External Email - Use Caution
It might be an issue with the current freesurfer dev version because when I change it back to the Freesurfer 6.0 version it works perfectly fine? And has no issues reading them. On Tue, Apr 2, 2019 at 1:51 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
It is having problems reading both the bvals and the bvecs
On 4/2/19 9:34 AM, Daniel Callow wrote:
External Email - Use CautionHello,
I am running dt_Recon with the following specifications and am running into this issue? I wasn't running into this issue previously. Two changes I made are I added the --eres-save flag and I am running the code on the dev version instead of the freesurfer6.0 version. Any idea what could be contributing to this issue?
I am running the following
mri_convert image000001.dcm /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/dwi.nii.gz
dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/dwi.nii.gz --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --eres-save --o /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}
and get an error at this point
#@#-------------------------------
Fitting Tensors
Mon Apr1 15:16:29 EDT 2019
cd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES114.Rest
mri_glmfit --y /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz --glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 --nii.gz --dti dwi.bvals dwi.voxel_space.bvecs --eres-save
$Id: mri_glmfit.c,v 1.246 2017/02/15 21:04:18 greve Exp $
cwd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES114.Rest
cmdline mri_glmfit --y /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz --glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 --nii.gz --dti dwi.bvals dwi.voxel_space.bvecs --eres-save
sysnameDarwin
hostname 255a-280.umd.edu http://255a-280.umd.edu
machinex86_64
user amos
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz
logyflag 1
usedti1
glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory
/Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114
Loading y from /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz
... done reading.
Using DTI
Loading BValues from dwi.bvals
ERROR: DTIloadBValues(dwi.bvals): could not scan value(s)
Found 65 bvalues
ERROR: DTIloadBValues(dwi.bvals): could not scan value(s)
Loading BVectors from dwi.voxel_space.bvecs
ERROR: DTIloadBValues(dwi.voxel_space.bvecs): could not scan value(s)
Found 0 bvectorss
ERROR: DTIloadBValues: no bvectors found in dwi.voxel_space.bvecs
Best,
*Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park _ddcc2442@gmail.com mailto:ddcc2442@gmail.com_ 443-254-6298
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