[Freesurfer] Question about 3T images and brain atlas compatibility

External Email - Use Caution Hello, I wanted to extract brain morphometry data (cortical thickness, surface areas, volume, etc) using PALS-B12 atlas. I have some 3T MRI images that I have preprocessed using Freesurfer 3T flag. I am wondering if it would be ok to extract MRI data

[Freesurfer] Mapping labels from left hemisphere to right hemisphere in fsaverage space

External Email - Use Caution Hi all, I have manually drawn roi onto fsaverage space on the left hemisphere. Is there a way to transfer these labels to the right? The end goal is to extract cortical measures from labels in both hemispheres and then will be averaged for further an

[Freesurfer] Problem with skull strip & general beginner questions

External Email - Use Caution Hello everyone, I hope you can help me with my little problem I encountered after manually editing the skull strip. Because my internet provider crashed I'm unable to upload the log file right now and writing this from my phone. For context: I'm analy

[Freesurfer] mri_aparc2aseg with flag --a2005s

External Email - Use Caution Hello, I am trying to run mri_aparc2aseg with the flag --a2005s on a subject that I previously ran recon-all --all on. When trying to run mri_aparc2aseg with --a2005s I get the following error: could not read annot file 010/label/lh.aparc.a2005s.annot

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

Dear Jenna, 1.Manually editing aseg.mgz fixes the initialization (super important). 2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important) If it’s only 1 subject in a bigger study, I’d probably call it a QC fail and leave it out. If it’s a single case you’r

[Freesurfer] Freesurfer Hippocampal Subfield Misalignment

External Email - Use Caution Hi Experts, I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical boundaries of the hippocam

[Freesurfer] Atlas question

External Email - Use Caution Hi FS developers I'm doing an ROI analysis with data data and was wondering if there exists a merged Freesurfer white matter parcellation and Johns Hopkins University white matter label atlas. If yes what is it called and where can I find it? I am tryin

[Freesurfer] (no subject)

External Email - Use Caution Dear experts, I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6. I got the recon-all.log error message: ERROR: cannot find /share/apps/freesurfer-7.1.0/average/RB_all_2008-03-26.gca Thanks for your help. Sincerely, Peka -- Peka Ch

[Freesurfer] The European Neuroscience Institute in Göttingen (ENI-G) Germany announces positions for Group Leaders (m/f/d)

External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany announces positions for Group Leaders (m/f/d) - Limitation: fixed-term - Working period: full-time - Tariff: salary according to TV-L - Announcement published on 06.07.2020

[Freesurfer] bbregister using freesurfer v7

External Email - Use Caution Dear experts, I am running bbregister and have a couple questions: 1) I am using freesurfer version 7. My understanding is that I do not need any --init argument anymore, and without it, by default it uses init-coreg. Could you confirm this? (I test