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I don’t see what FREESURFER _HOME is set to, but if you used the .deb package
installer, it would be /usr/local/freesurfer/7.4.0, i.e.
$ wget
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Hi Dr. Doug,
Thanks for your prompt reply!
I’m sorry it was not clear. Basically, I would like to extract the cortical
volume for each subject using a pre-defined ROI. As I have already created the
surface ROI, thanks to your answer on the official
On 1/19/2024 3:45 PM, Na, Xiaoxu wrote:
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Dear Freesurfer Expert,
While the sphere can only be drawn using that Dr. Doug suggested, the
sphere option would mess up.
Do you need help with this? If so, can you give more info?
I have a further question
mmm, still not sure. I'm assuming that you don't really have those
backslashes ("\") in there. Can you try it with mcz instead of perm just
to see if you can get it running. I would also try version 7.4.1;
version 6.0 is from a long time ago and so hard to debug.
On 1/19/2024 3:03 PM,
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Dear Freesurfer Expert,
While the sphere can only be drawn using that Dr. Doug suggested, the sphere
option would mess up.
I have a further question as using this ROI to extract surface information from
?h.area and ?h.volume. I'm using the command
I'm just trying now to run the "recon-all -version", also without any arguments.
Both produce the same error.
Thanks!
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: Friday, January 19, 2024 3:10 PM
To: Freesurfer support
I'm wondering how you ran recon-all. Do you see the error even running it w/o
any arguments?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all cannot execute:
Hi Doug,
Thanks so much for getting back to me. Below is our previous correspondence:
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Date: Friday, January 12, 2024 at 4:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Issue with mri_glmfit-sim
Thanks Yujing,
Yes, I looked for the file permissions using ls -l. It does have execute
permissions.
I also tried running chmod which didn't help.
Thanks,
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: Friday, January 19,
After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.
1. 'ls -l $FREESURFER_HOME/bin/recon-all' to check if your recon-all has the
execute permissions?
2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission
Best,
Yujing
From:
Sorry, I already forgot what the problem was. Can you include our
previous correspondence? Also, make sure to reply to the list. Thanks!
On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote:
Hi Doug,
Thank you for getting back to me. Unfortunately, the issue is
persisting, and the command
Dear group,
I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10
(GNU/Linux 5.19.0-46-generic x86_64)
I Downloaded freesurfer 7.4.0
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)
After sourcing Freesurfer, recon-all gives following error:
Maybe you can give us more details about what you are trying to do? Generate an
fMRI time-series that is the average response in each cortical parcel? And
subcortical structure? The subcortical segmentation is not Talairach, although
I'm not sure that is relevant. Generating the average time
what is the wang atlas? volume or surface?
On 1/19/2024 12:20 AM, Sujeevini Sujanthan wrote:
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Hi,
I would like to apply the wang atlas over the group activation maps
produced from Freesurfer analysis. I would appreciate any
guidance/instructions you can
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Dear Juan Eugenio Iglesias,
We are a biomedical engineering company (BIOREM) in Barcelona, and we are
collaborating in a research and innovation project with the University of
Barcelona.
For this project we use EasyReg to do brain registrations.
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