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Thanks Juan! It looks like the -xmask is available only for newer distributions
of FreeSurfer. I’m using v7.1.1.
I appreciate the help though!
Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSHR BC/PARF Postdoctoral
Dear Narlon,
I believe you can add -xmask [mask_volume_file] to your recon-all command.
To generate such external mask, maybe you could use mri_synthseg with the
--robust flag and binarize the output?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From: on behalf of "Boa
Hello,
I am trying to register a full volume to a single slice, and I follow example 3
of mri_robust_register's help. I get the following error:
Input image is smaller than min dimension: 1 < 16
Input dimensions (after conformalizing) MOV: 64 64 64
Input dimensions (after conformalizing) DST:
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Thanks Martin. I assume in GLM approach I should calculate change for
session 1 and 2 and then 3 and 4 and then run difference of difference.
We actually randomized the order so half day1 is plcebo and half drug. So I
just need to be caretabout the
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Issues with surface placement in harder areas (e.g., white matter surface
placement in heavily myelinated cortex; pial surface placement in lightly
myelinated cortex).
Matt.
From: on behalf of "Lee, Sang Hoon"
Reply-To: Freesurfer support list
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On Mon, Jan 30, 2023 at 12:40 PM Lee, Sang Hoon
wrote:
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>
> Dear, Matt,
>
>
>
> What kind of issues did you have with version 7.x and the hires stream?
>
> It would help us to know what we are facing…
>
> Thanks.
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Dear, Matt,
What kind of issues did you have with version 7.x and the hires stream?
It would help us to know what we are facing…
Thanks.
Sang
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Glasser, Matt
Sent: Monday, January 30, 2023
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Thank you so much for the information, Matt!
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Glasser, Matt
Sent: Monday, January 30, 2023 1:23 PM
To: Freesurfer support list
Subject: [EXTERNAL] Re: [Freesurfer] High resolution T1
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We showed improved data (more accurate surface placement leading to more
accurate myelin maps) in prior publications (Glasser et al., 2013; 2014
Neuroimage). It makes a difference for cortical thickness too (e.g., falsely
too low cortical thickness
Hi Amirhossein,
So you have session 1 , placebo , session 2
Another day session 3, drug, session 4 ?
Again if this is for all subjects, easiest is to subtract session 2 from 1, and
4 from 3, to get thickness/volume differences for each condition. Then compute
the difference of the differences
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Thanks a lot Martin for the information.
We have actually 2 sessions of placebo for each subject. How do you suggest
to do the analysis including that data?
BR
On Mon, 30 Jan 2023 at 16:30, Reuter, Martin,Ph.D.
wrote:
> Hi Amirhossein,
>
> - If you
Hi Amirhossein,
- If you have two time points for all participants,
- and the time difference is the same for all
you can simply subtract the thickness (or volume) values per participant and
run a regular GLM. LME is a little overkill here.
In LME, you have one column of ones, and one of the
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I understand that from Version 7.0, better high resolution surface
reconstruction with -hires is done.
My question is, if we use higher resolution T1, such as 0.8mm, will it improve
the accuracy of the cortical thickness measurement? If yes, is
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Hi,
I have 2 sessions of data acquired in the same day for each participant
before and after the drug intake. I wonder how to analyse this with LME
tool. I create design matrix X in 2 columns, first all ones and second the
time differences(which are
I see talairach check failed. Can you try the steps that are suggested in
recon-all.log?
“
#@# Talairach Failure Detection Wed Jan 4 15:13:30 IST 2023
/Volumes/Rakshathi/Freesurfer/subj55_anat/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
ERROR: talairach_afd: Talairach
Hi Adriana,
I don't seem to see your previous message posted. Can you share the images
again, and recon-all.log too?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of adriana.jo...@unibe.ch
Sent: Monday, January 30, 2023 7:50 AM
To: freesurfer@nmr.mgh.harvard.edu
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Hello,
I'm just checking to see if you have received the images and if you are still
working on my issue? I don't think I got any more replies from you and just
want to make sure if you're still working on it.
Best,
Adriana
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