Hi Skyler - When you say it's been working fine, have you checked that the orientations are correct by viewing dtifit_V1.nii.gz and dtifit_FA.nii.gz, like in the snapshot that I sent you? If those orientations aren't correct, the gradient table isn't correct either.

a.y

On Tue, 21 May 2013, Skyler Gabriel Shollenbarger wrote:

Hi Anastasia,

Thank you for all of your help! 'trac-all' has been working fine with the other subjects, so it doesn't appear to be the gradient vector file. Yes, unfortunately the resolution is not the best.

Would you consider this subject a loss or are there other fixes you suggest?

Thanks again! Skyler

----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, May 21, 2013 10:40:59 AM Subject: Re: [Freesurfer] tracula error

Hi Skyler - A couple of things. I'm attaching a screenshot of the FA map and primary tensor eigenvectors of your subject. First, it looks like your gradient directions are incorrect, given how the eigenvectors are oriented in the corpus callosum (yellow arrows in the coronal and axial slice). The eigenvectors follow the shape of the corpus callosum in the axial view but not in the coronal view. My guess is your gradient vectors need to be flipped in the z-direction.

Second, your resolution is 4mm. There's going to be a lot of partial voluming. You'll have to give up on the thinner tracts, like ccg/cab (see purple arrow in sagittal view pointing to cingulum, you can barely resolve it from the corpus callosum).

Third, you have 14 gradient directions, so fitting the ball-and-stick model to this data, which is done by bedpostx and which you need for the tract reconstruction step, is going to be challening.

I don't want to discourage you, but tractography may be a bit more than this data can support.

Please let me know if you have more questions, a.y

On Mon, 20 May 2013, shollen2@uwm.edu wrote:

...

Hi Anastasia,

They were uploaded. Thanks for your help!

Skyler

Sent from my iPhone

On May 20, 2013, at 10:20 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

...

Hi Skyler - If you upload the dmri/dmri.bedpostX/dlabel/scripts directories of your subject for me, I'll take a look.

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

a.y

On Fri, 17 May 2013, shollen2@uwm.edu wrote:

...

Hi Anastasia,

The brain mask looks fine. Any other suggestions?

Thanks for your help, Skyler Sent from my iPhone

On May 17, 2013, at 12:24 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

...

Hi Skyler - How does the brain mask look like? Any major chunks of brain missing in the area of the left uncinate? That's the tract where the error occurs, and based on this info in the log file, I'm guessing it's a masking issue:

[...] INFO: Rejected 4221 streamlines for straying off mask INFO: Rejected 2 streamlines for reversing direction INFO: Rejected 9 streamlines as length outliers INFO: Have 56 total streamlines (min/mean/max length: 1/13/33) [...]

Hope this helps, a.y

On Wed, 15 May 2013, Skyler Gabriel Shollenbarger wrote:

...

Hi all,

We ran tracula prep stage and it exited with errors: 'Selected streamline has fewer than 5 points'. We have attached the log and error files if needed.

Thank you in advance! Skyler

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