We are pleased to release freesurfer 8.1.0. This contains an important
bug fix so we recommend that you this instead of 8.0.0. It will give the
same output as 8.0.0 while avoiding the "symlink" bug described below.
The biggest new feature is the new infant freesurfer pipeline. Congrats
to Lilla
External Email - Use Caution
Dear FreeSurfer team,
I would like to obtain a FreeSurfer license for academic research use. Due to
the registration page can't run properly and gives the 'FreeSurfer Registration
Error reCAPTCHA not checked' error message, I wrote this email to requ
External Email - Use Caution
Dear FreeSurfer Team,
I previously submitted a license request but only received a mailing list
notification.
Could you please send me the license file directly?
My details:
- Full Name: Li Xuelian
- Institution: University of Electronic Scie
External Email - Use Caution
Dear FreeSurfer Team,
I am unable to complete the online registration due to reCAPTCHA issues.
Could you please send me a FreeSurfer license file?
My details:
- Full Name: Li Xuelian
- Institution: University of Electronic Science and Technolo
Good afternoon,
I hope this finds you well.
I am a research assistant at MGH, recently took the freesurfer course in June,
trying to install it on an arm64 M3 chip Mac (OS Sequoia 15.5), 24GB
RAM/memory. I followed the online installation guides and troubleshooting for
V8.0.0, yet am getting st
@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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OK, thank you Yujing
I'll see if we can update the installation
Simon
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The information i
edu
On Behalf Of Simon Jones
Sent: Friday, May 16, 2025 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer 8 + PetSurfer talairach.m3z
External Email - Use Caution
Dear FS
I tried to perform PetSurfer following recon-all pipeline using FreeSurfer 8.
When I ru
External Email - Use Caution
Dear FS
I tried to perform PetSurfer following recon-all pipeline using FreeSurfer 8.
When I run
gtmseg -s $sub
I get error
ERROR: cannot find talairach.m3z
I was able to create the file talairach.m3z which is omitted from version 8
recon-all pip
stions or
suggestions. Sincerely,Nagesh___Freesurfer
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listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear FreeSurfer development team,
Could you kindly let us know if FreeSurfer 8 native installer for Ubuntu 24.04
would be released sometime in the near future? Thank you so much for the help
and guidance. Please let us know if you have any questions
External Email - Use Caution
The freesurfer_ubuntu22-8.0.0_amd64.deb installer may work if you are
running an early version of Debian 12. The system may refuse to do the
install on the current version of Debian 12 because of system library
conflicts. I don’t see a container i
have a development build running on Ubuntu24 in the next several
months.
I’m not sure what 7.X version it runs, but there is a freesurfer docker
container available fromhttps://hub.docker.com/r/freesurfer/freesurfer/
Alternately, you could install VirtualBox, create and run a VirtualBox VM
running
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Hi Freesurfers,
I updated my Ubuntu OS to 24.04 and successfully installed Freesurfer 7.4.0
in it. I am saying it was successful because I was able to open 'freeview'
through the terminal.
However, the real problem started when I tried to execute the '
://surfer.nmr.mgh.harvard.edu/fswiki/ChildBrainManualEdits
Lilla
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Stefanie Bradley
Sent: Wednesday, March 19, 2025 9:55 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology
External Email - Use Caution
I'm attempting to run freesurfer 8 on debian 12.
Are there any tips on making the Ubuntu package work on debian?
or
Is there a freesurfer 8 docker container out there?
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Hello,
Sorry to message the wider list; I emailed the fscourse address previously but
did not hear back. Is there a course planned for this spring, and if so, is the
timing known? Thank you!
Best,
Kevin
-
mentioned?
Thank you,
Stefanie
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Stefanie Bradley
Sent: Monday, March 17, 2025 10:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology
You don't often
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zollei, Lilla,Ph.D.
Sent: Monday, March 17, 2025 10:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology
You don't often get email from lzol...@mgh.harvard.edu.
11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Question - Pediatric pathology
Hi Stef,
The infant FreeSurfer pipeline does rely on an infant training data set. What
atlas did you have in mind?
At the moment, there is no way to include a lesion mask into the pipeline, b
pipeline you might
want to try. Le me know whether you are interested,
Lilla
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Stefanie Bradley
Sent: Monday, March 17, 2025 9:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer
External Email - Use Caution
Hi there,
I'm working with MRI scans from children aged 3-6 years old. I was wondering if
there's a way to integrate pediatric atlases into the Freesurfer recon-all
pipeline?
