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Hello, I found FreeSurfer can segment brain areas automatically these days,
and it really meets my requirements. therefore, this tool is really useful
for me! But this process is only a part of my work, and I notice FreeSurfer
isn't designed for
Phew!
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Michael
Sent: Wednesday, June 17, 2020 5:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correcting recon-all output (missing parts in pial
surface)
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Thank you for your quick
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Hi Doug,
Thanks for this. I sent the file; it’s called yannquide.tar.gz.
Yann
> On 16 Jun 2020, at 11:56 pm, Douglas N. Greve wrote:
>
> Can you upload the subject so I can take a look? Instructions below
>
>
> From the linux command line,
>
Yes, we will release a v7 container on dockerhub as soon as we can. Hopefully
by next week once we release a new 7.1 patch.
From: on behalf of David Pagliaccio
Reply-To: FS Help
Date: Tuesday, June 16, 2020 at 4:20 PM
To: FS Help
Subject: [Freesurfer] version 7 docker container
Hi Mason,
My guess is that freesurfer is still grabbing the initial license. Have you
been sure to remove the original one? It might be hiding as a .license file
Best
Andrew
From: on behalf of Mason Wells
Reply-To: FS Help
Date: Wednesday, June 17, 2020 at 5:34 AM
To:
Maybe those 88 vertices have a value lower than the thresh or are not in
the mask.
On 6/17/2020 6:42 AM, Marina Fernández wrote:
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Dear experts,
I am using the mri_surfcluster function to cluster the surface results:
mri_surfcluster --subject fbb_average
you're not running it correctly. Run it with just --help to get info on
how to set up the command line
On 6/17/2020 3:48 AM, Ian Hardingham wrote:
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Hi Doug, just an FYI that I think this requires extra recon-all files
that are only output by v7 ?
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Perfect, thanks Tim.
On 17/06/2020 10:50, Tim Schäfer wrote:
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>
> To find the code, look at FreeSurferColorLUT.txt, e.g., you may be interested
> in a subset of these:
>
>grep -i vent
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Are the ventricles currently in V6 Surf directory as a set of vertices,
or a labelled list of voxels, or anything like that?
Ian
On 16/06/2020 13:39, Ian wrote:
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Hi Freesurfers.
I'm looking to find the center
Hi Nick,
Would it be possible to send us the surface file and the merged gift file so we
can take a look?
Best,
Ruopeng
On Jun 17, 2020, at 1:14 AM, Nick Blauch
mailto:bla...@cmu.edu>> wrote:
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Hello Freesurfer experts,
I recently upgraded to Freesurfer
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Hi Doug, just an FYI that I think this requires extra recon-all files
that are only output by v7 ?
./mri_segcentroids --i freesurfer/surf --o results.txt
error: corRead(): can't open file freesurfer/surf/COR-.info
On 16/06/2020 15:44, Douglas N.
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Dear experts,
I am using the mri_surfcluster function to cluster the surface results:
mri_surfcluster --subject fbb_average --mask mask.mgh --hemi lh --olab
label --in sig_results_tvalues.mgh --thmin 0.001
When I count vertices different
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To find the code, look at FreeSurferColorLUT.txt, e.g., you may be interested
in a subset of these:
grep -i vent $FREESURFER_HOME/FreeSurferColorLUT.txt
The last 4 values on each line make up a color code (RGBA, in range 0-255 per
channel). The
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The 2nd line are actually 2 commands, you have to split them:
The first one downloads a file:
sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
-o rca-long-tp-init
The second command makes it
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Hi Expets,
I am trying to work with the Ciftify package, a great tool for converting
non-HCP data into cifti format. I am running the following docker command.
However, I get an error with the return code 255
sudo docker run --entrypoint
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Dear all,
As evidently experienced by others, a certain percentage of subjects failed to
run on freesurfer 7.1 version, stopping at the segmentation step, while they
could run in version 6.
I read that this is bug is present in Mac os, which I am
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