-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of FSL automatic digest system
Sent: 17 September 2015 17:23
To: [log in to unmask]
Subject: FSL Digest - 16 Sep 2015 to 17 Sep 2015 - Special issue (#2015-82)
There are 24 messages totaling 10303 lines in this issue.
Topics in this special issue:
1. tbss_2_reg -T error (2)
2. FIRST: Questions in source code modification
3. 3 x 2 x 3 within subject design
4. cluster volume per subject
5. Fwd: [FSL] 3D rendering shape analysis (8)
6. Longitudinal analyses with/without subject specific regressors
7. bet error
8. EDDY parallelization
9. eddy_correct via matlab
10. Parallelising bedpost (2)
11. plotting brain activation
12. Cost Measure Flirt
13. FEAT GLM design question
14. FSL on OS X 10.11 El Capitan (2)
----------------------------------------------------------------------
Date: Thu, 17 Sep 2015 10:41:49 +0800
From: 邓凤 <[log in to unmask]>
Subject: tbss_2_reg -T error
hello,
when I run tbss_2_reg -T,there is an error
task file (.commands) does not exist
$/fsl/bin/fsl_sub:332:exit:illegal number: -1
what can i do to solve this p
------------------------------
Date: Thu, 17 Sep 2015 10:52:54 +0800
From: 邓凤 <[log in to unmask]>
Subject: tbss_2_reg -T error
hello,
when I run tbss_2_reg -T,there is an error
task file (.commands) does not exist
$/fsl/bin/fsl_sub:332:exit:illegal number: -1
when I run the same commanline in another computer,there is an another error:
wc: .commands: No such file or directory
32340
what can i do
------------------------------
Date: Thu, 17 Sep 2015 07:22:08 +0100
From: Ryana Fok <[log in to unmask]>
Subject: FIRST: Questions in source code modification
Dear Experts,
I would like to conduct a project using FIRST, we would like to modify FIRST source code to suit our project aim.
However, I have no idea on where to find the source code of FIRST. I am using FSLvm on Windows, and installed FSL using the FSL installer. In the FSLvm, I checked the inside of /Computer/Filesystem/ , but don't know where I can access the source code. I had perform "run_first_all" for a few times, and I am sure the FSL is in the FSLvm, but I am not sure about the location of source file. May I ask anyone who know where to access the source code and modify it?
Besides, I downloaded an "Uncompiled sources" from the download page, which I found there is /first/ and /firstlib/ inside the src directory. Are these two /first/ & /firstlib/ the source code of FIRST? Does it mean I need to compile this "Uncompiled sources" in Ubuntu, or in Windows?
Also, will there be any guidelines to modifying the source code? And how to build it after modification of the code?
I am new to Linux system and virtual machine settings, if I have any thing wrong, please help clarify me. Thank you for any advice in advance.
Thank you very much!
Best Regards,
Ryana
------------------------------
Date: Thu, 17 Sep 2015 08:07:27 +0000
From: "Thijssen, S." <[log in to unmask]>
Subject: Re: 3 x 2 x 3 within subject design
Hi Anderson,
Thank you for your reply. In a lower level feat analysis, I think I would create EVs for all conditions (A1B1, A2B1, A1B2, A2B2, A1B3, A2B3). I would additionally create contrasts for A1-A2, B1-B3, B2-B3, B1-B2, B2-B1 and all A*B interactions (A*B1-B3, A*B2-B3 etc.). I have attached an image of the model.
For all three sessions (hormone A, B and placebo), I would feed the cope images of contrast 7 until 15 in a higher level analysis, comparing the effect of the different hormones and creating F-tests for variable A, B, hormones H1 to H3 and for the interactions (see attached image). I haven't written out all EVs for all hormones, but instead focused on one the effect of hormone 1 (H1) vs. placebo (H3).
I am not sure if I am going about this correctly, as I think this model looks pretty messy. We would be interested in controlling for the effects of other non-investigational hormones and dietary factors that would differ per visit (i.e. per hormone) but not per condition. Would it be possible to add such variables to the model as well? There would be a lot of identical values in the model.
Perhaps it would be wise to drop one of the experimental conditions of B1 (e.g. B2) to make the model a bit more comprehensible.
Thank you for you help!
Kind regads,
Sandra
________________________________
Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Anderson M. Winkler [[log in to unmask]]
Verzonden: vrijdag 11 september 2015 9:44
Aan: [log in to unmask]<mailto:[log in to unmask]>
Onderwerp: Re: [FSL] 3 x 2 x 3 within subject design
Hi Sandra,
With purely within-subject effects and interactions, yes, it should be possible. If you want to assemble a draft of the design now for your hypotheses, before even beginning the data collection, it'd be better as if there is a problem you can make changes now as needed.
All the best,
Anderson
On 10 September 2015 at 10:08, Thijssen, S. <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear experts,
We're planning to set up an fMRI study on the effects of several hormones on behavior. The study will be a within-subject study, with all participants receiving 2 hormones and a placebo in three visits. Our paradigm consists of two variables, say A and B. Variable A has two levels (experimental and control), and variable B has three levels (2 experimental and 1 control). This results in a total of 6 different conditions (A1-B1, A2-B1, A1-B2, A2-B2, A1-B3, A2-B3). Would it be possible to assess a 3 (hormonal, different runs) x 2 (variable A) x 3 (variable B) within-subject ANOVA using FEAT, or would you suggest simplifying our design?
Thank you very much for your help.
Kind regards,
Sandra Thijssen
------------------------------
Date: Thu, 17 Sep 2015 11:31:10 +0200
From: Maria Serra <[log in to unmask]>
Subject: cluster volume per subject
Dear FSL users,
I would like to know weather it is possible to obtain the volume of a given
cluster for every subject, instead of the whole structure (fslstats
*01_bet_brain_all_none_firstseg* -l 16.5 -u 17.5 -V ).
Thank you,
--
Maria Serra Blasco
------------------------------
Date: Thu, 17 Sep 2015 11:56:45 +0200
From: Niels Bergsland <[log in to unmask]>
Subject: Re: Fwd: [FSL] 3D rendering shape analysis
Hi - if you can make the mask and corrp image available, I can try to
take a look.
On Wed, Sep 16, 2015 at 11:42 AM, Maria Serra <[log in to unmask]> wrote:
> Hi,
>
> please find attached a screenshot of my 3D rendering.
>
> Also, the output of the fslstats corrp_fstat1_output_randomise -R coomand is
> the following:
>
> 0.000000 0.985800
>
> And finally, I just realized that when I run the first3Dview, it comes up
> with this error:
>
> 80
> ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkDecimatePro.cxx, line 163
> vtkDecimatePro (0x482b6c80): No data to decimate!
