Hi Douglas,

I actually solved it! So, if yours is the same problem, you need to change your bval and bvec file format. I used mricron to convert from dicom to nifti, then used the bvec and bval files it produced for me. What it gives as output doesn't match with tracula's format.

bvec file should look like:

0  0  0
 0  0  0
 0  0  0
 1  0  1
-1  0  1
 0  1  1
 0  1 -1
 1  1  0

bval file should look like:

0
0
0
1000
1000
1000
1000
1000 
1000

​If you adjust yours accordingly, it should work.

Best,​

On Mon, Nov 9, 2015 at 6:47 PM, Douglas Merkitch <Douglas_Merkitch@rush.edu> wrote:

Hey D,

I also had the same error in the same spot, although I'm using an earlier version of tracula and Mac OS. This is my first time using tracula for DWI processing so I am a little confused as to how to best troubleshoot this issue.

Any help from the experts would be great!

Thanks,

Doug

Douglas Merkitch

Neurological Sciences

Rush University Medical Center
Email: Douglas_Merkitch@rush.edu

On Nov 9, 2015, at 6:39 AM, denizzgursel <denizzgursel@gmail.com>

 wrote:

Dear all,

I am running Tracula preprocessing on NIFTI files. 

After running the command: trac-all -prep -c 

I get the error:

...

processing /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_tmp0032

mv -f /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs.norot

xfmrot /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi.ecclog /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs.norot /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs

ln -sf /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi.nii.gz /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/data.nii.gz

awk: fatal: cannot open file `1000' for reading (No such file or directory)

mri_concat --i /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_frame.nii.gz --mean --o /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/lowb.nii.gz

niiRead(): error opening file /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_frame.nii.gz

ninputs = 1

Checking inputs

ERROR: reading /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_frame.nii.gz

Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Nov  9 12:47:20 CET 2015

I checked the folder and 'dwi_frame.nii.gz' file was never created.

I attached the trac-all.log file.

Does anybody know how to solve this?

Best,

--

D.

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