Hi Joelle - The last command in the trac-all.log file (mri_probedicom) works fine for me, when I run it on your dicoms. So there must be something else after that command that causes the error. What do you see when you run "ls /Users/joelle/Documents/Tracula_new/tmp/5047_3_3T.long.5047_3T_base/dmri"?
Thanks! a.y ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joëlle Ismay Rosanne Van Der Molen [joelle.vandermo...@etu.unige.ch] Sent: Tuesday, April 25, 2017 4:54 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA tract reconstruction Of course, here it is. Thank you for taking a look at it! Best, Joëlle ________________________________ De : freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Yendiki, Anastasia <ayend...@mgh.harvard.edu> Envoyé : mardi 25 avril 2017 10:25 À : Freesurfer support list Objet : Re: [Freesurfer] TRACULA tract reconstruction Hi Joëlle - I can't come up with a config file without knowing the locations of your files. If you send me the trac-all.log, I can figure out at what step it fails. Best, a.y ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joëlle Ismay Rosanne Van Der Molen [joelle.vandermo...@etu.unige.ch] Sent: Tuesday, April 25, 2017 4:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA tract reconstruction Hi Anastasia, I still can't seem to make it run when I don't specify the gradient tables, so I think I'm probably doing something wrong in the configuration of the dmrirc file... Would you mind sending me the dmrirc file you would use to run this subject? Best, Joëlle ________________________________ De : freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Yendiki, Anastasia <ayend...@mgh.harvard.edu> Envoyé : mercredi 12 avril 2017 19:35 À : Freesurfer support list Objet : Re: [Freesurfer] TRACULA tract reconstruction Hi Joelle – I tested one of your dicoms and the gradient table that mri_convert reads from it works just fine. So you can just pass your dicoms to TRACULA and it’ll do the rest. No need for you to specify the gradient tables. Best, 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: Friday, March 31, 2017 at 7:44 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] TRACULA tract reconstruction Hi Anastasia, I sent the links for the dicom files to you and just want to make sure - did you receive them? Best, Joëlle ________________________________ 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 30 mars 2017 15:20 À : Freesurfer support list Objet : Re: [Freesurfer] TRACULA tract reconstruction Hi Joëlle - Can you please send the filedrop upload to me too? Thanks! 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 Joëlle Ismay Rosanne Van Der Molen [joelle.vandermo...@etu.unige.ch<mailto:joelle.vandermo...@etu.unige.ch>] Sent: Thursday, March 30, 2017 7:27 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA tract reconstruction Hi Barbara, Thank you for the tip, I managed to anonymize my dicom images. I uploaded them on filedrop. The scanner used for the acquisition is a Siemens Prisma 3 Tesla. Best, Joëlle ________________________________ 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 Barbara Kreilkamp <bakk....@googlemail.com<mailto:bakk....@googlemail.com>> Envoyé : mercredi 29 mars 2017 14:18 À : Freesurfer support list Objet : Re: [Freesurfer] TRACULA tract reconstruction Hi Joëlle, Which scanner was used to acquire the images? I have used Osirix light in the past to anonymize my dicom images, maybe you'd like to try that? Best wishes, Barbara On 29/03/2017 13:30, Joëlle Ismay Rosanne Van Der Molen wrote: Hi Anastasia, Yes, I use dicom images as input for Tracula. I also specify the bvecs files, as Tracula returns an error if I try to run it with a configuration file that does not contain them. Unfortunately, our dicom images are not anonymised, so I cannot provide them. Best, Joëlle ________________________________ 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 : mercredi 22 mars 2017 15:40 À : Freesurfer support list Objet : Re: [Freesurfer] TRACULA tract reconstruction 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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