Hi Jon - Can you please send all of trac-all.log? Sometimes there are hints earlier than where the error actually occurs.
Thanks, a.y On Fri, 22 Mar 2013, Jon Wieser wrote: > Hi > I ran trac-all -prep -c dmrirc_single_subject > and got the following error: > > here's the end of the output from trac-all: > > > RegMat --------------------------- > 1.000 -0.016 -0.000 4.210; > 0.000 -0.005 1.000 2.417; > -0.016 -1.000 -0.005 0.018; > 0.000 0.000 0.000 1.000; > FSLOUTPUTTYPE NIFTI_GZ > tkreg2FSL: mov det = -64, ref det = -1 > Cleaning up > > Started at Fri Mar 22 11:35:44 CDT 2013 > Ended at Fri Mar 22 11:38:10 CDT 2013 > BBR-Run-Time-Sec 146 > > bbregister Done > To check results, run: > tkregister2 --mov > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/dwi.nii.gz > --reg > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.dat > --surf > > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat > -inverse > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.bbr.mat > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat > -concat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat > > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2anatorig.mat > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat > -inverse > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat > #------------------------------------- > #@# Inter-subject registration Fri Mar 22 11:38:10 CDT 2013 > flirt -in > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat.nii.gz > -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_mni.nii.gz > -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat > -cost mutualinfo > > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anat.mat > -inverse > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat > -concat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat > > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.flt.mat > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.flt.mat > -inverse > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat > -concat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat > > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.bbr.mat > -inverse > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat > -concat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat > > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2anat.mat > convert_xfm -omat > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anatorig.mat > -inverse > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat > #------------------------------------- > #@# Masks Fri Mar 22 11:41:27 CDT 2013 > flirt -in > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz > -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz > -applyxfm -init > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat > -interp nearestneighbour > flirt -in > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz > -ref > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_orig.nii.gz > -out > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz > -applyxfm -init > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.flt.mat > -interp nearestneighbour > Error: failed to open file > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz > ERROR: Could not open image > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt > Image Exception : #23 :: Failed to open volume > /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt > for writing > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > Abort > Darwin cerebrum.uwm.edu 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 > > trac-preproc exited with ERRORS at Fri Mar 22 11:41:39 CDT 2013 > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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