Re: [Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hi again Also the same when run via X11 from a beastly compute node. As it runs just fine on Ubuntu 16.04 with the very same NFS storage backend we are at a loss, but the finger points at something with CentOS Stream I guess. Anyone using it on Cen

Re: [Freesurfer] Question about hippocampal sub-volume extraction

External Email - Use Caution Hi, Abdalla Z Mohamed Thanks for your reply, but this is code is for T1 scan only according to the instruction, I want to extract the volume from the T2 (for segmentation based only on the additional scan ) Best, Wei On Mon, May 3, 2021 at 7:55 PM w

Re: [Freesurfer] Question about hippocampal sub-volume extraction

External Email - Use CautionHi Wei, You can directly extract the volumes from all subjects within your Freesurfer Analysis folder by using the following command quantifyHAsubregions.sh hippoSf T1 result.txt Best regards, Abdalla Z Mohamed.   From: Wei ShaoSent: Tuesday, 4 May 2021 5

[Freesurfer] mri_ribbon does not return the ribbon

External Email - Use Caution Hi! I am trying to make a ribbon.mgz from a non-human primate surface recon that does not have an aseg. Following this prior discussion: Re: [Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com)

[Freesurfer] Question about hippocampal sub-volume extraction

External Email - Use Caution Hello,Dear Freesurfer exports I have a question about the pipeline of hippocampal sub-volume extraction: quantifyHAsubregions.sh hippoSf - Let's say I have two different groups of analysisID such as sub-AVP and sub-BAY I can pass a wildcar

[Freesurfer] PET seeding with hippocampal subfields

External Email - Use Caution Dear Freesurfer Development Team I've used freesurfer with hippocampal subfields module to get GM and Thickness in this region in detail. but now I need this subfields' mask to use it on my PET data. So I'll appreciate it if you tell me how I can get t

Re: [Freesurfer] QA in longitudinal processing

Was the aseg correct in the cross? If you can upload this subject (all the cross and long timepoints) we can take a look Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Malo Gaubert Sent: Monday, May 3, 2021 10:19 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Frees

Re: [Freesurfer] QA in longitudinal processing

External Email - Use Caution Hello, Any idea on how to correct pial & white matters segmentation splitting out on lateral ventricle while aseg is correct (see previous message below)? Thank you. Le lun. 26 avr. 2021 à 08:38, Malo Gaubert a écrit : > Hello, > > Any idea on how

Re: [Freesurfer] Out of memory from longitudinal segmentation of hippocampus

Yeah that’s what we do at the Martinos cluster ;-) I’m glad it’s working! From: on behalf of Wei Shao Reply-To: Freesurfer support list Date: Friday, April 30, 2021 at 19:19 To: Freesurfer support list Subject: Re: [Freesurfer] Out of memory from longitudinal segmentation of hippocampus