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