External Email - Use Caution
Hi Bruce,
Thank you for your helpful suggestion - re-running it seems to have fixed the
issue.
Harriet Cornwell
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Subject: Freesurfer Digest, Vol 208, Issue 38
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Contents of Freesurfer digest..."
Today's Topics:
1. Re: External 3D View Issue (Fischl, Bruce)
2. Yeo atlas for children! (Martin Juneja)
3. Running Freesurfer in the Desktop (Rosalia Dacosta Aguayo)
----------------------------------------------------------------------
Message: 1
Date: Fri, 18 Jun 2021 17:25:18 +0000
From: "Fischl, Bruce" <bfis...@mgh.harvard.edu>
Subject: Re: [Freesurfer] External 3D View Issue
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<bl0pr04mb660946eb4496cca774bcc1f4ef...@bl0pr04mb6609.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
Hi Harriet
Is that a parcellation overlaid on the brain? Usually this means something was
not regenerated when you reran (like the parcellation). Try just recreating it
an see if it fixes your problems. Should just take a couple of min to run just
the parcellation stage
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Harriet Cornwell
Sent: Friday, June 18, 2021 9:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] External 3D View Issue
External Email - Use Caution
External Email - Use Caution
Hello,
We thought we had finished manually editing a T1 scan and so opened it in the
external 3D view to perform final checks and it looks incredibly messy (see
attached screenshot). Are you able to advise whether this is an issue? If so,
is it possible to fix it and, if it can be fixed, how we should go about doing
so? Also, do you have any idea what might have caused this to happen?
Thank you in advance!
Harriet Cornwell
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Message: 2
Date: Fri, 18 Jun 2021 18:16:20 -0500
From: Martin Juneja <mj70...@gmail.com>
Subject: [Freesurfer] Yeo atlas for children!
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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<CAAf3GeSnjMTJp6QPA=tdbta6bkcvjxw4ajwh7r0mbl6gvkr...@mail.gmail.com>
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Dear experts,
I used Yeo's 17-network parcellation to study the association between
network-wise cortical volume and a clinical variable in adolescents. I received
the following two questions from the reviewers regarding the use of Yeo's
atlas. I would really appreciate if someone could help us in addressing these
questions:
*1) Could the author justify their choice to use a functional parcellation on
structural data? How is using this parcellation helpful in understanding the
brain? All in all, the authors need to justify the superiority of using Yeo's
17-area parcellations on structural data over other methods of
parcellation/analysis. *
*2) One issue with Yeo's parcellation also stems from the fact that this
parcellation was derived from adult connectomes. Could the authors also address
this issue and provide examples that justify their approach.*
Thanks.
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Message: 3
Date: Sat, 19 Jun 2021 13:35:58 +0200
From: Rosalia Dacosta Aguayo <rdacos...@gmail.com>
Subject: [Freesurfer] Running Freesurfer in the Desktop
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<capbdvhhe5ir_kxewdttx3txebhy1jgms8k_ohvsnuwn0z7+...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Freesurfer's team,
I am trying to run FreeSurfer recon-all -all in a folder placed *on my
Desktop* and I am having some trouble.
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -subject
sub-003_ses-BSL_T1w.nii -i /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii
-T2 /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T2w.nii -T2pial -all
mkdir: cannot create directory
'/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied
mkdir: cannot create directory
'/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied
mkdir: cannot create directory
'/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied
cp: cannot create regular file
'/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt':
No such file or directory
cat:
/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt:
No such file or directory
INFO: FreeSurfer build stamps do not match Subject Stamp:
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/patchdir.txt:
No such file or directory.
I would greatly appreciate your help.
Kind regards,
Rosie
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