[Freesurfer] Cerebellum ROI

External Email - Use Caution Hello Freesurfer developers, I want to create a ROI in fsaverage space including only certain regions of the cerebellum cortex. Is it possible to use/extract the labels from the "# Cerebellar parcellation labels from SUIT" or "# Cerebellar lobule par

Re: [Freesurfer] [EXTERNAL] Re: Longitudinal PET analysis

statistics. On Wed, Sep 21, 2022 at 12:39 PM Gomar, Jesus mailto:jgo...@northwell.edu>> wrote: External Email - Use Caution Thank you Doug, I will follow your suggestion. From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu&g

Re: [Freesurfer] [EXTERNAL] Re: Longitudinal PET analysis

2)/2). --paired-diff-norm1 Same as --paired-diff, but normalizes by time point 1, ie, (Input1-Input2)/Input1. --paired-diff-norm2 Same as --paired-diff, but normalizes by time point 2, ie, (Input1-Input2)/Input2. On 9/20/2022 3:31 PM, Gomar, Jesus wrote: External Email - Use Caution

[Freesurfer] Longitudinal PET analysis

External Email - Use Caution Hello Freesurfer developers, I am interested in analyzing PET data following a longitudinal design. I have co-registered each PET image to the closest MRI in time processed through the longitudinal stream. I have sampled each co-registered PET image t

[Freesurfer] Update aseg stats file

Good morning, I have a group of subjects reconed with v5.1 and a group reconed with v5.3. In order to get the same aseg structures for all subjects in the stats file: Is there an option to update the aseg file only (like flags -cortparc & -parcstats for cortical measures)? Best, Jesus The i

Re: [Freesurfer] (no subject)

the recon-all.log file doug On 9/17/13 10:34 PM, Gomar, Jesus wrote: Hi Doug, I have run recon-all -s subject -cortparc -parcstats and the process finished without errors, but the aparc files do not have the perirhinal cortex on it. I have noticed that when I recon with 5.3 perirhinal labels are cr

[Freesurfer] (no subject)

Hi Doug, I have run recon-all -s subject -cortparc -parcstats and the process finished without errors, but the aparc files do not have the perirhinal cortex on it. I have noticed that when I recon with 5.3 perirhinal labels are created on the label folder, but when I run recon-all -s subject -c

[Freesurfer] mris_anatomical_stats

Dear Freesurfer experts, I hope someone can help me with a couple of questions regarding the use of mris_anatomical_stats command: 1. I am using mris_anatomical_stats to compute perirhinal thickness but with subjects I had previously recon through v5.1.0, and of course the mris_anatomical_sta

Re: [Freesurfer] Peirhinal cortex thickness

Thank you very much Bruce, I have used mris_anatomical_stats and it worked beautifully. Cheers Jesus -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, August 29, 2013 1:19 PM To: Gomar, Jesus Cc: 'freesurfer@nmr.mgh.harvard.edu' S

[Freesurfer] Peirhinal cortex thickness

Dear all, I am interested on getting thickness measures of the perirhinal cortex. I am using version 5.3 and I am aware that a label for the perirhinal cortex has been created in version 5.2. However, when I run recon-all I don't get thickness measures of the perirhinal cortex (just as I do for