Can you do this in two steps? First, convert the dicom to a volume format (eg,
mgz or nii.gz) with
mri_convert image0000001.dcm dwi.nii.gz
This may or may not create bvals and bvecs. If not, then you will have to
supply them. If they are created, look at them and make sure they are right.
Next run dt_recon specifying the input and the bvals/bvecs
On 2/15/19 9:22 AM, Daniel Davidson Callow wrote:
External Email - Use Caution
Hello,
I tried to run dt_recon, however, I received the following error message.
Attached is the error log.
dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm
--s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon/
MatrixReadTxT: could not scan value [1][1]
No such file or directory
WARNING: matlab elment type is 1852050003, which is not a matrix.
mri_glmfit.bin(51624,0x7fffaff913c0) malloc: *** mach_vm_map(size=9155227648)
failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
could not allocate 1684305759 x 1144402954 matrix
Cannot allocate memory
mri_glmfit.bin(51624,0x7fffaff913c0) malloc: *** mach_vm_map(size=13474447360)
failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
could not allocate 1684305759 x 1144402954 matrix
Cannot allocate memory
unsupported matlab format 540094003 (unknown)
Cannot allocate memory
It also seems when dt_Recon is trying to process different subjects in parallel
they are being processed in the same folder? does this create an issue?
Any help you can provide in debugging the issue would be greatly appreciated!
Thanks,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
[email protected]<mailto:[email protected]>
443-254-6298
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