External Email - Use Caution When running on freesurfer 6.0 I get the following pop-up screen as well.
*“tkregister2.bin” is not optimized for your Mac and needs to be updated.* This software will not work with future versions of macOS and needs to be updated to improve compatibility. Contact the developer for more information. Just FYI. It does work on the freesurfer 6.0 version despite the pop-up. It seems like trac-all is not compatible with the development version then? Best, *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 On Thu, Jul 4, 2019 at 8:08 AM Daniel Callow <ddcc2...@gmail.com> wrote: > 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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