Hi Mahtab - If your dicom file is anonymized, can you upload it here for us to take a look?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Please address the upload to ayendiki and greve.

Thanks, a.y

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Farahbakhsh, Mahtab [m.farahbakhsh.16@ucl.ac.uk] Sent: Monday, January 02, 2017 5:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Problem with trac-all correction step for DTI image processing

Dear FreeSurfer,

I am trying to pre-process my DTI data using TRACULA. But I receive an error when I run the pre-processing stage of DTI image processing. On the Correction step (1st step) I receive this error:

------------------------------------------------------------- MRIresample(): error inverting matrix; determinant is nan, matrix is: -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; Darwin Mahtabs-MBP 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Jan 2 03:23:23 IRST 2017 ------------------------------------------------------------

My DTI images are in enhanced DICOM format. In addition, I receive a warning earlier in the processing stage. The warning is:

WARNING: it appears that the image position for all slices is the same. This is a problem with the DICOM file. Using direction cosines from col and row to compute slice direction, but the output may be misoriented.

Please also find my log file attached to the mail.

Any kind guidance from you is much appreciated.

Kind Regards, Mahtab. -- Mahtab Farahbakhsh PhD Candidate Dept. Visual Neuroscience, UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL