Hello,
I am having trouble with the pre-processing step. When I enter the recon-all
<subject-id> command I get an error:
[Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018
ERROR: nothing to do
When I enter 'recon-all -s ms_018 -qcache' I get a long list of output but I
don't think it worked correctly:
[Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018
-qcache
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r-- 1 root wheel 87913 Nov 8 10:52
/Applications/freesurfer/subjects/ms_018/scripts/recon-all.log
Darwin Lisa-Koskis-iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7
16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer/
Previous: /Applications/freesurfer
/Applications/freesurfer/subjects/ms_018/surf
#--------------------------------------------
#@# Qdec Cache lh thickness fsaverage Thu Nov 8 11:46:43 EST 2012
INFO: File lh.thickness does not exist!
Skipping creation of smoothed data for lh.thickness
#--------------------------------------------
#@# Qdec Cache lh area fsaverage Thu Nov 8 11:46:43 EST 2012
INFO: File lh.area does not exist!
Skipping creation of smoothed data for lh.area
#--------------------------------------------
#@# Qdec Cache lh area.pial fsaverage Thu Nov 8 11:46:43 EST 2012
INFO: File lh.area.pial does not exist!
Skipping creation of smoothed data for lh.area.pial
#--------------------------------------------
....etc
recon-all -s ms_018 finished without error at Thu Nov 8 11:46:43 EST 2012
done
My goal is to eventually be able to bring up my T1 images with the qdec
application and segment the motor cortex.
When I use the tkmedit command it works correctly (I have converted my files to
.mgz already).
Do you know if it is a pre-processing error that is preventing me from getting
the qdec application to work with my own brain images? I cannot open files in
qdec currently.
Many thanks,
Julia
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