Re: [Freesurfer] -qcache and thickness questions

Objet : Re: [Freesurfer] -qcache and thickness questions Yes, looks like small registration errors. I don't think it is problematic. Any vertex where even a single subject has a 0 should be masked out of the final analysis. On 12/3/2019 1:42 PM, Joëlle Ismay Rosanne Van Der Molen

Re: [Freesurfer] Keep manual edits of older freesurfer versions?

Rosanne Van Der Molen wrote: > > External Email - Use Caution > > Dear FreeSurfer experts, > > > I have a question regarding manual edits and change of FreeSurfer version. > > > In our lab, we have thus far processed most of our T1 scans using FS version > 5.1

[Freesurfer] Keep manual edits of older freesurfer versions?

External Email - Use Caution Dear FreeSurfer experts, I have a question regarding manual edits and change of FreeSurfer version. In our lab, we have thus far processed most of our T1 scans using FS version 5.1 and have performed manual edits when needed. We are now updating ou

Re: [Freesurfer] TRACULA tract reconstruction

Hi Anastasia, Ok thanks a lot! I will download the 6.0 version. Best, Joëlle De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Joëlle Ismay Rosanne Van Der Molen Envoyé : mercredi 3 mai 2017 13:39:34 À : Freesurfer support list Objet : Re

Re: [Freesurfer] TRACULA tract reconstruction

ments/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, 20

Re: [Freesurfer] TRACULA tract reconstruction

-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 speci

Re: [Freesurfer] TRACULA tract reconstruction

hat 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: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Joëlle Ismay Rosanne Van Der Molen m

Re: [Freesurfer] TRACULA tract reconstruction

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 inpu

Re: [Freesurfer] TRACULA tract reconstruction

ishes, 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

Re: [Freesurfer] TRACULA tract reconstruction

pass the dicom itself, or a converted file? Happy to look at your dicom, if it’s anonymized. a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Joëlle Ismay Rosanne Van Der Molen mailto:joelle.vandermo...@etu.unige.ch>> Reply-To: Freesurfer support list mailt

[Freesurfer] TRACULA tract reconstruction

??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 st