>
> ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkSmoothPolyDataFilter.cxx, line
> 211
> vtkSmoothPolyDataFilter (0x3f4ac400): No data to smooth!
>
> which is probably related with my problem.
>
> Hope this information helps.
>
> Maria
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
[log in to unmask]
------------------------------
Date: Thu, 17 Sep 2015 12:14:46 +0200
From: Maria Serra <[log in to unmask]>
Subject: Re: Fwd: [FSL] 3D rendering shape analysis
Hi Niels,
please find attached the mask and corrp image.
Thank you!
On Thu, Sep 17, 2015 at 11:56 AM, Niels Bergsland <[log in to unmask]>
wrote:
> Hi - if you can make the mask and corrp image available, I can try to
> take a look.
>
> On Wed, Sep 16, 2015 at 11:42 AM, Maria Serra <[log in to unmask]>
> wrote:
> > Hi,
> >
> > please find attached a screenshot of my 3D rendering.
> >
> > Also, the output of the fslstats corrp_fstat1_output_randomise -R
> coomand is
> > the following:
> >
> > 0.000000 0.985800
> >
> > And finally, I just realized that when I run the first3Dview, it comes up
> > with this error:
> >
> > 80
> > ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkDecimatePro.cxx, line 163
> > vtkDecimatePro (0x482b6c80): No data to decimate!
> >
> > ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkSmoothPolyDataFilter.cxx,
> line
> > 211
> > vtkSmoothPolyDataFilter (0x3f4ac400): No data to smooth!
> >
> > which is probably related with my problem.
> >
> > Hope this information helps.
> >
> > Maria
>
>
>
> --
> Niels Bergsland
> Integration Director
> Buffalo Neuroimaging Analysis Center
> 100 High St. Buffalo NY 14203
> [log in to unmask]
>
--
Maria
P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
fer-ho.
------------------------------
Date: Thu, 17 Sep 2015 12:43:13 +0200
From: Niels Bergsland <[log in to unmask]>
Subject: Re: Fwd: [FSL] 3D rendering shape analysis
Hi Maria,
I am not having any trouble created it (see attached). I don't think
there have been major changes to the first3Dview script (the most
recent one is in fact from 2012), but can you try downloading the
script again (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide?action=AttachFile&do=view&target=first3Dview.zip)
and redoing the process?
On Thu, Sep 17, 2015 at 12:14 PM, Maria Serra <[log in to unmask]> wrote:
> Hi Niels,
>
> please find attached the mask and corrp image.
>
> Thank you!
>
> On Thu, Sep 17, 2015 at 11:56 AM, Niels Bergsland <[log in to unmask]>
> wrote:
>>
>> Hi - if you can make the mask and corrp image available, I can try to
>> take a look.
>>
>> On Wed, Sep 16, 2015 at 11:42 AM, Maria Serra <[log in to unmask]>
>> wrote:
>> > Hi,
>> >
>> > please find attached a screenshot of my 3D rendering.
>> >
>> > Also, the output of the fslstats corrp_fstat1_output_randomise -R
>> > coomand is
>> > the following:
>> >
>> > 0.000000 0.985800
>> >
>> > And finally, I just realized that when I run the first3Dview, it comes
>> > up
>> > with this error:
>> >
>> > 80
>> > ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkDecimatePro.cxx, line 163
>> > vtkDecimatePro (0x482b6c80): No data to decimate!
>> >
>> > ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkSmoothPolyDataFilter.cxx,
>> > line
>> > 211
>> > vtkSmoothPolyDataFilter (0x3f4ac400): No data to smooth!
>> >
>> > which is probably related with my problem.
>> >
>> > Hope this information helps.
>> >
>> > Maria
>>
>>
>>
>> --
>> Niels Bergsland
>> Integration Director
>> Buffalo Neuroimaging Analysis Center
>> 100 High St. Buffalo NY 14203
>> [log in to unmask]
>
>
>
>
> --
> Maria
>
>
> P Abans d'imprimir aquest correu electrònic pensa bé si és necessari fer-ho.
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
[log in to unmask]
------------------------------
Date: Thu, 17 Sep 2015 13:11:13 +0200
From: Maria Serra <[log in to unmask]>
Subject: Re: Fwd: [FSL] 3D rendering shape analysis
Niels,
I've tried to download the script again but it still does not work.
When I run the script the images open correctly, but when I open the 3D
view, this error comes out:
[image: Inline image 1]
I just realized that, although I am using the FSL version 5.0.8, the FSL
view is using the version 4.0.1. Maybe the problem rely on this fact? If
so, how could I fix it? I downloaded the whole package and FSL opens FSL
view with this old version by default.
Many thanks again
On Thu, Sep 17, 2015 at 12:43 PM, Niels Bergsland <[log in to unmask]>
wrote:
> Hi Maria,
> I am not having any trouble created it (see attached). I don't think
> there have been major changes to the first3Dview script (the most
> recent one is in fact from 2012), but can you try downloading the
> script again (
> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide?action=AttachFile&do=view&target=first3Dview.zip
> )
> and redoing the process?
>
>
>
> On Thu, Sep 17, 2015 at 12:14 PM, Maria Serra <[log in to unmask]>
> wrote:
> > Hi Niels,
> >
> > please find attached the mask and corrp image.
> >
> > Thank you!
> >
> > On Thu, Sep 17, 2015 at 11:56 AM, Niels Bergsland <[log in to unmask]>
> > wrote:
> >>
> >> Hi - if you can make the mask and corrp image available, I can try to
> >> take a look.
> >>
> >> On Wed, Sep 16, 2015 at 11:42 AM, Maria Serra <
> [log in to unmask]>
> >> wrote:
> >> > Hi,
> >> >
> >> > please find attached a screenshot of my 3D rendering.
> >> >
> >> > Also, the output of the fslstats corrp_fstat1_output_randomise -R
> >> > coomand is
> >> > the following:
> >> >
> >> > 0.000000 0.985800
> >> >
> >> > And finally, I just realized that when I run the first3Dview, it comes
> >> > up
> >> > with this error:
> >> >
> >> > 80
> >> > ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkDecimatePro.cxx, line
> 163
> >> > vtkDecimatePro (0x482b6c80): No data to decimate!
> >> >
> >> > ERROR: In
> /build/buildd/vtk-5.8.0/Graphics/vtkSmoothPolyDataFilter.cxx,
> >> > line
> >> > 211
> >> > vtkSmoothPolyDataFilter (0x3f4ac400): No data to smooth!
> >> >
> >> > which is probably related with my problem.
