I'm not sure what is going on here, but I would guess that the v6 hires
stream is not behaving very well. I would suggest using a patch I
created the HCP. If you are in the version 6 environment, you can run
recon-all.v6.hires the same way you did recon-all, but do not use -hires
and instead
Hi Mona, not sure what you are trying to do. When you say "native"
space, do you mean native functional space or native anatmical space?
If you want to analyze the data on the native surface, you can use
--surf self when you run preproc-sess and mkanalysis-sess (instead of
specifying
What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
subcortical ROIs added? If so, you can try merging it with the aparc, eg,
mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
aparc+BN_Atlas_subcotex.mgz
Then use aparc+BN_Atlas_subcotex.mgz as input to
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Yes, you can disable the gatekeeper security software and allow software to be
installed anywhere. This may not be the best choice for everyone if you
prefer to have this security (or do not have sudo privs). Anyway, we
will endeavor to not require
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Yes, you can disable the gatekeeper security software and allow software to be
installed anywhere. This may not be the best choice for everyone if you
prefer to have this security (or do not have sudo privs). Anyway, we
will endeavor to not require
Yes, you should be following the instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
rather than the wiki page for 6.0 here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research
Dear Freesurfer experts
Hi
I was trying to do selxavg in native space for individual subjects which I have
analyzed them in "fsaverage" space before.
I have two sessions of functional data for each subject. In order to register
them on one T1, I put the functional data from both sessions in
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Dear Eugenio,
I noticed what was the problem. I used freesurfer dev version with the
following command:
segmentHA_T2.sh
I tried to export the hippocampal and amygdala results of several subjects
with these commands and now everything works fine.
Dear Steve,
Can you please send us:
- The segmentation command you used for a sample subject
- A list of the files under the mri directory for that subject.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on
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Hello,
sudo spctl - -master -disable
Running this command before installing freesurfer will solve your problem ..
There is no space between the two hyphens
Sent from my iPhone
> On 11-Dec-2019, at 2:33 PM, fsbuild wrote:
>
> External
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Hello CM,
We are looking at how Freesurfer can work with the new security and file system
changes added in Catalina (Mac OS 10.15). I am not aware of an issue if
Freesurfer had been installed on a machine running an older version of Mac OS,
e.g.,
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Dear Freesurfer experts,
I used the freesurfer dev version to estimate hippocampal subfields using
mode B (additional scan).
All have worked fine although when I tried to export the results I can not
find the txt file created
This is the output
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Dear all,
I keep getting a warning on my Mac that Freesurfer will not be compatible with
the latest update to MacOS Catalina. Does anyone have any information about how
critical this issue is/ if Freesurfer will be updated to be compatible with
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