-rwxrwxr-x 1 rd521 rd521 4951 Oct 30 04:45 /usr/local/freesurfer/dev/bin/slicedelay

Thanks!

From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Friday, October 30, 2020 10:38 AM
To: Peled, Noam <NPELED@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Gumenyuk, Valentina <VGUMENYUK@mgh.harvard.edu>; Stufflebeam, Steven M. <SMSTUFFLEBEAM@mgh.harvard.edu>; Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: preproc-sess error with FreeSurfer 7.1

can you send the result of
ls -l `which  slicedelay`

On 10/29/2020 8:47 PM, Peled, Noam wrote:

Dear FreeSurfer experts!

We are running FsFast pipeline to analysis our language task for epilepsy patients.

Usually we are using FreeSurfer 5.3. We want to use a newer version, so I decided to jump right to 7.1 (dev)

When trying to run

preproc-sess -surface {trg_subject} lhrh -s {subject} -fwhm {fwhm} -fsd {fsd} -mni305 -per-run -stc siemens

I got the following error:

mri_info --nslices --o /autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/tmp.110620/nslices.dat /autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/fmcpr.nii.gz

nslices =  44

slicedelay --nslices 44 --siemens --o /autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/tmp.110620/sdf.txt --ngroups 1

  File "/usr/local/freesurfer/dev/bin/slicedelay", line 9

    print "USAGE: slicedelay --help";

                                   ^

SyntaxError: Missing parentheses in call to 'print'

When I reran the same pipeline with FreeSurfer 5.3, it seems to work.

Is it a bug in 7.1? Or should we change something in the call?

Thanks,

Noam