[Freesurfer] Question about statistical data for cerebellar segmentation ?

External Email - Use Caution Hi Freesurfer I would like to perform statistical analesys on cerebellar segmentation data. For my purposes, The atlases that come with Freesurfer don't give enough parcellation of the cerebellum. I tried looking online and found this email conversati

Re: [Freesurfer] Sulcal probability maps

What format is your sulcus in? On 2/16/2021 2:38 PM, Kristi Drudik wrote: External Email - Use Caution Good afternoon, I hope this email finds you well. I am in the process of “painting” MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the su

Re: [Freesurfer] convert BA probability labels to volume

Try adding --label-stat statvol.mgz to the command On 2/17/2021 10:16 AM, julienbesle wrote: > External Email - Use Caution > > Hello, > > I'm trying to convert label files containing probability values for > Brodmann areas (e.g. rh.BA1_exvivo.label) to volume files using > mri_label2vol.

Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits

That is fine. You could save a few min by not starting from scratch, but the brainmasking happens very close to the beginning. On 2/17/2021 3:57 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi, We are finding that the skull-stripping  in standard  FS 7.1.1. in a fe

Re: [Freesurfer] 3 groups comparison question (mri_glmfit)

How you solve this depends a little on what you want to analyze. If CPZ is a nuisance variable, you can run a DOSS (different-offset-same-slope) analysis. In this case, it will fit CPZ to all the data and not to each group separately (use --fsgd fsgdfile doss). If you want to look at the diff

Re: [Freesurfer] multiple comparisons correction

You have to use --grf. I never computed the cache tables for volumes On 2/19/2021 9:58 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution Dear Douglas, I have another question regarding multiple comparisons correction: Can I use --cache  with volume analyses? Or should I

Re: [Freesurfer] Sulcal probability maps

External Email - Use Caution Hi Doug, The sulci are .label format because they were painted directly on the surface using FreeSurfer 7.1. Best, Kristi From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: February 19, 2021 10:16 AM To: freesurfer@nm

Re: [Freesurfer] Sulcal probability maps

Hi Kristi I use mris_spherical_average for this, but I think Doug has something better documented Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kristi Drudik Sent: Friday, February 19, 2021 11:37 AM To: Freesurfer support list Subject: Re: [Freesurfer] Sulcal probabil

Re: [Freesurfer] multiple comparisons correction

External Email - Use Caution Dear Douglas, I have another question regarding multiple comparisons correction: Can I use --cache with volume analyses? Or should I use --grf? Thank you very much, Kind regards, Agurne El mar, 9 feb 2021 a las 18:11, Agurne Sampedro Calvete (

[Freesurfer] Hippocampal subfield segmentation by T2 scan

External Email - Use Caution Hi, dear Freesurfer team I used sagittal T1(MPRAGE-sag_T1w.nii.gz) to recon-all and did the hippo-subfield segmentation on T1, but when I tried to use the additional scan by segmentHA_T2.sh : segmentHA_T2.sh sub-AVP14352 /home/weishao/sub-AVP14352/Ses

Re: [Freesurfer] multiple comparisons correction

External Email - Use Caution Dear Douglas, And can I include abs to the --grf 3 command? I read this in the tutorial: "NOTE: the "abs" for GRF is only approximate. For volumes, it may give very conservative results" Is it better to include neg or pos? Thank you! Regards, Agurne

Re: [Freesurfer] Hippocampal subfield segmentation by T2 scan

External Email - Use Caution Hi Wei, I'm not one of the developers but std::bad_alloc probably means you ran out of memory, so it would be beneficial to the developers if you could include the details like - which version of FreeSurfer you're running, - how much memory that lin