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 2016/08/02 21:19:09 greve Exp $
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
-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


root@andraderenew:/home/andraderenew/Downloads/barrios/project# ls  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
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# cd 1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold/1# ls

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.


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