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Hello,
Im wondering if there is an update regarding etiv differences between recon all
and using sclimbic. I want to divide the volumes extracted from using sclimbic
on t1s by etiv. Im not sure given the discrepancy if I should use etiv
extracted fr
I think we are on the right track, but it looks like there was a space between
FREESURFER_HOME and the equal (=) sign? It also looks like there was no space
between '$FREESURFER_HOME' and './fs_install_mcr'?
The command should be copied exactly as written:
sudo FREESURFER_HOME=$FREESURFER_HOME .
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Hi Paul,
I have taken your advice and run the command as shown below:
ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME
=$FREESURFER_HOME./fs_install_mcr R2019b
sudo
Ah ok, let's try this:
cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
We are appending `./` to fs_install_mcr to tell it it's in the same directory.
We are also passing the definition of FREESURFER_HOME into the 'sudo'ed'
environment, because t
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Hi Paul,
I have entered the command under this directory
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$
sudo fs_install_mcr R2019b and the following error persists. (sudo:
fs_install_mcr: command not found)
Could there be a reason for this?
S
Hi Justina,
Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?
Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr
R2019b`?
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Justina Lee
Sent: Tuesday, Sept
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Hi Paul,
When I try to run the installation command with sudo, the following error
command shows:
sudo: fs_install_mcr: command not found
I'm terribly sorry for the inconvenience.
Sincerely,
Justina
On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul
wr
Thanks R, those are very good points.
-Paul
From: fsbuild
Sent: Tuesday, September 13, 2022 2:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: r.lud...@eni-g.de ; Wighton, Paul
; fsbu...@contbay.com
Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
Hi Justina,
Ok so it looks like the install script is getting further and has extracted the
matlab runtime environment into a temporary directory
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is
trying to move that temporary directory to a location inside the FreeSurfer
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The glibc version has changed in newer versions of Ubuntu. That and/or
changes to encryption related functions is likely preventing the license
decoding from working. Binary backwards compatibility cannot assure old
binaries will indefinitely run
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Thank you Paul for your help!
This seems to have solved the issue, as I can now run the command
fs_install_mcr R2019b. It has ended successfully with this end message
stated below:
mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
'/usr/l
Hi Rüdiger,
This is really interesting.. I'm able to reproduce this issue in a docker
container. Anyone else who would like to reproduce or look into this issue can
use the following containers
- The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16.04
(glibc v2.23) and eve
Hello again,
I realized I might have missed some important information in my question about
freesurfer 5.3 license files a few days ago:
We use Ubuntu 20 with lmod. FREESURFER_HOME is ''/opt/apps/freesurfer/5.3/''
for freesurfer 5.3
When we try ''mri_convert sample-001.mgz sample-001.nii.gz
Hi Justina,
It looks like the matlab installer is trying to use unzip but it can't find it.
Can you try running:
`sudo apt-get install unzip`
To install unzip then try the matlab installer again?
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
We do not have this functionality in FreeSurfer.
Best, Lilla
From: Greve, Douglas N.,PHD
Sent: Tuesday, September 13, 2022 9:46 AM
To: freesurfer@nmr.mgh.harvard.edu ; Zollei,
Lilla,PHD
Subject: Re: [Freesurfer] Extract Fetal Brain MRI
I don't think that we do.
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Thank you, Douglas!
Kind regards,
Olga
> On Sep 13, 2022, at 3:41 PM, Douglas N. Greve wrote:
>
> Once you have the vertex number, you can get the MNI coordinate through some
> combination of operations shown on this page
> https://secure-web.cisco.
I don't think that we do. I'm cc'ing Lilla in case she knows
On 9/12/2022 6:37 PM, Xuchu Liu wrote:
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Hi Dear,
We are a research team at Rush University Medical Center. We are
working on the Fetal MRI data. In this step,*we need to extract the
"Fetal Brain
I'm not sure of the order. You can run recon-all passing in the flair
with -flair flair.mgz. At some point in the process it will apply a
normalization to the flair (it will not necessarily be the same
normalization that is applied to the t1)
On 9/12/2022 4:01 PM, James Brown wrote:
I dont think you did anytyhing wrong. You can use mri_vol2vol with the
lta from the base/mri/transforms to map the seg into the base (same as
long) space. But this resample will probably change the volume by 5%
On 9/12/2022 2:11 PM, Bernardoni, Fabio wrote:
> External Email - Use Cauti
try
mri_convert --downsample 3 input.mgz downsampled.mgz
On 9/12/2022 12:54 PM, Marina Fernández wrote:
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Dear experts,
I would like to downsample the GM mask, which is at 1mm isotropic
voxel size (freesurfer subject space), at 3mm isotropic. What is the
m
Once you have the vertex number, you can get the MNI coordinate through
some combination of operations shown on this page
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
Getting the minimum vertex is a little trickier. I would probably load
the thickness into matlab, eg,
thickness =
External Email - Use CautionTo whom it may concern, Apologies for my first post, I was a little bit confounded as to how I can reach for help. I would like to use the segmentation of hippocampal subfields and the nuclei of the amygdala. Currently, I am working with Ubuntu on windows
External Email - Use CautionTo whom it may concern, I would like to post on the freesurfer mailing list. Please let me know if the access is granted.I look forward to hearing from you soon. Sincerely,You Na Lee Sent from Mail for Windows
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