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png +
sll.png EF_U_edges.gif
/usr/local/fsl/bin/whirlgif -o EF_UD_movie.gif -time 50 -loop 0
EF_D_edges.gif EF_U_edges.gif; /bin/rm -f sla* slb* slc* sld* sle* slf* slg*
slh* sli* slj* slk* sll* grot*
/usr/local/fsl/bin/imcp example_func_undistorted ../example_func
/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat
example_func2highres.mat
/usr/local/fsl/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png
-x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45
slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z
0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png example_func2highres1.png ;
/usr/local/fsl/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png
-x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45
slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z
0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png example_func2highres2.png ;
/usr/local/fsl/bin/pngappend example_func2highres1.png -
example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png
example_func2highres2.png
/bin/rm example_func2highres1.png
did not find file: highres2standard.mat. Generating transform.
/usr/local/fsl/bin/flirt -in highres -ref standard -out highres2standard
-omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry
-90 90 -searchrz -90 90 -interp trilinear
/usr/local/fsl/bin/fnirt --iout=highres2standard_head --in=highres_head
--aff=highres2standard.mat --cout=highres2standard_warp
--iout=highres2standard --jout=highres2highres_jac --config=T1_2_MNI152_2mm
--ref=standard_head --refmask=standard_mask --warpres=10,10,10
/usr/local/fsl/bin/applywarp -i highres -r standard -o highres2standard -w
highres2standard_warp
/usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat
highres2standard.mat
/usr/local/fsl/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x
0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png
-y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55
slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png +
slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png +
slj.png + slk.png + sll.png highres2standard1.png ;
/usr/local/fsl/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x
0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png
-y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55
slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png +
slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png +
slj.png + slk.png + sll.png highres2standard2.png ;
/usr/local/fsl/bin/pngappend highres2standard1.png - highres2standard2.png
highres2standard.png; /bin/rm -f sl?.png highres2standard2.png
/bin/rm highres2standard1.png
/usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat
highres2standard.mat example_func2highres.mat
/usr/local/fsl/bin/convertwarp --ref=standard
--premat=example_func2highres.mat --warp1=highres2standard_warp
--out=example_func2standard_warp
/usr/local/fsl/bin/applywarp --ref=standard --in=example_func
--out=example_func2standard --warp=example_func2standard_warp
/usr/local/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat
example_func2standard.mat
/usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35
sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y
0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png
-z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png example_func2standard1.png ;
/usr/local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35
sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y
0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png
-z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png +
slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png +
sli.png + slj.png + slk.png + sll.png example_func2standard2.png ;
/usr/local/fsl/bin/pngappend example_func2standard1.png -
example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png
example_func2standard2.png
/usr/local/fsl/bin/imcp ../example_func ../example_func_distorted
/usr/local/fsl/bin/imcp example_func ../example_func
On Apr 16, 2013, at 1:35 PM, Mark Jenkinson wrote:
> Dear Mary,
>
> It is hard to know exactly what went wrong from just this info. Can you
send the whole contents of your log file?
>
> All the best,
> Mark
>
>
> Mary Elizabeth Sutherland <[log in to unmask]> wrote:
>
>
> Dear Jake,
>
> The log file seems to show that the initialisation, prestats, stats, and
registration run (the last lines are in the registration:
/usr/local/fsl/bin/imcp ../example_func ../example_func_distorted
> /usr/local/fsl/bin/imcp example_func ../example_func
> However, in the stats directory in the output I only have
> Corrections.nii.gz
> dof
> logfile
> pe1.nii.gz
> pe2.nii.gz
> res4d.nii.gz
> sigmasquareds.nii.gz
> smoothness
> threshac1.nii.gz
>
> Thank you so much for your help!
>
> ~ mary
------------------------------
End of FSL Digest - 15 Apr 2013 to 16 Apr 2013 - Special issue (#2013-117)
**************************************************************************
|