> >> >
> >> > Hope this information helps.
> >> >
> >> > Maria
> >>
> >>
> >>
> >> --
> >> Niels Bergsland
> >> Integration Director
> >> Buffalo Neuroimaging Analysis Center
> >> 100 High St. Buffalo NY 14203
> >> [log in to unmask]
> >
> >
> >
> >
> > --
> > Maria
> >
> >
> > P Abans d'imprimir aquest correu electrònic pensa bé si és necessari
> fer-ho.
>
>
>
> --
> Niels Bergsland
> Integration Director
> Buffalo Neuroimaging Analysis Center
> 100 High St. Buffalo NY 14203
> [log in to unmask]
>
--
Maria
P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
fer-ho.
------------------------------
Date: Thu, 17 Sep 2015 13:45:54 +0200
From: Niels Bergsland <[log in to unmask]>
Subject: Re: Fwd: [FSL] 3D rendering shape analysis
Hi,
I'm pretty sure the latest fslview version is 4.0.1. That's what I am using
at least, so it shouldn't be related to that.
I have been able to reproduce your problem though - are you perhaps not
following the instructions as given in the wiki? Only the basestruct image
should be set to mask/label. If set the corrp image to mask/label as well,
it won't display the significant areas. This should be set to "Statistic"
(which is the default for me for this image).
On Thu, Sep 17, 2015 at 1:11 PM, Maria Serra <[log in to unmask]>
wrote:
> Niels,
>
> I've tried to download the script again but it still does not work.
>
> When I run the script the images open correctly, but when I open the 3D
> view, this error comes out:
>
> [image: Inline image 1]
>
> I just realized that, although I am using the FSL version 5.0.8, the FSL
> view is using the version 4.0.1. Maybe the problem rely on this fact? If
> so, how could I fix it? I downloaded the whole package and FSL opens FSL
> view with this old version by default.
>
> Many thanks again
>
> On Thu, Sep 17, 2015 at 12:43 PM, Niels Bergsland <[log in to unmask]>
> wrote:
>
>> Hi Maria,
>> I am not having any trouble created it (see attached). I don't think
>> there have been major changes to the first3Dview script (the most
>> recent one is in fact from 2012), but can you try downloading the
>> script again (
>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide?action=AttachFile&do=view&target=first3Dview.zip
>> )
>> and redoing the process?
>>
>>
>>
>> On Thu, Sep 17, 2015 at 12:14 PM, Maria Serra <[log in to unmask]>
>> wrote:
>> > Hi Niels,
>> >
>> > please find attached the mask and corrp image.
>> >
>> > Thank you!
>> >
>> > On Thu, Sep 17, 2015 at 11:56 AM, Niels Bergsland <[log in to unmask]
>> >
>> > wrote:
>> >>
>> >> Hi - if you can make the mask and corrp image available, I can try to
>> >> take a look.
>> >>
>> >> On Wed, Sep 16, 2015 at 11:42 AM, Maria Serra <
>> [log in to unmask]>
>> >> wrote:
>> >> > Hi,
>> >> >
>> >> > please find attached a screenshot of my 3D rendering.
>> >> >
>> >> > Also, the output of the fslstats corrp_fstat1_output_randomise -R
>> >> > coomand is
>> >> > the following:
>> >> >
>> >> > 0.000000 0.985800
>> >> >
>> >> > And finally, I just realized that when I run the first3Dview, it
>> comes
>> >> > up
>> >> > with this error:
>> >> >
>> >> > 80
>> >> > ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkDecimatePro.cxx, line
>> 163
>> >> > vtkDecimatePro (0x482b6c80): No data to decimate!
>> >> >
>> >> > ERROR: In
>> /build/buildd/vtk-5.8.0/Graphics/vtkSmoothPolyDataFilter.cxx,
>> >> > line
>> >> > 211
>> >> > vtkSmoothPolyDataFilter (0x3f4ac400): No data to smooth!
>> >> >
>> >> > which is probably related with my problem.
>> >> >
>> >> > Hope this information helps.
>> >> >
>> >> > Maria
>> >>
>> >>
>> >>
>> >> --
>> >> Niels Bergsland
>> >> Integration Director
>> >> Buffalo Neuroimaging Analysis Center
>> >> 100 High St. Buffalo NY 14203
>> >> [log in to unmask]
>> >
>> >
>> >
>> >
>> > --
>> > Maria
>> >
>> >
>> > P Abans d'imprimir aquest correu electrònic pensa bé si és necessari
>> fer-ho.
>>
>>
>>
>> --
>> Niels Bergsland
>> Integration Director
>> Buffalo Neuroimaging Analysis Center
>> 100 High St. Buffalo NY 14203
>> [log in to unmask]
>>
>
>
>
> --
> Maria
>
>
> P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
> fer-ho.
>
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
[log in to unmask]
------------------------------
Date: Thu, 17 Sep 2015 12:59:33 +0100
From: SUBSCRIBE FSL Jay <[log in to unmask]>
Subject: Longitudinal analyses with/without subject specific regressors
Hello Anderson,
I wanted to know your opinion to understand the design for longitudinal analyses (paired two-sample t-test) mentioned at (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Randomise/UserGuide#Two-Sample_Paired_T-test_.28Paired_Two-Group_Difference.29)
Can you please tell me the role of the subject specific regressors (used to model the individual subject means)? What would be the difference if i did not model for the individual subject means and still use the design.grp file to pair them?
BW
Jay
------------------------------
Date: Thu, 17 Sep 2015 14:03:59 +0200
From: Maria Serra <[log in to unmask]>
Subject: Re: Fwd: [FSL] 3D rendering shape analysis
Hi,
I have followed and double checked the instructions of the wiki in detail.
The parameters you referred were set the same way as yours... so really do
not know what could be wrong.
Thank you for the efforts
On Thu, Sep 17, 2015 at 1:45 PM, Niels Bergsland <[log in to unmask]>
wrote:
> Hi,
> I'm pretty sure the latest fslview version is 4.0.1. That's what I am
> using at least, so it shouldn't be related to that.
>
> I have been able to reproduce your problem though - are you perhaps not
> following the instructions as given in the wiki? Only the basestruct image
> should be set to mask/label. If set the corrp image to mask/label as well,
> it won't display the significant areas. This should be set to "Statistic"
> (which is the default for me for this image).
>
>
>
> On Thu, Sep 17, 2015 at 1:11 PM, Maria Serra <[log in to unmask]>
> wrote:
>
>> Niels,
>>
>> I've tried to download the script again but it still does not work.
