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Hello experts,
I am going through FreeSurfer's repeated measures anova tutorial using
fspalm. I understand that fspalm frontend can only do t-tests at the moment
and NOT F tests as noted in this thread:
https://secure-web.cisco.com/1t11cJOK6FCdHxqm_O6W
Thanks for reporting this bug, Victor. I just fixed it. The fix will be
propagated to the development version in the next couple of days but, if you
want, you can keep using the version you’ve got by adding the flag --crop 1000
(where 1000 is a number bigger than your image size in any dimensio
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Hi,
My name is Nina and I'm a PhD Student from Department of Knowledge technologies At Jožef
Stefan Institute, Ljubljana. I downloaded " Freesurfer VirtualBox Image" and I
need the paswword
to login as the user "developer" in the login menu.
Thank y
I usually just divide the volume by the eTIV (you can do this in
asegstats2table with the --etiv flag). Some people will use it as a
nuisance regressor in the GLM
On 7/27/2022 3:11 PM, Bouchra Guelib wrote:
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-- Forwarded message -
De : *Bo
how are you converting them?
On 7/27/2022 11:20 AM, Ariana Fei wrote:
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Hi,
We are recently trying to get cortical thickness from freesurfer and
converting them to 32k. A problem we notice is that after converting
to 32k, all the cortical thickness values
Yes, see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation
On 7/25/2022 6:56 PM, Angela Fang wrote:
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Hi Freesurfer community,
I have run participants through an event-related fMRI task in which
subjects rate whether trait adjectives ar
Have you looked at the input volume to see if there is anything strange
about them? What kind of scans are you passing to it? What is the
resolution?
On 7/25/2022 9:03 PM, Miriam Taza wrote:
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Hello,
I noticed 20 out of ~240 subjects left basal forebrain vo
What version of FS are you using for recon-all?
On 7/25/2022 9:45 PM, Miriam Taza wrote:
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I reran sclimbic and I get the same result as the first time I ran
sclimbic.
I also reran recon all on one subject. The etiv now differs from the
original recon all a
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Hi,
I signed up last night to send a freesurfer question, but I figured it out. Now
I am getting bombarded with emails from this thread and can’t see a
‘unsubscribe’ button. Can you help with this??
Thanks in advance,
Jessica
Jessica Archibald M.Sc
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is it not these two lines?
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cvs_version dev
if not, for the new recon-all I also have this:
freesurfer-darwin-macOS-dev-20220328-fc008d0
How do i check the old recon all? It wa
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Go to this page
http://secure-web.cisco.com/1IpGkreM7YsvDG2-JYbE4U8Y6p41OF4g_aIz5Jna6INo3-xXKZsj2Rmdtc-Y9cGr3OCH0AdP3ZfXPaptXW8xG6yWzA6Y-6o7Wgj0xNnxzA-OXsf5IdZ_7jnYKDYQC3lSRqdPLf9rb1l0S8H5bZuzI8ckjWndats7QLp5RuPbml8HEuWPfQYhrwMIPYV0ynwJXR0dWMZ_YohvHfno
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I'm attaching a list of command I used to convert freesurfer cortical
thickness output to native space:
$Caret5_Command -file-convert -fsc2c
"$FreeSurferFolder"/surf/"$hemisphere"h.thickness
"$FreeSurferFolder"/surf/"$hemisphere"h.white
"$AtlasSpaceFol
The "cvs_version" is just for that particular binary. look in
$FREESURFER_HOME/build-stamp.txt. There should also be a build stamp
file in $SUBJECTS_DIR/subject/scripts (should be in the recon-all.log too)
On 7/28/2022 1:41 PM, Miriam Taza wrote:
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is it n
those look like hcp commands so you should contact them
On 7/28/2022 2:00 PM, Ariana Fei wrote:
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I'm attaching a list of command I used to convert freesurfer cortical
thickness output to native space:
$Caret5_Command -file-convert -fsc2c
"$FreeSurferFold
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new recon all: freesurfer-darwin-macOS-dev-20220328-fc008d0
old recon all: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Th
Thanks Doug. This wiki page is extremely helpful. However, my question is about
individual subject responses. I could see how you could include a summary
(e.g., average) value of the parametric variable across subjects in your
“weight” column but it’s not clear to me how you could integrate indi
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If the brain scans went through successfully already, in an older dev version,
do they need to be reprocessed?
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: freesurfer-boun...@nmr.mgh.harvard.e
Hi FreeSurfer Developers,
I'm trying to run TRACULA in FreeSurfer v7.3 on OS Monterey.
I was unable to download R2014b Runtime on my newer OS, so instead of the
segmentThalamicNuclei.sh script, I tried running the newer segmentation
tool segment_subregions thalamus (
https://surfer.nmr.mgh.harvar
Nothing strange about them.
They’re T1w scans 1x1x1mm3
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Thursday, July 28, 2022 1:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] sclimbic sometimes does not dete
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