Hi Linnea Marie - Screenshot 3 doesn't look that bad actually. You could use that and see if the FA comes out to be an outlier compared to other subjects. Increasing the controls points for the fminor from 5 to 6 would be another option.
Best,
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Linnea Marie Dramdal Borg [lmborg@stud.ntnu.no] Sent: Wednesday, October 18, 2017 5:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA qc: forceps minor and major
Hi,
Thank you, we did that successfully on every file except one. There is one forceps minor left with bad voxel distribution. Would you recommend reinitializing it again, or can we use it as it is? Or should we attempt to increase the number of control points?
I've attached the three examples, and "210_fminor1.png" is the worst. In pictures "210_fminor2.png" and "210_fminor3.png" TRACULA has obviously found the tract, but I'm not sure what the best option is. What would you recommend?
Thank you,
Linnea Marie
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Sent: Friday, October 6, 2017 11:26:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA qc: forceps minor and major
Hi Linnea Marie – You’re right in your assessment. Are you using 6.0? You can reinitialize those bad cases, by adding “set reinit = 1” in your config file and changing the path list and subject list to specify only the tract and subjects that you want. Then rerun trac-all --prior and trac-all —path for those cases.
Best,
a.y From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Linnea Marie Dramdal Borg <lmborg@stud.ntnu.nomailto:lmborg@stud.ntnu.no> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, October 6, 2017 at 6:13 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA qc: forceps minor and major
Hi,
We have run into some issues with our forceps major and forceps minor tractographies. I have attached examples: In "fminor_bro_139.png", there is a "bridge" in forceps minor in the space between the hemispheres. We've also come across other cases of bridging in forceps minor, with somewhat unusual voxel intensity distribution, such as in "fminor_onestripe_otherwOK.png" and" fminor_litenbro_OKornot_210.png". Also, "fmajor_132_toolateral.png", fmajor brances out in the left hemisphere (right in the picture). All of these cases seem pretty bad to us. Do you agree?
In contrast, "fminor_allslicesOKbutone_158.png" looks fine, but there is one slice where it branches out to some extent. Are we correct in assuming this won't affect the results too much, or is there something we can/should do about this?
Thank you,
Linnea Marie