Hi Joëlle – What images do you pass as input to TRACULA? Do you pass the dicom itself, or a converted file? Happy to look at your dicom, if it’s anonymized.
a.y From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Joëlle Ismay Rosanne Van Der Molen <joelle.vandermo...@etu.unige.ch<mailto:joelle.vandermo...@etu.unige.ch>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, March 22, 2017 at 3:55 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] TRACULA tract reconstruction Hi Anastasia and Antonin, I apologize for the late response. Thank you very much for the explanations! Regarding the gradient tables, I realized that I was indeed using the old version of mrtrix3, and was getting tables with a flipped x component (sign inversion), which corresponds to the bug that is highlighted in the blog link you sent me. After having updated mrtrix3, the tables now look correct. What seems odd, however, is that in fact mri_convert outputs the same gradient tables as the old version of mrtrix3, that is, with a flipped x component. I tried running tracula on one of our subjects using gradient tables obtained with the updated mrtrix3, versus those obtained with mri_convert, and the results are quite different. I attached several files, so that you could maybe take a look and tell me how to best interpret this: - the bvecs from the updated mrtrix3 (mrtrix3up_bvecs) - a screenshot from the gradient directions (FA map overlaid with V1 map) resulting from usage of the bvecs tables from the updated mrtrix3 (mrtrix3up_graddirs) - a screenshot from the path reconstruction resulting from usage of the bvecs tables from the updated mrtrix3 (mrtrix3up_tracts) - the bvecs from mri_convert (mriconvert_bvecs) - a screenshot from the gradient directions resulting from usage of the bvecs tables from mri_convert (mriconvert_graddirs) - a screenshot from the path reconstruction resulting from usage of the bvecs tables from mri_convert (mriconvert_tracts) Note that the TRACULA steps were done using version 6.0. Based on these outputs, my guess is that the correct bvec table is the one obtained with the updated version of mrtrix and not the one obtained with mri_convert. But I would appreciate your opinion on that. Thanks again for your help! Best, Joëlle van der Molen ________________________________ De : freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> de la part de Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> Envoyé : jeudi 16 mars 2017 22:27 À : Freesurfer support list Objet : Re: [Freesurfer] TRACULA tract reconstruction One potential difference is that TRACULA does not need the gradient vectors to be flipped. It needs to get them the way they are stored in the DICOM header, and that's what mri_convert outputs. Best, a.y ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Antonin Skoch [a...@ikem.cz<mailto:a...@ikem.cz>] Sent: Wednesday, March 08, 2017 10:03 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA tract reconstruction Dear Joelle, regarding the conversion to .bvecs, could you please show the example of difference between bvecs converted by mri_convert of FreeSurfer and mrconvert of mrtrix3? Do you have most recent version of mrtrix3? There have been a quite extensive discussion on implementation of FSL .bvec convention in mrtrix3 in spring 2016: http://www.mrtrix.org/2016/04/15/bug-in-fsl-bvecs-handling/ However, there have been quite a big effort to settle this issue and I am pretty convinced that the recent versions should have this issue resolved. Maybe you can also post this to the mrtrix community forum, they are usually responding very quickly and each post gives detailed attention. Regards, Antonin Skoch ??Dear Tracula experts, I am applying Tracula on a longitudinal data set, and have some questions I am hoping you could help me with: Firstly, upon visual inspection, several tracts appear to be quite messy, or small (on the default freeview threshold) for most subjects. However, the -stat step from Tracula does not necessarily flag these tracts as outliers. What is then the best way to decide whether tracts are not correctly reconstructed and need to be rerun separately once more? Can I rely on the flagged outliers? Or should I rerun all the tracts that do not look ok after visual inspection? And in the last case, for tracts that look small, are they considered as correctly reconstructed if looking ok at lower thresholds than the default of freeview? Second, concerning the rerunning of poorly reconstructed tracts, I was wondering if there might be a more automated way to configure the dmrirc file in order to adapt it for each subject/each tract to rerun (and its corresponding control points). Third, I was wondering if there is a recommended software for obtaining bvecs and bvals. For the moment I used mrconvert (from MRtrix, using the -export_grad_fsl option) and the new mri_convert from freesurfer 6.0. As they give different outputs, I was wondering if this may impact the reconstruction. Lastly, would you recommend using freesurfer 5.3 or 6.0 for applying the longitudinal stream of Tracula? Related to this, is it recommended to use the same freesurfer version to obtain the long/base images, and to run Tracula? Thank you for your time, Best regards, Joëlle van der Molen
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