External Email - Use Caution Hello Anastasia,
I was running this on freesurfer's dev version. I will try running it on freesurfer 6.0. Best, *Daniel Callow* *PhD Student, Neuroscience and Conitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2...@gmail.com <ddcc2...@gmail.com>* 443-254-6298 On Thu, Jul 4, 2019 at 4:26 AM Yendiki, Anastasia <ayend...@mgh.harvard.edu> wrote: > Hi Daniel - Yes, this seems to be the problem: " tkregister2: Command not > found." What version of freesurfer are you using? > > > a.y > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow < > ddcc2...@gmail.com> > *Sent:* Wednesday, July 3, 2019 2:06:27 PM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Trac-all error > > > External Email - Use Caution > > Hello, > > I am running trac-all preproc with the following code > > setenv FREESURFER_HOME /Applications/freesurfer_dev > > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > *#Must set SUBJECTS_DIR to where data is or else uses what was set up when > installing freesurfer* > > setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurfer_MCIP/diffusion_recons > > > *#Must set up configuration file - see trac-all-config-file in > dti_analysis compository* > > *#In configuration file can change number of subject to perform analysis > on each cluster* > > > *#RUN FIRST* > trac-all -prep -c /Volumes/DANIEL/dmrirc.long.MCIP.example.sh > > > *and the attached configuration file. * > > *However, I get the following error.* > > #@# Intra-subject registration Tue Jul 2 18:21:42 EDT 2019 > > mri_convert > /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > > mri_convert > /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > > > $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ > > reading from > /Volumes/DANIEL/freesurfer_MCIP/MCIP0006_post.long.base_MCIP0006/mri/brain.mgz... > > TR=9.62, TE=3.90, TI=450.00, flip angle=12.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... > > orientLAS > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz > > INFO: input image orientation is LIA > > INFO: input image determinant is -1 > > mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 > -oc -6.32147 -1.97853 6.55573 -rt nearest > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz > > mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 > -oc -6.32147 -1.97853 6.55573 -rt nearest > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz > > > $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ > > reading from > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz... > > TR=9.62, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > Reslicing using nearest > > writing to > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz... > > tkregister2 --mov > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat_orig.nii.gz > --targ > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/brain_anat.nii.gz > --regheader --noedit --fslregout > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anatorig2anat.mat > --reg > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_post.long.base_MCIP0006/dmri/xfms/anat2anatorig.dat > > tkregister2: Command not found. > > Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 > 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Tue Jul 2 18:21:47 EDT 2019 > > > #------------------------------------- > > /Applications/freesurfer_dev/bin/trac-preproc > > #------------------------------------- > > #@# Inter-subject registration (base template) Tue Jul 2 18:21:49 EDT > 2019 > > cp > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat > /Volumes/DANIEL/dti_freesurf_MCIP/trac/base_MCIP0006/dmri/xfms > > cp: > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/mni2anatorig.mat: > No such file or directory > > cp: > /Volumes/DANIEL/dti_freesurf_MCIP/trac/MCIP0006_pre.long.base_MCIP0006/dmri/xfms/anatorig2mni.mat: > No such file or directory > > Darwin 255a-280.umd.edu 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 > 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Tue Jul 2 18:21:49 EDT 2019 > > *What might be causing the issue? Does it seem like tkregister2 isn't > working?* > > *Thank you for help or assistance you can provide.* > > *Daniel Callow* > *PhD Student, Neuroscience and Cognitive Science* > Exercise for Brain Health Lab > University of Maryland, College Park > *ddcc2...@gmail.com <ddcc2...@gmail.com>* > 443-254-6298 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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