Hi Guillaume,

not sure what is going on. It could be missing permissions or it could be that the disk is full?

You could also try to drop the --do-label and see if that works.

Best, Martin

On Fri, 2020-02-14 at 10:12 +0100, Guillaume Carey wrote:

Hello everyone, I’m currently working on a longitudinal FreeSurfer pipeline in order to compare cortical thickness changes across the time. I’m using FreeSurfer version 6.0.0 (OS: Scientific Linux 7.3). I already processed the recon-all, -base and -long processing steps. Now I’m trying to run the “long_mris_slopes“ processing in order to prepare the data for a two stage model analyze. But there is an error. The command: long_mris_slopes --qdec ./qdec.dat --meas thickness --hemi lh --do- spc --do-label --time month --qcache fsaverage --sd $SUBJECTDIR

At first everything seems to work well for the 1st subject and then:

SUBJECT CBTPD-001/template_CBTPD-001 mapping label to QCache (…) Writing label file /data/guillaume/ParkAnx3/freesurfer/results/CBTPD- 001/template_CBTPD-001/label/lh.long.cortex.fsaverage.label 167889 mri_label2label: Done

Traceback (most recent call last): File "/opt/mumc/apps/freesurfer-6.0.0/bin/long_mris_slopes", line 868, in <module> dirname = tempfile.mkdtemp('',prefix,'') File "/usr/lib64/python2.7/tempfile.py", line 329, in mkdtemp _os.mkdir(file, 0700) OSError: [Errno 2] No such file or directory: './tmp-CBTPD- 001/template_CBTPD-001_lh_thickness_wuK7ZI'

It seems like the output “lh.long.cortex.fsaverage.label” has been created for this subject. But then there is a missing “tmp” folder. I haven’t find this error in the archives. Does anyone have an idea of how to fix it ?

Best, Guillaume _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer