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 https://urldefense.proofpoint.com/v2/url?u=http-3A__slow.mri.tu-2Dmuenchen.de&d=AwMFaQ&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=s-VxZTdPXY4S0rcW6kW0YDWh-kEouGyhAJYX2FeNt9k&s=UgWTkYEmMlIN-Hlk4yHyg4ju4GkOcEg-PPBSX3ofvJU&e= 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. <trac-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at

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Hi Doug - This post from the archives addresses the same error message. Please check if this fixes it for you, too:

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37920.html

Best, a.y

On Mon, 9 Nov 2015, Douglas Merkitch 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. <trac-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... B_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=s-VxZTdPXY4S0rcW6kW0YDWh-kEouGyhAJYX2FeNt9k&s=BPpkxmOt6lD2bo BPcdkhoEqRqXkxUFMJ2PyVZHTK570&e=

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... 8rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=s-VxZTdPXY4S0rcW6kW0YDWh-kEouGyhAJYX2FeNt9k&s=zdzB6sXyVr17dm8l1VCBJnSkdKlvwvM74uaW sSp6spo&e=  . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.