[Freesurfer] mris_make_surfaces - longitudinal stream - questions

Dear experts, I am trying to understand what is the specificity of the pial and white surface generation in longitudinal stream, i.e. how the information from processing of base template is used for surface estimation in -long step of recon-all. Specifically: Why the maximal thickness is constr

Re: [Freesurfer] how does the content of the curv files compare to that of smoothwm.H.crv

Hi Fabio I'll cc Rudolph who has worked with the curvature much more than I have, but some points: 1. The negative gyral/positive sulcal curvature is a consequence of adopting an outwards pointing surface normal direction. 2. I think the smoothwm.H.crv is generated from the ?h.smoothwm surf

[Freesurfer] Fwd: [HCP-Users] HCP to FreeSurfer Resampling

Just following up on the message below. Respectfully, -Tim FreeSurfer experts, I am attempting to resample HCP data into FreeSurfer space with the following how to document: https://wiki.humanconnectome. org/display/PublicData/HCP+Users+FAQ.

Re: [Freesurfer] Fwd: [HCP-Users] HCP to FreeSurfer Resampling

Hi Tim we need your full command line and screen output. cheers Bruce On Tue, 22 Nov 2016, Timothy Hendrickson wrote: > > Just following up on the message below. > > Respectfully, > > -Tim > > FreeSurfer experts, > > I am attempting to resample HCP data into FreeSurfer space with the > fo

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, (also inline) > On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte > wrote: > > Hi Martin, > > Thanks for replying. Please see inline below: > >> Le 21 nov. 2016 à 20:26, Martin Reuter > > a écrit : >> >> Hi Matthieu, >> >> a few quick answer

Re: [Freesurfer] mris_make_surfaces - longitudinal stream - questions

Hi Antonin, I had answered that in my email from Nov. 18.. Thickness is not constrained to 3.5mm, but see my email for the full answer. Best, Martin > On Nov 22, 2016, at 12:15 PM, Antonin Skoch wrote: > > Dear experts, > > I am trying to understand what is the specificity of the pial and

Re: [Freesurfer] Fwd: recon-all -s Prueba2 exited with ERRORS

Hello, This is a known issue with ubuntu16 platforms and other distributions that include perl 5.22. That version of perl is incompatible with the version of the mni tools shipped with freesurfer 5.3 The issue has been fixed in the freesurfer v6-beta release (https://surfer.nmr.mgh.harvard.edu

[Freesurfer] quantifyHippocampalSubfields.sh

Hi Eugenio - Hope all is well with you at UCL. I have the run the subfields algorithm on a set of subjects using Freesurfer 6.0. All the brains were processed without much fuss. However, when I ran the following: quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt It yielded nothing. Can yo

Re: [Freesurfer] quantifyHippocampalSubfields.sh

Hi Alan, Can you please send the the command line that you used to generate the results, and a listing of the files in the mri directory of any subject you’ve analyzed? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://w

Re: [Freesurfer] quantifyHippocampalSubfields.sh

Hi Eugenio - The command I used was : [afrancis-mac:/Applications/freesurfer/subjects] afrancis% quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt Here are a listing of the files in the mri directory of a given brain: [afrancis-mac:subjects/DM_130/mri] afrancis% ls -la total 89392 drwxr-x

Re: [Freesurfer] quantifyHippocampalSubfields.sh

Hi again, The command should be: quantifyHippocampalSubfields.sh T1 Cannabis_HSF.txt Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 22 Nov 2016, at 18:00, Alan Francis mailto:alan

Re: [Freesurfer] quantifyHippocampalSubfields.sh

Wonderful. Thank you so much. best, Alan On Tue, Nov 22, 2016 at 1:42 PM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Hi again, > The command should be: > quantifyHippocampalSubfields.sh T1 Cannabis_HSF.txt > > > > Juan Eugenio Iglesias > ERC Senior Research Fellow > Translation

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Martin, Please see inline below: > Le 22 nov. 2016 à 17:04, Martin Reuter a écrit : > > Hi Matthieu, > (also inline) > >> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte >> mailto:matthieuvanhou...@gmail.com>> wrote: >> >> Hi Martin, >> >> Thanks for replying. Please see inline below:

Re: [Freesurfer] mris_make_surfaces in longitudinal stream - explanation of parameters

Dear Martin, thank you for the explanations, and sorry, I missed your previous response. Just I am wondering, what is the reason of the shrinkage? Why not to start directly from pial surface of the base? And, I also found a binary mris_longitudinal_surfaces, which is, however, not used in reco

Re: [Freesurfer] mris_make_surfaces in longitudinal stream - explanation of parameters

Hi Antonin in the case of severe atrophy or a long period between scans the pial surface from time 1 may be far enough outside the pial surface of time 2 that the deformation cannot recover it. We have found that starting it a bit inside makes it more robust. As for the mris_longitudinal_sur

Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces

Dear Bruce, thank you very much for your time. Concerning transformations, that is weird since I adopted my code from HCP pipelines https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/scripts/FreeSurferHiresPial.sh and there I think they use the surfaces precisely this

Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces

the vox2ras. Not sure about the HCP pipeline. They use a deprecated version of FS, but in any case what you had would not work as the ?h.pial surface didn't match the ?h.white.deformed one. If you also deformed the pial it would be ok On Wed, 23 Nov 2016, Antonin Skoch wrote: > Dear Bruce,