Re: [Freesurfer] calculating geodesic distances between vertices

Hello Burke, you might want to check out https://github.com/NeuroanatomyAndConnectivity/surfdist . It works directly on Freesurfer output. The approach is described here: Margulies, D.S., Falkiewicz, M. and Huntenburg, J.M., 2016. A cortical surface-based geodesic distance package for Python. Gi

Re: [Freesurfer] volume parcellation

Well, it's a pretty straightforward format, but we have created all the icosahedral supersamplings there are in that range. On Thu, 30 Mar 2017, Almarshad F. wrote: > hi Bruce; > > thanks for your help, i needed to create tri file with a different number of > areas to use it with mris_make_face

Re: [Freesurfer] volume parcellation

hi Bruce; thanks for your help, i needed to create tri file with a different number of areas to use it with mris_make_face_parcellation? can you help with the best way to do that? any tool or functions outside freesurfer thank in advance From: freesur

[Freesurfer] calculating geodesic distances between vertices

I am interested in finding the distance between two vertices along the cortical surface. So far I have used two methods: (1) Compute the shortest path with a variant of Dijkstra's algorithm on the white surface. (2) Compute the great circle distance on the sphere surface. (as done by Risk et.al.

[Freesurfer] HCP Course 2017: Faculty and Course Schedule Available -- Register Now!

Faculty listings and the full schedule of covered topics are now available for the 2017 HCP Course: "Exploring the Human Connectome"

Re: [Freesurfer] Recon-all after edits

Hello Bruce, I think this ties to one of my previous questions. Most of the volumes I processed need both wm and pial edits (typically deleting incorrectly added voxels for both). More recently, I was editing wm.mgz for wm and brainmask.mgz for pial. From the wiki, if changes are made for both wm/

Re: [Freesurfer] smoothing kernel

Hi Bruce What I mean is - labeled sulci in volume space, overlaid onto surfaces and then averaged across subjects. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Mar 30, 2017 at 12:56 PM, Bruce Fischl wrote: > what is a sulcal probability

[Freesurfer] Trying to compare 2 scans from same person, 6 months apart.

First scan is 005_IHD_1 Second scan is 005_IHD_1_post These were in $SUBJECTS / ihd I moved them into $SUBJECTS (i.e. no subfolder within $SUBJECTS folder). I am following this; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing FsTutorial/LongProcessing - Free Surfer

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

you are not giving it the proper glmdir dir. the glmdir is /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova On 03/30/2017 01:12 PM, Clara Kühn wrote: > I tried this command: > > mri_glmfit-sim --glmdir > /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

I tried this command: mri_glmfit-sim --glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post --cache-dir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces and got this error: ERROR: cannot find

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

what do you mean that it did not seem to work? On 03/30/2017 11:25 AM, Clara Kühn wrote: > Thank you! I completely didn't see that. It worked. > > I was wondering how to proceed next. The tutorial ends with running the > glmfit command. I've tried correcting for multiple comparisons with Monte

Re: [Freesurfer] smoothing kernel

what is a sulcal probability map? On Thu, 30 Mar 2017, Trisanna Sprung-Much wrote: > thanks, Bruce - that is what I am learning. And if it was to smooth data > from a sulcal probability map? A FWHM of 10 seems pretty high > best > > Trisanna > > -- > Ph.D. CandidateMcGill University > Integ

Re: [Freesurfer] Parahippocampal subfields huge memory demands

Ha, that’s funny. The dimensions seem perfectly fine to me … Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 30 Mar 2017, at 09:16, Ferdi van de Kamp mailto:ferdivdk...@gmail.com>> w

Re: [Freesurfer] smoothing kernel

thanks, Bruce - that is what I am learning. And if it was to smooth data from a sulcal probability map? A FWHM of 10 seems pretty high best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Mar 30, 2017 at 12:17 PM, Trisanna Sprung-Much < t

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

Thank you! I completely didn't see that. It worked. I was wondering how to proceed next. The tutorial ends with running the glmfit command. I've tried correcting for multiple comparisons with Monte Carlo but that doesn't seem to work. How can I interpret the files that are the output from the

[Freesurfer] Open position at Boston/Children's Hospital for bilingual research assistant (Spanish-English) {Disarmed}

The Gaab Lab

[Freesurfer] Open position at Boston/Children's Hospital for bilingual research assistant (Spanish-English)

The Gaab Lab

Re: [Freesurfer] Recon-all after edits

Hi Manuel -autorecon2-cp runs all the steps that autorecon2-wm does so it is redundant. If you run autorecon2-cp and autorecon3 you will get everything (unless you edit the aseg) cheers Bruce On Thu, 30 Mar 2017, Manuel Delgado wrote: > Dear list, > There is an issue that I have been concerned

Re: [Freesurfer] smoothing kernel

Hi Trisanna sorry, there is no easy answer to this question. It depends on what you are trying to do. Bruce On Wed, 29 Mar 2017, Trisanna Sprung-Much wrote: > Hi there > I am wondering whether there is an acceptable FWHM to use to smooth surface > data (for instance, a probability map)? > > Ma

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 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joëlle Ismay Rosanne Van Der Molen [joelle.vandermo...@etu.unige.ch] Sent: Thursday, Mar

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 de la part de Barbara Krei

[Freesurfer] Recon-all after edits

Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits have been made to a subject? For example, if you have edited all the po

[Freesurfer] Qcache

Dear list, When processing the data for longitudinal analysis (or even for cross sectional) the -qcache has to be run before editing or after all the edits have been done? Thank you -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, I

Re: [Freesurfer] Parahippocampal subfields huge memory demands

Hi Eugenio, I've been trying figure out what is going on and part of the problem seems to be a buggy scheduler, which cannot be remedied at the moment. E.g. 64G maxvmem is reached in one subject within 12 seconds (when running a batch of over 100 participants). Running it again later (in a very sm

[Freesurfer] FREEVIEW: Registration visualization

Hello everyone, I am quite new to FreeSurfer and I have a doubt for the visualization of the data on a registered surface.Is it enough to load in freeview the surface.reg with overlayed the data like in: freeview -f lh.sphere.reg:overlay=lh.sulc or  freeview -f lh.sphere.reg:annot=aparc.annot Doi