[Freesurfer] Tutorial Data Set - Won't Download

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to download the tutorial dataset, as described on the FreeSurfer Tutorial Datasets page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data). It is able to download majority of the buckner_data file

Re: [Freesurfer] Matlab Segmentation error when running hippocampal segmentation in dev version

External Email - Use Caution Hi, Right after calling the command and getting the segmentation error it only prints out this: # #@# Hippocampal Subfields processing (T1) left Mon Nov 5 11:37:11 CET 2018

[Freesurfer] problems concerning mris_prepoc

External Email - Use CautionDear Sir or Madam,   I am currently trying to run a group analysis on FreeSurfer. After having created a FSGD-File I tried mris_prepoc. As a command I use   mris_preproc --fsgd FSGD_File_Aggression.fsgd --cache-in thickness.fwhm10.fsaverage --target

[Freesurfer] How to combine and divide surface-based fMRI data?

External Email - Use Caution Hello FreeSurfer experts, May I ask how can I modify the surface-based fMRI data, such as combing two independent sessions into one or dividing one 4D into a series of 3D surface-based fMRI files in which each one denotes a single volume/TR? Thank you

[Freesurfer] Compiling same-subject data across multiple scanning sessions

External Email - Use Caution Hi all, I'm wondering whether there's a way to compile same-subject data across multiple sessions into the same analysis. More specifically, I've run all my individual scanning sessions through preproc-sess (same subject, different scanning days)

Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

External Email - Use Caution Can anyone help? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruss, Joel E Sent: Friday, October 19, 2018 9:26:39 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Nonsensical

[Freesurfer] Longitudinal brainstem structures / thalamic nuclei

External Email - Use Caution Hi Eugenio, Just wanted to ask quickly if there is plan to implement longitudinal processing for the brainstem structures and thalamic nuclei modules? Thanks! Niels ___ Freesurfer mailing list Freesurfer@nmr.m

Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

Hi Joel Doug is on vacation so I'll try to help. You can use mris_curvature -w ... to recreate the curv files, but I think that is a red herring. Can you summarize what is going on? Have you used mris_info to extract the various transforms from the surface file? Did you fix the off-by-one that

Re: [Freesurfer] İlt: Desikan Atlas in volume space

Hi Ece for a given subject the Desikan parcellation is sampled into the volume alread in the file aparc+aseg.mgz in the subject's mri dir. Is that what you are looking for? cheers Bruce On Mon, 5 Nov 2018, ece ulug wrote: External Email - Use Caution Dear Experts, I am

Re: [Freesurfer] Tutorial Data Set - Won't Download

External Email - Use Caution ​Hello Emma, We're taking a look at those links which seem to not be working right now, so stay tuned. On Nov 5, 2018, at 05:30, Bunting, Emma wrote:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data __

[Freesurfer] help with subjects concatenation/dimension inconsistency error

Dear FreeSurfers, I am trying to apply surface processes to concatenate my cohort, but for some subjects I am getting this error: mri_surf2surf --srcsubject Ctrl034_R01_07 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval /autofs/space/alicu

Re: [Freesurfer] Longitudinal brainstem structures / thalamic nuclei

External Email - Use Caution Hi Niels, There is, but not in the short term. For the time being, you can run the module on longitudinally processed subjects. Cheers, /Eugenio -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biome

Re: [Freesurfer] Longitudinal brainstem structures / thalamic nuclei

External Email - Use Caution Hi Eugenio, Thanks as always for the speedy response! I was already going that route just wanted to make sure that something else wasn’t just around the corner. Thanks again! Niels On Mon, Nov 5, 2018 at 9:44 PM Iglesias Gonzalez, Eugenio < e.igles...@

[Freesurfer] Ynt: İlt: Desikan Atlas in volume space

External Email - Use Caution Thanks for your reply doctor. Actually I want to access Desikan K. Atlas coordinates as x, y, z. (each regions. for example caudalanteriorcingulate). In that case, one expert said that ; the closest to what you want is probably $FREESURFER_HOME/sub

Re: [Freesurfer] help with subjects concatenation/dimension inconsistency error

Hi Valeria that means there is a mismatch between the surface overlay and the surface. Maybe you sampled: /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh to the surface then recreated the surfaces after editing?

Re: [Freesurfer] Ynt: İlt: Desikan Atlas in volume space

I don't think there is an lh.aparc.label file - I don't know what it would be if it existed. Maybe we can take a step back and you can let us know what you are trying to achieve? On Mon, 5 Nov 2018, ece ulug wrote: External Email - Use Caution Thanks for your reply doctor.

[Freesurfer] Recon-all run error

External Email - Use Caution Dear FS, When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the mri_convert command is executed. The specific errors are as follows: /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core

Re: [Freesurfer] Recon-all run error

that certainly looks like something is running out of ram. Can you run the command that failed directly on the command line and see if it works? Was anything else running on the machine at the time? We do report total and free memory at the start of the recon in the recon-all.log file cheers B

[Freesurfer] ?????? Recon-all run error

External Email - Use Caution Dear Bruce, I found the error location in the recon-all.log folder. Here is the place where it went wrong??I don't think it's the reason for insufficient memory.. ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.''

[Freesurfer] Triangular mesh sampling problem

External Email - Use Caution Dear FS We now have high and low resolution images, we want to resample each triangular surface mesh generated from low-resolution data onto the corresponding triangular surface mesh generated from high-resolution data and vice versa as follows: For

[Freesurfer] 回复： 回复： Recon-all run error

External Email - Use Caution Dear fsbuild, Thank you very much for your help, I will try to enter this line of statements and then run high-resolution data, but I did not find the putget.c file, is it under the installation of freesurfer file, or a system file. yours yujunjie