>>
>> When I run the script the images open correctly, but when I open the 3D
>> view, this error comes out:
>>
>> [image: Inline image 1]
>>
>> I just realized that, although I am using the FSL version 5.0.8, the FSL
>> view is using the version 4.0.1. Maybe the problem rely on this fact? If
>> so, how could I fix it? I downloaded the whole package and FSL opens FSL
>> view with this old version by default.
>>
>> Many thanks again
>>
>> On Thu, Sep 17, 2015 at 12:43 PM, Niels Bergsland <[log in to unmask]>
>> wrote:
>>
>>> Hi Maria,
>>> I am not having any trouble created it (see attached). I don't think
>>> there have been major changes to the first3Dview script (the most
>>> recent one is in fact from 2012), but can you try downloading the
>>> script again (
>>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide?action=AttachFile&do=view&target=first3Dview.zip
>>> )
>>> and redoing the process?
>>>
>>>
>>>
>>> On Thu, Sep 17, 2015 at 12:14 PM, Maria Serra <[log in to unmask]>
>>> wrote:
>>> > Hi Niels,
>>> >
>>> > please find attached the mask and corrp image.
>>> >
>>> > Thank you!
>>> >
>>> > On Thu, Sep 17, 2015 at 11:56 AM, Niels Bergsland <
>>> [log in to unmask]>
>>> > wrote:
>>> >>
>>> >> Hi - if you can make the mask and corrp image available, I can try to
>>> >> take a look.
>>> >>
>>> >> On Wed, Sep 16, 2015 at 11:42 AM, Maria Serra <
>>> [log in to unmask]>
>>> >> wrote:
>>> >> > Hi,
>>> >> >
>>> >> > please find attached a screenshot of my 3D rendering.
>>> >> >
>>> >> > Also, the output of the fslstats corrp_fstat1_output_randomise -R
>>> >> > coomand is
>>> >> > the following:
>>> >> >
>>> >> > 0.000000 0.985800
>>> >> >
>>> >> > And finally, I just realized that when I run the first3Dview, it
>>> comes
>>> >> > up
>>> >> > with this error:
>>> >> >
>>> >> > 80
>>> >> > ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkDecimatePro.cxx, line
>>> 163
>>> >> > vtkDecimatePro (0x482b6c80): No data to decimate!
>>> >> >
>>> >> > ERROR: In
>>> /build/buildd/vtk-5.8.0/Graphics/vtkSmoothPolyDataFilter.cxx,
>>> >> > line
>>> >> > 211
>>> >> > vtkSmoothPolyDataFilter (0x3f4ac400): No data to smooth!
>>> >> >
>>> >> > which is probably related with my problem.
>>> >> >
>>> >> > Hope this information helps.
>>> >> >
>>> >> > Maria
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> Niels Bergsland
>>> >> Integration Director
>>> >> Buffalo Neuroimaging Analysis Center
>>> >> 100 High St. Buffalo NY 14203
>>> >> [log in to unmask]
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > Maria
>>> >
>>> >
>>> > P Abans d'imprimir aquest correu electrònic pensa bé si és necessari
>>> fer-ho.
>>>
>>>
>>>
>>> --
>>> Niels Bergsland
>>> Integration Director
>>> Buffalo Neuroimaging Analysis Center
>>> 100 High St. Buffalo NY 14203
>>> [log in to unmask]
>>>
>>
>>
>>
>> --
>> Maria
>>
>>
>> P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
>> fer-ho.
>>
>
>
>
> --
> Niels Bergsland
> Integration Director
> Buffalo Neuroimaging Analysis Center
> 100 High St. Buffalo NY 14203
> [log in to unmask]
>
--
Maria Serra Blasco
Institut d'Investigació Biomèdica de l'Hospital de la Santa Creu i Sant
Pau, IIB-Sant Pau
Av. Sant Antoni Ma. Claret, 167
Tlf: +34 93 5537836
08025 Barcelona- Spain
P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
fer-ho.
------------------------------
Date: Thu, 17 Sep 2015 14:20:37 +0200
From: Niels Bergsland <[log in to unmask]>
Subject: Re: Fwd: [FSL] 3D rendering shape analysis
Hmm, are you adjusting the brightness/contrast settings? You shouldn't need
to do that. I ask because I notice in your screenshot that the minimum is 0
and the maximum is 1 (which in this case shouldn't be a problem, but it
should open with 0.95 and 1 by default).
On Thu, Sep 17, 2015 at 2:03 PM, Maria Serra <[log in to unmask]> wrote:
> Hi,
>
> I have followed and double checked the instructions of the wiki in detail.
> The parameters you referred were set the same way as yours... so really do
> not know what could be wrong.
>
> Thank you for the efforts
>
> On Thu, Sep 17, 2015 at 1:45 PM, Niels Bergsland <[log in to unmask]>
> wrote:
>
>> Hi,
>> I'm pretty sure the latest fslview version is 4.0.1. That's what I am
>> using at least, so it shouldn't be related to that.
>>
>> I have been able to reproduce your problem though - are you perhaps not
>> following the instructions as given in the wiki? Only the basestruct image
>> should be set to mask/label. If set the corrp image to mask/label as well,
>> it won't display the significant areas. This should be set to "Statistic"
>> (which is the default for me for this image).
>>
>>
>>
>> On Thu, Sep 17, 2015 at 1:11 PM, Maria Serra <[log in to unmask]>
>> wrote:
>>
>>> Niels,
>>>
>>> I've tried to download the script again but it still does not work.
>>>
>>> When I run the script the images open correctly, but when I open the 3D
>>> view, this error comes out:
>>>
>>> [image: Inline image 1]
>>>
>>> I just realized that, although I am using the FSL version 5.0.8, the FSL
>>> view is using the version 4.0.1. Maybe the problem rely on this fact? If
>>> so, how could I fix it? I downloaded the whole package and FSL opens FSL
>>> view with this old version by default.
>>>
>>> Many thanks again
>>>
>>> On Thu, Sep 17, 2015 at 12:43 PM, Niels Bergsland <[log in to unmask]>
>>> wrote:
>>>
>>>> Hi Maria,
>>>> I am not having any trouble created it (see attached). I don't think
>>>> there have been major changes to the first3Dview script (the most
>>>> recent one is in fact from 2012), but can you try downloading the
>>>> script again (
>>>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide?action=AttachFile&do=view&target=first3Dview.zip
>>>> )
>>>> and redoing the process?
>>>>
>>>>
>>>>
>>>> On Thu, Sep 17, 2015 at 12:14 PM, Maria Serra <
>>>> [log in to unmask]> wrote:
>>>> > Hi Niels,
>>>> >
>>>> > please find attached the mask and corrp image.
>>>> >
>>>> > Thank you!
>>>> >
>>>> > On Thu, Sep 17, 2015 at 11:56 AM, Niels Bergsland <
>>>> [log in to unmask]>
>>>> > wrote:
>>>> >>
>>>> >> Hi - if you can make the mask and corrp image available, I can try to
>>>> >> take a look.
>>>> >>
>>>> >> On Wed, Sep 16, 2015 at 11:42 AM, Maria Serra <
>>>> [log in to unmask]>
>>>> >> wrote:
>>>> >> > Hi,
>>>> >> >
>>>> >> > please find attached a screenshot of my 3D rendering.
>>>> >> >
>>>> >> > Also, the output of the fslstats corrp_fstat1_output_randomise -R
>>>> >> > coomand is
>>>> >> > the following:
>>>> >> >
>>>> >> > 0.000000 0.985800
>>>> >> >
>>>> >> > And finally, I just realized that when I run the first3Dview, it
>>>> comes
>>>> >> > up
>>>> >> > with this error:
>>>> >> >
>>>> >> > 80
>>>> >> > ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkDecimatePro.cxx,
>>>> line 163
>>>> >> > vtkDecimatePro (0x482b6c80): No data to decimate!
>>>> >> >
>>>> >> > ERROR: In
>>>> /build/buildd/vtk-5.8.0/Graphics/vtkSmoothPolyDataFilter.cxx,
>>>> >> > line
>>>> >> > 211
>>>> >> > vtkSmoothPolyDataFilter (0x3f4ac400): No data to smooth!
>>>> >> >
>>>> >> > which is probably related with my problem.
>>>> >> >
>>>> >> > Hope this information helps.
>>>> >> >
>>>> >> > Maria
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >> Niels Bergsland
>>>> >> Integration Director
>>>> >> Buffalo Neuroimaging Analysis Center
>>>> >> 100 High St. Buffalo NY 14203
>>>> >> [log in to unmask]
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > Maria
>>>> >
>>>> >
>>>> > P Abans d'imprimir aquest correu electrònic pensa bé si és necessari
>>>> fer-ho.
>>>>
>>>>
>>>>
>>>> --
>>>> Niels Bergsland
>>>> Integration Director
>>>> Buffalo Neuroimaging Analysis Center
>>>> 100 High St. Buffalo NY 14203
>>>> [log in to unmask]
>>>>
>>>
>>>
>>>
>>> --
>>> Maria
>>>
>>>
>>> P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
>>> fer-ho.
>>>
>>
>>
>>
>> --
>> Niels Bergsland
>> Integration Director
>> Buffalo Neuroimaging Analysis Center
>> 100 High St. Buffalo NY 14203
>> [log in to unmask]
>>
>
>
>
> --
> Maria Serra Blasco
> Institut d'Investigació Biomèdica de l'Hospital de la Santa Creu i Sant
> Pau, IIB-Sant Pau
> Av. Sant Antoni Ma. Claret, 167
> Tlf: +34 93 5537836
> 08025 Barcelona- Spain
>
> P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
> fer-ho.
>
>
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
[log in to unmask]
------------------------------
Date: Thu, 17 Sep 2015 14:39:39 +0200
From: Maria Serra <[log in to unmask]>
Subject: Re: Fwd: [FSL] 3D rendering shape analysis
yey! you hit the nail on the head!
thanks Niels
On Thu, Sep 17, 2015 at 2:20 PM, Niels Bergsland <[log in to unmask]>
wrote:
> Hmm, are you adjusting the brightness/contrast settings? You shouldn't
> need to do that. I ask because I notice in your screenshot that the minimum
> is 0 and the maximum is 1 (which in this case shouldn't be a problem, but
> it should open with 0.95 and 1 by default).
>
> On Thu, Sep 17, 2015 at 2:03 PM, Maria Serra <[log in to unmask]> wrote:
>
>> Hi,
>>
>> I have followed and double checked the instructions of the wiki in
>> detail. The parameters you referred were set the same way as yours... so
>> really do not know what could be wrong.
>>
>> Thank you for the efforts
>>
>> On Thu, Sep 17, 2015 at 1:45 PM, Niels Bergsland <[log in to unmask]>
>> wrote:
>>
>>> Hi,
>>> I'm pretty sure the latest fslview version is 4.0.1. That's what I am
>>> using at least, so it shouldn't be related to that.
>>>
>>> I have been able to reproduce your problem though - are you perhaps not
>>> following the instructions as given in the wiki? Only the basestruct image
>>> should be set to mask/label. If set the corrp image to mask/label as well,
>>> it won't display the significant areas. This should be set to "Statistic"
>>> (which is the default for me for this image).
>>>
>>>
>>>
>>> On Thu, Sep 17, 2015 at 1:11 PM, Maria Serra <[log in to unmask]>
>>> wrote:
>>>
>>>> Niels,
>>>>
>>>> I've tried to download the script again but it still does not work.
>>>>
>>>> When I run the script the images open correctly, but when I open the 3D
>>>> view, this error comes out:
>>>>
>>>> [image: Inline image 1]
>>>>
>>>> I just realized that, although I am using the FSL version 5.0.8, the
>>>> FSL view is using the version 4.0.1. Maybe the problem rely on this fact?
>>>> If so, how could I fix it? I downloaded the whole package and FSL opens FSL
>>>> view with this old version by default.
>>>>
>>>> Many thanks again
>>>>
>>>> On Thu, Sep 17, 2015 at 12:43 PM, Niels Bergsland <[log in to unmask]
>>>> > wrote:
>>>>
>>>>> Hi Maria,
>>>>> I am not having any trouble created it (see attached). I don't think
>>>>> there have been major changes to the first3Dview script (the most
>>>>> recent one is in fact from 2012), but can you try downloading the
>>>>> script again (
>>>>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide?action=AttachFile&do=view&target=first3Dview.zip
>>>>> )
>>>>> and redoing the process?
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Sep 17, 2015 at 12:14 PM, Maria Serra <
>>>>> [log in to unmask]> wrote:
>>>>> > Hi Niels,
>>>>> >
>>>>> > please find attached the mask and corrp image.
>>>>> >
>>>>> > Thank you!
>>>>> >
>>>>> > On Thu, Sep 17, 2015 at 11:56 AM, Niels Bergsland <
>>>>> [log in to unmask]>
>>>>> > wrote:
>>>>> >>
>>>>> >> Hi - if you can make the mask and corrp image available, I can try
>>>>> to
>>>>> >> take a look.
