Hi – The tractography is performed in the individual diffusion space of each subject, so the merged tract volumes are in that space. That’s why they align with the original FA map, which is also computed in diffusion space. I’m guessing that the FA map that you’re referring to in 1) is one that has been transformed to MNI space. That one will not align with the individual tracts.

Maybe the best way to troubleshoot this is for you to upload a zip file with all the output directories from a single subject, as well as the stats directory that contains the mean paths.
https://gate.nmr.mgh.harvard.edu/filedrop2/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Gabriela Longo <gabrielalongo.radiologia@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, February 23, 2018 at 3:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA registration

Yes, got it. But in these text files, the first line is already "#!ascii label, vox2ras=scanner".

It seems the problem is before the -stat step because I got many NaN in the group analysis. My impression is that the inter-subjects tracts are not well aligned. I also verified the registration:

1) dfifit_FA with MNI, that looks good;

2) merged_avg33_mni_bbr.mgz x dtifit_FA.nii.gz, that also looks good;

3) and then when I checked the merged_avg33_mni_bbr.mgz with MNI, it looks incorrect.

(I couldn't send the pictures due to the size of the email).   


2018-02-23 15:26 GMT-05:00 Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:
Sorry – I meant freeview, not trackvis!

From: Anastasia <ayendiki@mgh.harvard.edu>
Date: Friday, February 23, 2018 at 2:11 PM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA registration

So you may have been caught in that transition. The paths that you load into trackvis with the –w option are text files. Change the first line in those files to:
#!ascii label, vox2ras=scanner

When you do that and load the paths into freeview again, do they show up inside the brain?

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Gabriela Longo <gabrielalongo.radiologia@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, February 23, 2018 at 1:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA registration

Hi Anastasia,

thanks for your email.
I did the whole analysis in the developmental version, even the -stat.

Thanks, Gabriela

2018-02-23 13:21 GMT-05:00 Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:
Hi Gabriela – Any chance that you generated the paths with an older version of TRACULA, and viewed them in a newer version of freeview? There was a change in freeview at some point, in terms of the header that it expects those path files to have. This change happened between the 5.3 and 6.0 freesurfer releases, so if you ran TRACULA from the 5.3 release and used freeview from 6.0 or from a patched version that you downloaded in between 5.3 and 6.0, they may be incompatible. This would explain the outside the brain part. Now beyond that it seems that there's more strangeness going on, but let’s figure that part out first.

Thanks,
a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Gabriela Longo <gabrielalongo.radiologia@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, February 23, 2018 at 11:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA registration

Hi, 

I processed some subjects in TRACULA for a longitudinal evaluation.
I registered all of them in the MNI template (set doregmni = 1 
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz).

I checked the registration of my dtifit_FA.bbr.nii.gz with the MNI of all subjects.
However, when I performed the group analysis, I got more NaN than expected and I checked the images and the results are outside the MNI template (I am sending a picture).

I went back and checked the registration of the paths. Despite the dtifit_FA.bbr.nii.gz is correctly registered in the MNI, the paths aren't.

I am struggling here to find solutions. I really appreciate any insight to help me to solve this issue.

Thanks in advance, 

Gabriela Longo

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contains patient information, please contact the Partners Compliance HelpLine at
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