---------- Forwarded message ---------- From: "Salil Soman" salsoman@stanford.edu Date: Jan 12, 2014 1:28 PM Subject: Re: problem with bvecs file with new (12/13) TRACULA code To: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu Cc:

Hi,

Thank you for your email. Taking the .bval and bvec files outputed by dcm2nii (which are row format) and transposing them to column format was resulting in the blank rows that were causing troubles. Running this command got rid of the problems and allowed trac-all prep / bedp / and path to complete without errors:

sed '/^\s*$/d'

Thanks,

Sal

On Fri, Jan 10, 2014 at 3:57 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

...

Hi Sal - It looks like a problem with the spaces at the end of the lines of the bvecs file. If you remove those spaces, it should work. Thanks for bringing this to my attention - the row-formatted bvecs files are new in this version and I'll make sure to allow them to have spaces at the end of the lines in the future.

a.y

On Thu, 9 Jan 2014, Salil Soman wrote:

Hi,

...

I am re-running GE acquired 3T product DTI data which ran without trouble through the older tracula code. However, now when I run the code, the bvec file that gets generated has an extra 0 placed at the very end, and then trac-all -prep eventually fails because it complains the bvec and bvals files have non-matching number of entries. I do have the dorotbvecs option set to 1 (as I had before). Any suggestions on what I am doing incorrectly would be greatly appreciated. I have attached the bvec and bval files I am providing a input.

Best wishes,

Sal

Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System