>>>>> >>
>>>>> >> On Wed, Sep 16, 2015 at 11:42 AM, Maria Serra <
>>>>> [log in to unmask]>
>>>>> >> wrote:
>>>>> >> > Hi,
>>>>> >> >
>>>>> >> > please find attached a screenshot of my 3D rendering.
>>>>> >> >
>>>>> >> > Also, the output of the fslstats corrp_fstat1_output_randomise -R
>>>>> >> > coomand is
>>>>> >> > the following:
>>>>> >> >
>>>>> >> > 0.000000 0.985800
>>>>> >> >
>>>>> >> > And finally, I just realized that when I run the first3Dview, it
>>>>> comes
>>>>> >> > up
>>>>> >> > with this error:
>>>>> >> >
>>>>> >> > 80
>>>>> >> > ERROR: In /build/buildd/vtk-5.8.0/Graphics/vtkDecimatePro.cxx,
>>>>> line 163
>>>>> >> > vtkDecimatePro (0x482b6c80): No data to decimate!
>>>>> >> >
>>>>> >> > ERROR: In
>>>>> /build/buildd/vtk-5.8.0/Graphics/vtkSmoothPolyDataFilter.cxx,
>>>>> >> > line
>>>>> >> > 211
>>>>> >> > vtkSmoothPolyDataFilter (0x3f4ac400): No data to smooth!
>>>>> >> >
>>>>> >> > which is probably related with my problem.
>>>>> >> >
>>>>> >> > Hope this information helps.
>>>>> >> >
>>>>> >> > Maria
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >> --
>>>>> >> Niels Bergsland
>>>>> >> Integration Director
>>>>> >> Buffalo Neuroimaging Analysis Center
>>>>> >> 100 High St. Buffalo NY 14203
>>>>> >> [log in to unmask]
>>>>> >
>>>>> >
>>>>> >
>>>>> >
>>>>> > --
>>>>> > Maria
>>>>> >
>>>>> >
>>>>> > P Abans d'imprimir aquest correu electrònic pensa bé si és necessari
>>>>> fer-ho.
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Niels Bergsland
>>>>> Integration Director
>>>>> Buffalo Neuroimaging Analysis Center
>>>>> 100 High St. Buffalo NY 14203
>>>>> [log in to unmask]
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Maria
>>>>
>>>>
>>>> P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
>>>> fer-ho.
>>>>
>>>
>>>
>>>
>>> --
>>> Niels Bergsland
>>> Integration Director
>>> Buffalo Neuroimaging Analysis Center
>>> 100 High St. Buffalo NY 14203
>>> [log in to unmask]
>>>
>>
>>
>>
>> --
>> Maria Serra Blasco
>> Institut d'Investigació Biomèdica de l'Hospital de la Santa Creu i Sant
>> Pau, IIB-Sant Pau
>> Av. Sant Antoni Ma. Claret, 167
>> Tlf: +34 93 5537836
>> 08025 Barcelona- Spain
>>
>> P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
>> fer-ho.
>>
>>
>
>
> --
> Niels Bergsland
> Integration Director
> Buffalo Neuroimaging Analysis Center
> 100 High St. Buffalo NY 14203
> [log in to unmask]
>
--
Maria
P *Abans d'imprimir *aquest correu electrònic pensa bé si és necessari
fer-ho.
------------------------------
Date: Thu, 17 Sep 2015 13:49:39 +0100
From: Evgeny Chumin <[log in to unmask]>
Subject: bet error
Dear fsl experts,
I am doing brain extraction with fsl bet and I keep getting a NEWMAT::SIngularExemption error. I think it is related to c libraries, but I dont know what to do about it. I ran the same image on a different linux machine with no problem. The only difference I could find is that my machine has a later version of libc (2.21) and the other machine has version 2.20.
Any help is appreciated,
Evgeny CHumin
------------------------------
Date: Thu, 17 Sep 2015 23:55:04 +0900
From: Jun Miyata <[log in to unmask]>
Subject: Re: EDDY parallelization
Dear Matthew,
Thank you very much for your help. I tried to build full FSL package and got error messages for some (please see the attached build log). But at least I seemed to succeed to build EDDY.
I tried this re-built EDDY, but the processing was not parallelized. Could you guess the cause? I prepared in the following way:
1. installed the latest version of Xcode (ver.5 for Mavericks)
2. installed the latest command line tools
3. installed MacPorts
4. installed gcc5 using MacPorts (I created a link and call of gcc correctly refers to gcc5).
I think so far it's OK, but I'm not so sure if I correctly installed the libraries necessary for building.
GNU make: I read in a website that the make in Mac is already GNU make.
GNU install: I installed coreutils from MacPorts (actually it's ginstall).
expat : I installed from MacPorts.
libX11: I installed xorg-libX11 through MacPorts.
libGL: OpenGL is already installed in Mac.
zlib: I installed from MacPorts.
In addition, the environment variable omp_num_threads is not set. Is this critical?
I really appreciate if I can have a feedback.
Best,
Jun
> 差出人: Matthew Webster <[log in to unmask]>
> 件名: Re: EDDY parallelization
> 日付: 2015年9月16日 23:51:16 JST
>
>
> Hello,
> As you have upgraded your compiler, you probably need to do a full rebuild of FSL ( please see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/SourceCode for more information )
>
> Kind Regards
> Matthew
>
>> Dear Jesper and FSL experts,
>>
>> I have managed to install gcc5 on my Mavericks. I tried to build Eddy from the source, but I received error message as attached. Could you find what's wrong? I'm sorry I'm not experienced in building from the source.
>> Best,
>>
>> Jun
>> <error_log.txt>
>
------------------------------
Date: Thu, 17 Sep 2015 15:49:55 +0100
From: Christophe Maggia <[log in to unmask]>
Subject: eddy_correct via matlab
Hi everyone
I work on DTI images using matlab and FSL
i want to use eddy_correct on these images via matlab
i use the command "system" to run eddy_correct as in a terminal window
but i get this error :
/usr/local/fsl/bin/eddy_correct: line 92: fslroi: command not found
/usr/local/fsl/bin/eddy_correct: line 94: fslsplit: command not found
/usr/local/fsl/bin/eddy_correct: line 103: fslmerge: command not found
rm: ec_data_tmp???.*:No such file or directory
rm: ec_data_ref*: No such file or directory
Which is weird because when i run the same line in a terminal window, it works
According to the error, eddy_correct calls for other functions like fslroi, fslsplit and fslmerge that are not recognised
The thing that disturb me is that i do the same thing with topup and eddy and it works perfectly, (maybe they don't work the same way so i don't know if it is a matlab error or something else)
Does someone have an idea ?
