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Anastasia, thank you so much !
On Thu, Apr 30, 2020 at 8:03 PM Yendiki, Anastasia
wrote:
> Yes, this is fine.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Z
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Hello Mina,
On the setup page under the CentOS7 and 8 header,
https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_linux, it does mention you can
use the same archive and rpm installer for both CentOS7 and CentOS8. Or
the CentOS7 binaries should be backwa
Yes, this is fine.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
Sent: Thursday, April 30, 2020 2:22 PM
To: Freesurfer support list
Subject: [Freesurfer] trac-all -bedp error
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Hi,
I run trac-all, the
Hi Qi - "Subject IDs" should be just subject IDs (a.k.a. subject names), not
paths to subject directories. So one of the config files that you attached
should work, but the other should not.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
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Greetings FreeSurfer team,
I have some questions regarding the latest stable version of freesurfer;
1- I am currently using Centos 8, and the Freesurfer download link for this
version says centos 7 not 8.. is it compatible with centos 8?
2- Is it tr
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Hi Anastasia,
I think there are some misunderstandings here. I have created one
configuration file for each subject and it works processing longitudinal
data. And since all my subjects are stored following /subjects/ in one
directory, I assumed adding
You cannot have multiple SUBJECTS_DIR's. It is supposed to be the base
directory under which all subjects' dirs are saved. You could have a different
configuration file for each subject if you want each of them to have a
different SUBJECTS_DIR, but this hack won't work for longitudinal analyses
We are pleased to announce the release of FreeSurfer version 7.
You can get the new software from here
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
You can find the release notes here
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
Let us know how it goes
best
doug and th
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Dear experts,
Is it possible to run subfield analysis (hippcampal subfields, amygdalar,
thalamic nuclei, and brainstem structures) when we only run samseg on our
dataset?
Thank you,
Sneha
___
Freesurfer ma
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Hi,
I have my trac-all up and running with no error with individual subjects
when I set the subject directory to individual subjects.
as follow:
set SUBJECTS_DIR=/*/subjects/SUBJ1
set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2)
set baselist = (SUBJ1_base SUBJ
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Thank you. Can you please clarify, documentation for mri_convert states
default for resampling is -interpolate, does this mean trilinear? Also,
which method is preferable for bbregister (I am applying it for
intrasubject uni and multimodal registration
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Hi,
I run trac-all, the log file has the following endings.
"Queuing post processing stage"
or
"Queuing post processing stage
59 slices processed
All slices processed
/hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh:
line 345:
If you look at the bottom of the recon-all log file you will see that
this subject did not have an error
recon-all -s subjects02 finished without error at 2020年 04月 29日 星期三
06:01:19 CST
Send the recon-all log file of the subject that has the error
On 4/30/2020 7:41 AM, jiahui wrote:
how many subjects are there in your fsgd? How many groups in your fsgd
file? Also, you should not use --osgm and --fsgd
On 4/30/2020 1:09 PM, KennethSPrice wrote:
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Hello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running in
It will but, it will always be resampled with trilinear interpolation.
On 4/30/2020 12:55 PM, Octavian Lie wrote:
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Dear All,
I have seen bbregister command lines using --o option to get the final
output (say a .nii vol), and others where bbregister is use
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Thank you so much. I will upgrade the dev and run it again, fingers
crossed.
Best,
Qi
On Thu, Apr 30, 2020 at 1:25 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:
> Ah! I think you were unlucky enough to download the dev v
Ah! I think you were unlucky enough to download the dev version literally days
before we fixed these issues ;-)
If you upgrade to the latest dev, it should be fixed! Or, wait a bit until FS7
comes out, there’s rumors that it may be pretty soon.
Cheers,
/E
Juan Eugenio Iglesias
Senior research f
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Hello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running into an issue
with the mri_glmfit. I am running on just one subject pair.
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
I ran mris_prep
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Dear All,
I have seen bbregister command lines using --o option to get the final
output (say a .nii vol), and others where bbregister is used to get an lta
transform, which is used in a follow-up step (mri_convert with -ns 1 (no
scale), and -rl orig.mg
You can use mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only
segid segidreplace ... --o newseg.mgz
to create a new segmentation with merged segments, then using
vol2subfield with the newseg seg as --sf
On 4/29/2020 7:57 PM, std...@virgilio.it wrote:
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Hi Eugenio:
recon -all --version
freesurfer-linux-centos6_x86_64-dev-20180509-5a99f28
operating system: Linux
Best,
Qi
On Thu, Apr 30, 2020 at 12:06 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:
> This was very helpful,
This was very helpful, thanks. Can you please send me the output of the
following command?
recon-all --version
as well as your operating system?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Ze
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