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
443-254-6298


On Thu, Jul 4, 2019 at 4:26 AM Yendiki, Anastasia <AYENDIKI@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow <ddcc2442@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
443-254-6298
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