Thanks in advance
Christophe
------------------------------
Date: Thu, 17 Sep 2015 15:01:17 +0000
From: "Puechmaille, Danaele" <[log in to unmask]>
Subject: Re: Parallelising bedpost
Hi,
I'm on Linux.
I call bedpostx_gpu in $FSL_DIR/src/fdt/CUDA directory and this error occured :
/tools/FSL/fsl-5.0.8/fsl/bin/xfibres_gpu: error while loading shared libraries: libcudart.so.5.5: cannot open shared object file: No such file or directory
May be it's a wrong installation of FSL/CUDA but I don't know fix that.
Danaele
________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Moises Hernandez [[log in to unmask]]
Sent: Wednesday, September 16, 2015 5:42 PM
To: [log in to unmask]
Subject: Re: [FSL] Parallelising bedpost
Hi Danaele,
What problem did you have using the CUDA version of bedpostx ?
What OS do you have ?
Moises.
On 16 September 2015 at 22:24, Puechmaille, Danaele <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi Moises,
Yes I have a gpu and I tried to use the CUDA implementation of bedpostx but that didn't work. So I write a script which parallelized xfibres.
Thanks for your help
Regards,
Danaele
________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Moises Hernandez [[log in to unmask]<mailto:[log in to unmask]>]
Sent: Friday, September 04, 2015 5:08 AM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [FSL] Parallelising bedpost
Hi Danaele,
Do you have a GPU ?
It will be much faster if you use the CUDA implementation of bedpostx.
Moises.
On 3 September 2015 at 17:44, Danaele Puechmaille <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear experts,
I try to parallelise bedpostx in order to obtain bedpostx results faster.
So I have followed the FSL Tutorial - Parallelising bedpost : http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx_parallel.html
I set environment variables FSLMACHINELIST and FSLREMOTECALL like that :
setenv FSLMACHINELIST “mymachine mymachine mymachine”
setenv FSLREMOTECALL ssh
Moreover, I have a file called fsl.sh in this place : ${HOME}/.fslconf/
In this file I set the environment variable FSLDIR to my FSL directory.
Also I'm a tcsh user, so I have created a file fsl.csh in the same directory and I did the same thing : set the environment variable FSLDIR to my FSL directory.
At this point I have followed the tutorial and bedpost should be parallelised.
But when I execute the command bedpostx in my data directory, nothing is parallelised.
Furthermore, if I am connected to another machine (for example “myothermachine”) and I want to execute bedpost in mymachine with the environment variables set to the same values, the command bedpostx is executed in myothermachine and not parallelised too.
So, I think bedpostx never tried to be connected to another machine with shh.
If someone has already meet this problem and found a solution, please explain me. Otherwise if someone have a solution to parallelise bedpost, I am really interested and that could be very helpful for me!
Thank you,
Best regards,
Danaele Puechmaille
------------------------------
Date: Thu, 17 Sep 2015 11:20:36 -0400
From: Mayte Parada <[log in to unmask]>
Subject: plotting brain activation
Hello,
After running a basic contrast between two conditions (high arousal-low
arousal) I see that I have significant activation in the postcentral gyrus.
I would like to represent the activation in this brain region on a graph
for both conditions. I used Featquery to interrogate the stats/cope files
for high arousal and low arousal contrasts and I see that I get means, std.
deviations, and a timeseries that I can also display as %change for the
entire region. I also know I can do this for a specific voxel if I use
coordinates. I'm not quite sure what is the best representation of "brain
activity" from these data. I was plotting the means and std. deviations
(which are huge) and was told these means are the beta weights. Can anyone
clear this up for me or make a suggestion of what best represents activity?
--
Mayte Parada, PhD
Laboratory for the Biopsychosocial Study of Sexuality
1205 Avenue Dr. Penfield
Montreal, QC
H3A1B1
W8/24
------------------------------
Date: Thu, 17 Sep 2015 16:25:16 +0100
From: Herve Lemaitre <[log in to unmask]>
Subject: Cost Measure Flirt
Dear FSL list,
Using the following command line with flirt version 5.5 in fsl 4.1.9 to get the cost measure:
flirt -in toto.nii.gz -ref titi.nii.gz -schedule $FSLDIR/etc/flirtsch/measurecost1.sch -init tutu.mat -refweight tata.nii.gz
I get:
0.136744 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000
Final result:
0.999592 0.002647 0.028430 -42.797900
0.001663 0.988606 -0.150519 -34.175900
-0.028504 0.150505 0.988198 -20.129200
0.000000 0.000000 0.000000 1.000000
Using the same command line with flirt version 6 in fsl 5.0.8, I get:
0.224454 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000
Final result:
0.999592 0.002647 0.028430 -42.797900
0.001663 0.988606 -0.150519 -34.175900
-0.028504 0.150505 0.988198 -20.129200
0.000000 0.000000 0.000000 1.000000
I used the cost measure to compare different registrations and based on the old or the new flirt version I have opposite results. Could you tell me why and how to solve this issue.
Thanks,
Hervé Lemaître
PS: with the -v option
flirt version 5.5
WARNING: Both reference and input images have an sform matrix set
The output image will use the sform from the reference image
The output image will use the transformed sform from the input image
Init Matrix =
0.999592 0.002647 0.028430 -42.797900
0.001663 0.988606 -0.150519 -34.175900
-0.028504 0.150505 0.988198 -20.129200
0.000000 0.000000 0.000000 1.000000
>> # 1mm scale
>> setscale 1
>> setoption smoothing 1
>> setoption boundguess 1
>> clear U
>> setrow UA 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1
>> measurecost 7 UA 0 0 0 0 0 0 abs
>> printparams U
0.136744 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000
>>
>>
Final result:
0.999592 0.002647 0.028430 -42.797900
0.001663 0.988606 -0.150519 -34.175900
-0.028504 0.150505 0.988198 -20.129200
0.000000 0.000000 0.000000 1.000000
flirt version 6:
WARNING: Both reference and input images have an sform matrix set
The output image will use the sform from the reference image
The output image will use the transformed sform from the input image
Init Matrix =
0.999592 0.002647 0.028430 -42.797900
0.001663 0.988606 -0.150519 -34.175900
-0.028504 0.150505 0.988198 -20.129200
0.000000 0.000000 0.000000 1.000000
>> # 1mm scale
>> setscale 1
>> setoption smoothing 1
>> setoption boundguess 1
>> clear U
>> setrow UA 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1
>> measurecost 7 UA 0 0 0 0 0 0 abs
>> printparams U
0.224454 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000
>>
>>
Final result:
0.999592 0.002647 0.028430 -42.797900
0.001663 0.988606 -0.150519 -34.175900
-0.028504 0.150505 0.988198 -20.129200
0.000000 0.000000 0.000000 1.000000
------------------------------
Date: Thu, 17 Sep 2015 16:23:51 +0100
From: Jie Yu <[log in to unmask]>
Subject: FEAT GLM design question
Dear Expert
So here are 2 groups of people, and I'd like to address the different variances within each group by giving them different group variables.
