In the bold directory, it looks like you have one run directory called "1". Change this to "001"
On 11/29/2019 1:48 AM, Renew Andrade wrote:
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Dear FreeSurfer experts: I have some issues with "preproc-sess" because I cannot seem to get the setup of the directory structure or files to connect different things(the T1 subjects with functional bold or rest files). I have this output.
root@andraderenew:/home/andraderenew/Downloads/barrios/project# preproc-sess -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.sess1.log -------------------------------------------------------------- $Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $ root setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /usr/local/freesurfer/subjects Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 11:09:50 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux /home/andraderenew/Downloads/barrios/project /usr/local/freesurfer/fsfast/bin/preproc-sess -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run vie nov 29 07:33:28 CET 2019 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain sess1 Template ----------------------------- mktemplate-sess -s sess1 -d /home/andraderenew/Downloads/barrios/project -fsd bold -update
Session: /home/andraderenew/Downloads/barrios/project/sess1 ---------------- vie nov 29 07:33:28 CET 2019 ERROR: no run directories found
my working directory is
root@andraderenew:/home/andraderenew/Downloads/barrios/project# pwd /home/andraderenew/Downloads/barrios/project
and
root@andraderenew:/home/andraderenew/Downloads/barrios/project# ls copy.sh sess1 sess2 sess4 sess6 sess8 sessidlist log sess10 sess3 sess5 sess7 sess9 sessidlist~
root@andraderenew:/home/andraderenew/Downloads/barrios/project# cd sess1 root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1# ls bold rest subjectname
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1# cd bold root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# ls 1 root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# cd 1 root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold/1# ls sub-0030689_task-resthypnotic_bold.nii.gz
And that is all. If I try with tutorial data there is no problem. One of the obvious differences is SUBJECTS_DIR is pointing not to subjects in freesurfer but to another folder where also is fsaverage. I don't know if this is required or I am missing another linking file.
There you can see the files I have searched with terminal.
Sincerely, Andrade.
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