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Hello freesurfer developers,
When running trac-all the script seems to be getting tripped up on the epidewarp.fsl portion of the script and throwing a weird error about the fsl version? I am running trac-all -prep with bo homogeneity correction included in the configuration file.
I get the following error.
writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz...
orientLAS /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 10
mri_convert -oni 96 -onj 96 -onk 53 -oid -0.998405 -0.0247418 0.0507528 -ojd 4.61648e-10 0.898878 0.438199 -okd 0.0564624 -0.4375 0.897444 -oc 2.21634 10.523 31.9495 -rt nearest /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz
mri_convert.bin -oni 96 -onj 96 -onk 53 -oid -0.998405 -0.0247418 0.0507528 -ojd 4.61648e-10 0.898878 0.438199 -okd 0.0564624 -0.4375 0.897444 -oc 2.21634 10.523 31.9495 -rt nearest /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz
normalizing out_i_direction: (-0.998405, -0.0247418, 0.0507528) -> (-0.998405, -0.0247418, 0.0507528)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz...
TR=560.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998405, -0.0247418, 0.0507528)
j_ras = (-4.61648e-10, -0.898878, -0.438199)
k_ras = (0.0564624, -0.4375, 0.897444)
Reslicing using nearest
writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz...
mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/phase/TE7.38_image000001.dcm
/Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0info.dat
fslroi /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_eddy.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/lowb.nii.gz 0 1
epidewarp.fsl --mag /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0mag.nii.gz --dph /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz --exf /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/lowb.nii.gz --epi /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_eddy.nii.gz --tediff 2.46000000000000000000 --esp 0.7 --vsm /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/vsm.nii.gz --epidw /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi.nii.gz
FSLVersion 6.0.1
FSLVerMaj 6
FSL Version is 6.0.1, must be 3.X or 4.X or 5.X
Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Sat Apr 20 14:56:02 EDT 2019
Does this mean there is an issue with the trac-all script that makes it incompatable with fsl?
I notice the --vsm /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/vsm.nii.gz portion of the epidewarp.fsl script was not created. Everything else that should go into it was created.
Can anyone give me some guidance on why this might be happening?
Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298