EV3 and EV4 are ages (demeaned within all participants)
Group Variable EV1 EV2 EV3 EV4
1 1 0 20 0
1 1 0 30 0
2 0 1 0 30
2 0 1 0 40
Contrasts:
group difference 1 -1 0 0 and -1 1 0 0
group x age interaction 0 0 1 -1 and 0 0 -1 1
Hope it's correct?
Also, is it true that once group x age interaction is found, the group difference result (if there is any) will be meaningless?
Thanks so much!
------------------------------
Date: Thu, 17 Sep 2015 16:48:04 +0100
From: Leeron Rabinov <[log in to unmask]>
Subject: Re: FSL on OS X 10.11 El Capitan
The following got FSL up and running on the 10.11 GM:
0. (may not be necessary) remove FSL
1. Install latest version of XQuartz
2. Download fslinstaller.py
3. Open fslinstaller.py in text editor and change line 1090 to "for release in range(10,16):" and comment out line 1092. Save.
4. Run python fslinstaller.py
Good luck!
------------------------------
Date: Thu, 17 Sep 2015 16:53:48 +0100
From: Leeron Rabinov <[log in to unmask]>
Subject: Re: FSL on OS X 10.11 El Capitan
The following got FSL up and running on the 10.11 GM:
0. (may not be necessary) remove FSL
1. Install latest version of XQuartz
2. Download fslinstaller.py
3. Open fslinstaller.py in text editor and change line 1090 to "for release in range(10,16):" and comment out line 1092. Save.
4. Run python fslinstaller.py
Good luck!
------------------------------
Date: Thu, 17 Sep 2015 17:22:54 +0100
From: Moises Hernandez <[log in to unmask]>
Subject: Re: Parallelising bedpost
Ok,
You are getting that error because the GPU version of bedpostx in FSL 5.0.8
was compiled using CUDA 5.5, and
probably, you have another CUDA version (you can check it with 'nvcc
--version').
You can try this:
If you have CUDA 6.0 download:
http://users.fmrib.ox.ac.uk/~moisesf/bedpostx/CUDA-6_0.zip
If you have CUDA 6.5 download:
http://users.fmrib.ox.ac.uk/~moisesf/bedpostx/CUDA-6_5.zip
If you have CUDA 7.0 download:
http://users.fmrib.ox.ac.uk/~moisesf/bedpostx/CUDA-7_0.zip
If you have CUDA 7.5 download:
http://users.fmrib.ox.ac.uk/~moisesf/bedpostx/CUDA-7_5.zip
Unzip it and then copy all the files in:
\bin folder to your $FSLDIR\bin folder
and all the files in:
\lib folder to your $FSLDIR\lib folder
Then try to run again.
Moises.
On 17 September 2015 at 16:01, Puechmaille, Danaele <[log in to unmask]>
wrote:
> Hi,
> I'm on Linux.
> I call bedpostx_gpu in $FSL_DIR/src/fdt/CUDA directory and this error
> occured :
>
> /tools/FSL/fsl-5.0.8/fsl/bin/xfibres_gpu: error while loading shared
> libraries: libcudart.so.5.5: cannot open shared object file: No such file
> or directory
>
> May be it's a wrong installation of FSL/CUDA but I don't know fix that.
>
> Danaele
> ------------------------------
> *From:* FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
> Moises Hernandez [[log in to unmask]]
> *Sent:* Wednesday, September 16, 2015 5:42 PM
>
> *To:* [log in to unmask]
> *Subject:* Re: [FSL] Parallelising bedpost
>
> Hi Danaele,
>
> What problem did you have using the CUDA version of bedpostx ?
>
> What OS do you have ?
>
> Moises.
>
> On 16 September 2015 at 22:24, Puechmaille, Danaele <[log in to unmask]
> > wrote:
>
>> Hi Moises,
>>
>> Yes I have a gpu and I tried to use the CUDA implementation of bedpostx
>> but that didn't work. So I write a script which parallelized xfibres.
>> Thanks for your help
>> Regards,
>> Danaele
>>
>> ------------------------------
>> *From:* FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
>> Moises Hernandez [[log in to unmask]]
>> *Sent:* Friday, September 04, 2015 5:08 AM
>> *To:* [log in to unmask]
>> *Subject:* Re: [FSL] Parallelising bedpost
>>
>> Hi Danaele,
>>
>> Do you have a GPU ?
>> It will be much faster if you use the CUDA implementation of bedpostx.
>>
>> Moises.
>>
>> On 3 September 2015 at 17:44, Danaele Puechmaille <[log in to unmask]>
>> wrote:
>>
>>> Dear experts,
>>>
>>> I try to parallelise bedpostx in order to obtain bedpostx results faster.
>>> So I have followed the FSL Tutorial - Parallelising bedpost :
>>> http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx_parallel.html
>>> I set environment variables FSLMACHINELIST and FSLREMOTECALL like that :
>>> setenv FSLMACHINELIST “mymachine mymachine mymachine”
>>> setenv FSLREMOTECALL ssh
>>> Moreover, I have a file called fsl.sh in this place : ${HOME}/.fslconf/
>>> In this file I set the environment variable FSLDIR to my FSL directory.
>>> Also I'm a tcsh user, so I have created a file fsl.csh in the same
>>> directory and I did the same thing : set the environment variable FSLDIR
>>> to my FSL directory.
>>>
>>> At this point I have followed the tutorial and bedpost should be
>>> parallelised.
>>>
>>> But when I execute the command bedpostx in my data directory, nothing is
>>> parallelised.
>>> Furthermore, if I am connected to another machine (for example
>>> “myothermachine”) and I want to execute bedpost in mymachine with the
>>> environment variables set to the same values, the command bedpostx is
>>> executed in myothermachine and not parallelised too.
>>> So, I think bedpostx never tried to be connected to another machine with
>>> shh.
>>>
>>> If someone has already meet this problem and found a solution, please
>>> explain me. Otherwise if someone have a solution to parallelise bedpost, I
>>> am really interested and that could be very helpful for me!
>>> Thank you,
>>>
>>> Best regards,
>>>
>>> Danaele Puechmaille
>>>
>>
>>
>
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End of FSL Digest - 16 Sep 2015 to 17 Sep 2015 - Special issue (#2015-82)
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