Re: [Freesurfer] Registering preop and postop MRI scans

After running the longitudinal pipeline, it's still not registered well. Doug, I don't think I should attach the figures here, but you take a look at the registration here: freeview mg150.long.mg150_base/mri/T1.mgz mg150_postop.long.mg150_base/mri/T1.mgz Where the folders are in

Re: [Freesurfer] About segmentation of hippocampal subfields and nuclei of the amygdala

External Email - Use Caution Dear Dr. Iglesias, Thank you for your kind reply. My computer has 64GB of RAM. I have listed below the detailed information about my computer's specifications and version of FreeSufer. I would appreciate your advice.

[Freesurfer] Capture multiple images using freeview

External Email - Use Caution Dear FS developers, I know how to use freeview to capture one static image and save it to a file. For example, I can capture coronal view's slice 100 using this command: freeview \ -v $SUBJECTS_DIR/$subjectid/mri/orig.mgz \ -f $SUBJECTS_DIR/$

Re: [Freesurfer] Infant Freesurfer exiting without error

External Email - Use Caution Hello, Getting a list of the labels would be fantastic! Also, when relabeling the segmentations, do you normally just do that by hand? Thanks so much, Colleen From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf

Re: [Freesurfer] LGI error on FS7.1

This was fixed in 7.11. You can use that version or copy the attached file to this location $FREESURFER_HOME/matlab/freesurfer_read_surf.m On 5/11/2021 2:28 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: Hi, I am using Matlab R2014a, and FS7.1.0 and receiving this error when I

Re: [Freesurfer] mri_surf2surf fsaverage to fsaverage_sym

This is because it takes two passes through the transform. One takes each target vertex and finds the closest source vertex. The other takes each source vertex not already sampled and finds the closest target vertex to make sure that every source is represented. With the 2nd step, there may be

[Freesurfer] LGI error on FS7.1

Hi, I am using Matlab R2014a, and FS7.1.0 and receiving this error when I try to run -localGI. Is there a package I might be missing? Or am I using an outdated version of Matlab? = mris_smooth -nw -n 30

Re: [Freesurfer] About segmentation of hippocampal subfields and nuclei of the amygdala

Dear Daiki, Could this be a RAM memory issue? How much RAM do you have on this machine? Cheers, Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On May 11, 2021, at 06:16, 笹林大樹 mailto:ds...@med.u-toyama.ac.jp>> wrote:

Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker

External Email - Use Caution Hi Lara, What container are you using? Is it `freesurfer/freesurfer:7.1.1`? Can you share the docker run command you're using? -Paul On Mon, May 10, 2021 at 10:00 PM Lara Foland-Ross wrote: > External Email - Use Caution > > Sure. Here's

[Freesurfer] mri_surf2surf fsaverage to fsaverage_sym

External Email - Use Caution Hi experts, I am trying to resample some surface overlays from fsaverage to fsaverage_sym surface. I have used the following command: mri_surf2surf --srcsubject fsaverage --srcsurfreg fsaverage_sym.sphere.reg --trgsubject fsaverage_sym --trgsurfreg

Re: [Freesurfer] Error in SAMSEG preprocessing

External Email - Use Caution The lesion extension is memory hungry. The exact amount of RAM memory depends on the size and resolution of the scans. I'd say you need almost 16GB for 1mm (256x256x256) scans. Best, Stefano From: Hoopes, Andrew

Re: [Freesurfer] memory allocation error

External Email - Use Caution Sorry I forgot the attachment. Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences

Re: [Freesurfer] memory allocation error

External Email - Use Caution Dear Freesurfers, when running the longitudinal preprocessing on a subject, I get the same error as described here (see recon-all.log attached):