It's not an issue of compatibility. The tkregister2 executable doesn't exist in
whatever version you're sourcing when you run tracula. As far as I can see, it
should be there in both the stable6 and dev versions. Any chance that something
went wrong when you built the dev version on your system and tkregister2 did
not compile?
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow
<ddcc2...@gmail.com>
Sent: Thursday, July 4, 2019 8:24:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Trac-all error
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<mailto:ddcc2...@gmail.com>
443-254-6298
On Thu, Jul 4, 2019 at 8:08 AM Daniel Callow
<ddcc2...@gmail.com<mailto: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<mailto:ddcc2...@gmail.com>
443-254-6298
On Thu, Jul 4, 2019 at 4:26 AM Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Daniel Callow <ddcc2...@gmail.com<mailto: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<http://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<http://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<http://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<mailto:ddcc2...@gmail.com>
443-254-6298
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