[Freesurfer] Recon-all Ending Fast

External Email - Use Caution Hello, I am trying to run the recon-all function and the whole process is completing within a minute or so. I was told that the whole process would take between 6-24 hours. This is the output I am getting after entering the command: Akilas-MacBook-A

[Freesurfer] Cerebellum Segementation

External Email - Use Caution Hello Experts! This is the first time I am doing tractography and my aim is to do it specifically for the cerebellum. I saw online that FreeSurfurer can segment the cerebellum, to create the ROI but I’m not entirely sure how to go about this. So far

Re: [Freesurfer] Cerebellum Segementation

Segementation Hi Akila, Have you run recon_all on your structural data? Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Sent: Friday, May 14, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cerebellum Segementation

[Freesurfer] Cerebellum Segmentation

External Email - Use Caution Hello Experts! This is the first time I am doing tractography and my aim is to do it specifically for the cerebellum. I saw online that FreeSurfurer can segment the cerebellum, to create the ROI but I’m not entirely sure how to go about this. So far

Re: [Freesurfer] Cerebellum Segementation

2021 5:22:08 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segementation Is your question then how to isolate the cerebellar WM/GM labels from aseg? Lila From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Sent: Friday,

Re: [Freesurfer] Cerebellum Segementation

...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Sent: Sunday, May 16, 2021 4:34 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segementation External Email - Use Caution External Email - Use Caution Hi Lilla, That would be ideal! Thanks Akila Get Outlook for iOS<ht

Re: [Freesurfer] Cerebellum Segementation

t will result in 4 ROI files that you can use in your further analysis. Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Sent: Sunday, May 16, 2021 4:34 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segemen

Re: [Freesurfer] Cerebellum Segementation

surfer] Cerebellum Segementation Yes, you can use that one as well. Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Sent: Sunday, May 16, 2021 5:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segemen

Re: [Freesurfer] Cerebellum Segementation

found. Thanks for your help! Regards, Akila From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Date: Sunday, 16 May 2021 at 22:54 To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segementation External Email - Use Caution Hi Lilla, Thanks a lot

[Freesurfer] Expression Syntax Error

External Email - Use Caution Hello experts, I am doing cerebellar segmentation from one of my previous posts using the command: isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7,8,46,47 Following the command I am getting an expression syntax err

Re: [Freesurfer] Cerebellum Segementation

into diffusion space before using them for tractography. Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Sent: Sunday, May 16, 2021 7:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segementation

Re: [Freesurfer] Cerebellum Segementation

of A.R. Sekar Date: Tuesday, 18 May 2021 at 09:04 To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segementation External Email - Use Caution Hi Lilla, Thanks for your message, even if I put one label I am still getting the same error: Akilas-MacBook-Air:B301001

Re: [Freesurfer] Cerebellum Segementation

-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Sent: Tuesday, May 18, 2021 5:56 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segementation External Email - Use Caution External Email - Use Caution Hi Lilla, I completed the process and got my 4 ROI

Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution Hello, Just a follow up question: can I run the isolate function on 1. Co-registered nii files? Or do they have to be mgz files? Thanks! Akila From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Date: Tuesday, 18 May 2021 at

Re: [Freesurfer] Cerebellum Segementation

PM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segementation All of our binaries read any of our supported formats, so that should be fine as like as the direction cosines are correct Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of A.R. Sekar Sent: Wed

[Freesurfer] Labels #601-#628

External Email - Use Caution Hello Experts, I am trying to isolate ROIs using labels #601-#628 however I am getting the following output and it is the same for each label. Any idea what is wrong here? Thanks for your help! Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.

Re: [Freesurfer] Cerebellum Segementation

from the command line. Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of A.R. Sekar Sent: Tuesday, May 18, 2021 12:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum Segementation External Email - Use Caution

[Freesurfer] Tracula Anlsysis

External Email - Use Caution Hello Experts, I am using Tracula to analyse the white matter tracts of the cerebellum. I saw that the atlas has the Middle cerebellar peduncle

[Freesurfer] Isolate Function Error

External Email - Use Caution Hello Experts, Hope you are well! I am trying to extract ROIs from the aparc+aseg file after running recon all however, I am getting the following result for all my images: ciddrg@CIDDRGs-MacBook-Air C961060 % cd /Volumes/Akila/Cambridge/C961022 ci