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FSL  April 2013

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Subject:

Re: fsl_motion_ouliers??

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 15 Apr 2013 15:05:10 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (271 lines)

Hi,

This should have been fixed in 5.0.2.
Please update to the latest version and let us know if the problem persists.

All the best,
	Mark


On 13 Apr 2013, at 20:47, Estephan Moana <[log in to unmask]> wrote:

> I was wondering if there are any updates on the possible bug with the "--fd" option in fsl_motion_outliers. I am using it with FSL 5.0.1 and the confound EV file generated still outputs a number of rows that is equal to # of frames + 1. This is consistent regardless of using the option "--dummy" or not. I attached here some example files if it helps.
> 
> Also, I noticed that for both dvars and fd metrics the frames flagged as having spikes from the verbose output do not coincide with the row that is non-zero for that column - it is the # of frame flagged + 1. Shouldn't the frame number be exactly the same as the row contain "1"?
> 
> Thank you.
> 
> Estephan Moana, D.D.S., M.S.
> Ph.D. Candidate
> Clinical Fellow, Oral & Maxillofacial Pain Program
> Regional Center for Neurosensory Disorders
> UNC School of Dentistry
> [log in to unmask]
> 
> ________________________________________
> Hi Mark,
> Any news on this one??
> SD
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
> Sent: Monday, October 15, 2012 2:14 PM
> To: [log in to unmask]
> Subject: Re: [FSL] fsl_motion_ouliers??
> 
> Dear Sachin,
> 
> I'm afraid that there is a bug with the --fd option.
> I will try and fix it as soon as possible.
> In the meantime I suggest you use one of the other options for the metric.
> I'll send more news as soon as I have it.
> 
> All the best,
>        Mark
> 
> 
> 
> On 15 Oct 2012, at 20:01, "Dixit, Sachin" <[log in to unmask]> wrote:
> 
>> Hi,
>> The fsl_motion_outliers analysis in independent of Lev1 using feat. In any case we are not throwing any frames out using feat. The point is while using --dvars (which also is dependent on frame wise movement) I get correct number of frames in the txt file (ouput of fsl_motion_outlier), but using --fd as option I get one more the total number of frames (total frames + 1) in the text file. So is the first row is set to be zero or the last row? In principle should we get one more the number of total frames using --fd in the output.txt file?
>> 
>> Thanks
>> SD
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Stephen Smith [[log in to unmask]]
>> Sent: Monday, October 15, 2012 12:00 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] fsl_motion_ouliers??
>> 
>> Hi - is this because you told FEAT to exclude one timepoint from the raw data?  In which case I suggest using fslroi to exclude that timepoint in the first place before running FEAT or fsl_motion_outliers
>> 
>> Cheers.
>> 
>> 
>> 
>> On 15 Oct 2012, at 16:27, Dixit, Sachin wrote:
>> 
>>> Hi Folks,
>>> I am using latest version of FSL for our analysis. I would like to use output of fsl_motion_outliers script as confound in lev1 analysis. Below is the command I used.
>>> fsl_motion_outliers -i raw.nii.gz -o temp.txt --fd --thresh=0.3
>>> I am using fd as metrics (frame displacement). The temp.txt file it generates has one extra frame in the text file. For example raw file has 405 frames but the text file has 406 lines. The problem is apparent when I am trying to use another confound example Linear trend as a separate column before I run Lev1 analysis. The following exception is thrown:
>>> Exception in the log file is:
>>> /nrgpackages/tools/fsl5/bin/feat_model design confoundevs.txt
>>> terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException'
>>> 
>>> This is because Linear Trend file has 405 lines. The Lev1 analysis however gets completed.
>>> Can you please suggest me so that I don't get this exception or should I just ignore this or
>>> if this is a bug in fsl_moion_outlier?
>>> Thanks
>>> SD
>>> 
>>> 
>>> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>>> 
>> 
>> 
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>> 
>> ________________________________
>> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>> 
> 
> ________________________________
> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
> fsl_motion_outliers -i P018_20091209_painlock_frun01_BOLD_dentalvpress_painlock.nii.gz -o P018_test_nodels_dvars.txt --dvars -v
> 
> mcf = P018_20091209_painlock_frun01_BOLD_dentalvpress_painlock ; outfile = P018_test_nodels_dvars.txt ; ndel = 0 ; mask =  ; do_moco = yes ; thresh =  ; use_thresh = no ; metric = dvars
> refnum = 35
> Original_refvol = 35
> brainmed = 665.000000  ; maskmean = 0.271010 
> Calculating outliers
> Range of metric values: 18.501770 53.917145 
> Found 4 outliers over 42.1956445
> Generating EVs
> Found spikes at  23 24 53 54
> 
> 0   0   0   0  
> 0   0   0   0  
> 0   0   0   0  
> 0   0   0   0  
> 0   0   0   0  
> 0   0   0   0  
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> 0   0   0   0  
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> 0   0   0   0  
> 0   0   0   0  
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> 0   0   0   0  
> 0   0   1   0  
> 0   0   0   1  
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> 0   0   0   0  
> 0   0   0   0  
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> 
> 
> fsl_motion_outliers -i P018_20091209_painlock_frun01_BOLD_dentalvpress_painlock.nii.gz -o P018_test_nodels_fd.txt --fd -v
> 
> mcf = P018_20091209_painlock_frun01_BOLD_dentalvpress_painlock ; outfile = P018_test_nodels_fd.txt ; ndel = 0 ; mask =  ; do_moco = yes ; thresh =  ; use_thresh = no ; metric = fd
> refnum = 35
> Original_refvol = 35
> brainmed = 665.000000  ; maskmean = 0.271010 
> Calculating outliers
> Range of metric values: 0.000000 0.379768 
> Found 4 outliers over .1654840
> Generating EVs
> Found spikes at  24 33 54 55
> 
> 0   0   0   0  
> 0   0   0   0  
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> 
> 

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