Hi Sandra, is the environment variable SUBJECTS_DIR setup correctly ? in newer versions of the script this needs to be passed on the command line, but in 5.1 I think it needs to be set as an evironment variable.
Best, Martin On 06/21/2013 04:35 AM, Sandra Preissler wrote: > Dear freesurfer users, > > we wanted to do longitudinal analyses for two different time points. > So we did the longitudinal processing as described in the tutorial > (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#PreparingtheData-QCACHE) > > The "Post-Processing Longitudinal Data" step does not work. > (long_mris_slopes --qdec ./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 ) > > After starting the process we get the following error message: > > Parsing the qdec table: ./qdec/long.qdec.table.dat > Traceback (most recent call last): > File "/opt/freesurfer/bin/long_mris_slopes", line 521, in <module> > qdectable = LongQdecTable(options.qdec) > File "/srv/freesurfer/bin/LongQdecTable.py", line 30, in __init__ > self.parse(stpmap) > File "/srv/freesurfer/bin/LongQdecTable.py", line 58, in parse > if strlst[0].upper() == 'SUBJECTS_DIR': > IndexError: list index out of range > > We’ve already tried a lot of things, like removing subjects from the > longitudinal qdec table, except for one subject, or deleting every > command that was optional, but it still does not work. > > The information about the freesurfer version and linux version used are: > FREESURFER_HOME: /opt/freesurfer > Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Kernel info: Linux 2.6.34.10-0.6-default x86_64 > > Can you help us in fixing this problem? > > Thanks in advance! > > Sandra > > ---------------------------------------------------------------- > This message was sent through https://webmail.uni-jena.de > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: [email protected] [email protected] Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
