Hi Danny,
I have a total of 48 scans, 2 scans (pre and post) per subject (24 subjects).
In "FA" folder, there are 9,368 items including "tbss_logs" and "slicesdir" folders as well as all.msf, best.msf, target_mask.nii.gz, target_to_MNI 152.mat, target_to_MNI 152.nii.gz, target.nii.gz. There are 195 files for each scan as well.
I was also advised to do the following:
run
ulimit -s
on the system and add a line before the imglob:
ulimit -s <double the number returned in the above call>
I wasn't sure where to add the line though. I added a line before line 96 in my toss_non_FA file [please see attached an screenshot of what I did]. It is not still working. I guess I have to add this line somewhere else.
BTW, on this same computer, one of my labmate, Meisan, has been successful in running the same command with the same format of naming the files. The FSL is installed on her account. I don't know if that makes a different at all.
I can not get what I am doing wrong.
Many thanks,
Sara
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Danny Kim [[log in to unmask]]
Sent: Monday, October 16, 2017 10:53 AM
To: [log in to unmask]
Subject: Re: [FSL] tbss_non_FA not running
Sara
Could you give a brief description of what files are in the "FA" folder? How many subjects are in this process?
Cheers
Danny
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of [log in to unmask] [[log in to unmask]]
Sent: Monday, October 16, 2017 9:46 AM
To: [log in to unmask]
Subject: Re: [FSL] tbss_non_FA not running
Hi FSL team,
I want to run TBSS on my AD data. I followed the instruction on the website and I still get the following error:
/usr/local/fsl/bin/tbss_non_FA: line 96: /usr/local/fsl/bin/imglob: Argument list too long
merging all upsampled AD images into single 4D image
Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Cannot open volume all_AD for reading!
projecting all_AD onto mean FA skeleton
Image Exception : #22 :: ERROR: Could not open image all_AD
libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
/usr/local/fsl/bin/tbss_non_FA: line 105: 82036 Abort trap: 6
I also changes line 96 from
${FSLDIR}/bin/fslmerge -t ../stats/all_$ALTIM `$FSLDIR/bin/imglob *_to_target_${ALTIM}.*`
to
${FSLDIR}/bin/fslmerge -t ../stats/all_$ALTIM `$FSLDIR/bin/imglob *_to_target_${ALTIM}.nii.gz`
but it didn't help at all.
What else can I do to resolve this issue.
Thanks,
Sara
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