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#Prepar...)
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
Weve 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
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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#Prepar...)
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
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Sandra Preissler