Hi Jennifer,
I have never tested if the long_...slopes commands work when the data was processed with an old FS version. And 4.5 is very old. I'd recommend you re-run the data with 5.3 as sooo much has changed in the longitudinal pipeline since then.
Independent of that, do you have write permissions in the current directory? did the script create the ./tmp-CED01... directory ? The error message indicates that it cannot create that directory.
Best, Martin
On 05/15/2014 02:32 PM, Jennifer Addicks wrote:
Hello,
I recently installed FreeSurfer v5.3 on a Mac OS X 10.9.2. I am trying to run a longitudinal analysis (longitudinal two-stage model) on my data (26 participants, 2 time points each) which was processed (cross-sectionally and longitudinally) using a previous version of FreeSurfer (v4.5).
When running the long_mris_slopes command:
long_MRIS_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR
I get the following error message {CED01 is one of my fsid-base names}:
Traceback (most recent call last): File "/Applications/freesurfer/bin/long_MRIS_slopes", line 862, in
<module> dirname = tempfile.mkdtemp('',prefix,'') File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tempfile.py", line 329, in mkdtemp _os.mkdir(file, 0700) OSError: [Errno 13] Permission denied: './tmp-CED01_lh_thickness_34xA_9'
Any suggestions?
Sincerely, Jennifer
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