I'm also wondering if it's possible to integrate a lesion mask into the
pip
://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is
addressed. If you
--threads 1 --o apas+head.mgz
gtmseg exited with errors
Thank you very much
Best
--
*Miguel Ángel Rivas Fernández*
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I’m not familiar with the gtmseg command, but I think you can revert to
the old recon-all behavior by setting FS_V8_XOPTS=0 on the recon-all
command line. That is listed under recon-all behavior
at, https://secure-web.cisco.com/1sfWpao2icNI-saQsKdV
External Email - Use Caution
Dear Freesurfer developers,
I have run the recon-all command with version 8.0.0 and now I would like to
run the gtmseg command. However, I received the message below. It seems to
be looking for the file *talairach.m3z* in the transforms folder, but tha
That is good suggestion. ‘recon-all’ should check if any processing directive
presents before proceeding to process the data.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ben Wagner
Sent: Friday, March 7, 2025 10:44 AM
To: Freesurfer support list
Subject: Re: [Freesurfer
failing?
Ben
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Huang, Yujing
Sent: Thursday, March 6, 2025 3:37 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 8.0 without processing directives
Processing directive is always required by recon-all. If you would like
Processing directive is always required by recon-all. If you would like to
process the whole pipeline, use '-all'.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ben Wagner
Sent: Thursday, March 6, 2025 2:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [
External Email - Use Caution
Thank you so much, it worked!
Andreas
Von: freesurfer-boun...@nmr.mgh.harvard.edu
im Auftrag von Huang, Yujing
Gesendet: Mittwoch, 5. März 2025 16:11:21
An: Freesurfer support list
Betreff: Re: [Freesurfer
External Email - Use Caution
Hello Freesurfer devs,
I'm trying to test Freesurfer 8.0 but I am encountering an error importing the
T1 image. In previous versions I'd use this command "recon-all -s SUBJECT -i
T1.nii" to import the data and then run "recon-all -s SUBJECT -qcache
Sent: Wednesday, March 5, 2025 10:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 8 - ValueError: no field of name pixdim
External Email - Use Caution
Additional info:
The "fslhd" info I provided you in the last email was based on the origina
g, Andreas
Gesendet: Mittwoch, 5. März 2025 15:51:10
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer 8 - ValueError: no field of name pixdim
External Email - Use Caution
Dear freesurfer team,
I just tried to run recon-all on my T1 weighted images with the new freesurfer
8 ve
File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg",
line 324, in predict
image, aff, h, im_res, shape, pad_idx, crop_idx =
preprocess(path_image=path_images[i],
File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg",
line
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Hello FreeSurfer Community,
I am looking for any help/information/documentation in replicating the
transforms performed in FreeSurfer recon_all on a non-mri volume image. I am
trying to align the voxel space of a non-mri image with the masking (aseg,
d.edu/fswiki/mri_label2label
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yang Yifan
Sent: Friday, February 14, 2025 5:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer coordinates
External Email - Use Caution
Hi Yujing,
Many thanks for your repl
External Email - Use Caution
Hi Yujing,
Many thanks for your reply! The email didn’t come through to my inbox and I
just found it in the online archive.
Regarding the coordinate conversion, I had a look at the link but didn’t find
MNI 305 related information. It would be very h
5, 2025 8:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer coordinates
External Email - Use Caution
Hi FreeSurfer Developers,
I'm conducting manual ROI labelling on each participant's inflated surface
(after going through the 'recon-all' co
External Email - Use Caution
Hi FreeSurfer Developers,
I’m conducting manual ROI labelling on each participant’s inflated surface
(after going through the ‘recon-all’ command), but I wasn’t very sure if the
coordinates in the corresponding .label files are in MNI 305 space. At t
834 86 22166
e-mail:katharina.wittf...@uni-greifswald.de
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External Email - Use Caution
Dear FreeSurfer Developers,
I'm attempting to compute the local gyrification index but unfortunately the
calculations terminated with an error:
recon-all -subject XXX -localGI -hemi rh
FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-
/freesurfer
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you
*From:* Michael Eyre
*Sent:* 11 January 2025 21:21
*To:* dgr...@mgh.harvard.edu
*Subject:* Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and
normalization failures with 7T MP2RAGE data
Hi, thanks for your response, apologies for late reply.
nu.mgz
External Email - Use Caution
You don’t have permission to write to the default location of
SUBJECTS_DIR as set in the freesurfer shell environment, i.e.,
/Applications/freesurfer/7.4.1/subjects. The example subject data there
is on purpose meant to be read only along with the
External Email - Use Caution
I am trying to create a 3D brain model from a *.nii file (here: test.niiI),
which I have copied to the subjects folder.
A) Using the command line, the following error messages appear:
Phils-MacBook:~ cnaehle$ recon-all -s brain -all -i
/Applications
r-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Gonzalo
Rojas Costa
Sent: Monday, January 20, 2025 7:12 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer remotely
processing External Email
- Use CautionHi:Is there any
free impleme
@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer remotely processing
External Email - Use Caution
Hi:
Is there any free implementation that allows me to process images with
freesurfer remotely?
Sincerely
Gonzalo Rojas Costa
Medicine School
Finis Terrae University
External Email - Use Caution
Hi:
Is there any free implementation that allows me to process images with
freesurfer remotely?
Sincerely
Gonzalo Rojas Costa
Medicine School
Finis Terrae University
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Thanks，please don't send emails！
> -原始邮件-
> 发件人: freesurfer-requ...@nmr.mgh.harvard.edu
> 发送时间:2025-01-06 22:12:15 (星期一)
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: Freesurfer Digest, Vol 251, Issue 6
>
> Send Freesurfer mailing list submissio
er] Bug Report for Beta Version of FreeSurfer
> (8.0.0-beta)
> To: "freesurfer@nmr.mgh.harvard.edu"
> Message-ID:
>
>
>
> Content-Type: text/plain; charset="us-ascii"
>
> External Email - Use Caution
>
> Hello FreeSurfer D
27;s College London
St Thomas' Hospital
London SE1 7EH
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-inflated
inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1
-threads 1 sub-31 rh
best wishes
Mike
From: fsbuild
Sent: 29 December 2024 23:22
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack sm
dical Engineering &
Imaging Sciences, King's College LondonSt Thomas' Hospital London SE1
7EH<sub-04_recon-all.log><sub-06_recon-all.log><sub-31_recon-all.log>___Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.edu
External Email - Use Caution
I’m assuming you tried to install the freesurfer 7.4.1 release deb package for
Ubuntu 22 which is available via the
link,https://secure-web.cisco.com/1-8cAL3HeYSqkGt1gxwntnID8i3xh2XIP7o3oNj46aWRvzM1OdWL_6YCW3aou3M2mzul5sWVkT0j-Azlb9yR_oZD_Kfgg2a5lKMRz
External Email - Use Caution
Hello all,
I have a debian machine running on debian "bookworm". I tried to install
freesurfer ubuntu 7.4.1 deb package and had issues with dependencies.
1. Depends: language-pack-en but it is not installable
2. Depends: libc6 ( < 2.36) but 2.36-9+deb1
Hi John
It is mostly for background and other stuff outside of the brain
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Barsotti, Ercole
Sent: Friday, December 13, 2024 5:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer Labels Question
External Email - Use Caution
Hi all,
Sorry if this is a stupid question.
In the FreeSurferColorLUT.txt, there is a label for "Unknown" brain material.
What would most commonly be labelled as Unknown in an image?
Thanks,
John
___
Fre
-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj
-synthstrip -synthseg -synthmorph’?
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *???
*Sent:* Wednesday, December 11, 2024 11:53 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Freesurfer v8.0.0 error
freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer v8.0.0 error
External Email - Use Caution
Hello FreeSurfer Developers,
I installed freesurfer 8.0.0 successfully but failed to run "recon-all -i ***
-s *** -all -localGI -qcache" for any subjects. I tried this version 8.0.
External Email - Use Caution
Hello FreeSurfer Developers,
I installed freesurfer 8.0.0 successfully but failed to run "recon-all
-i *** -s *** -all -localGI -qcache" for any subjects. I tried this
version 8.0.0beta on both macos latest version and ubuntu 22.04, the
error was the s
External Email - Use Caution
The tutorial data exercises are not entirely up to date with the just announced
beta release. For now you could try running a pre 8.X stable dev build
fromhttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/stable/- or for
your M2 Mac, you w
External Email - Use Caution
Dear Freesurfer developers,
I have no previous experience in Freesufer and I am trying to go through the
tutorial before analyzing my own data.
I’m working on the dataset you shared on your website.
I work on MacBook Pro Apple M2 Pro 32 GB Sonoma 14.2.
m the Docker Hub.
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
noga.ker...@campus.technion.ac.il <noga.ker...@campus.technion.ac.il>
Sent: Wednesday, October 9, 2024 11:57
To: Freesurfer support list
Subject: Re: [Freesurfer]
noga.ker...@campus.technion.ac.il
Sent: Wednesday, October 9, 2024 11:57
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from
.ltafile
External Email - Use Caution
Sorry, I forgot to attached it.
Target, moving, moving_mask and the .lt
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
noga.ker...@campus.technion.ac.il
Sent: Wednesday, October 9, 2024 03:57
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer - extract rigidparameters from
.ltafile
External Email - Use Cauti
): could not allocate xforms
And the temp_moved_mask.nii.gz is not generated
Thanks,
Noga
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hoffmann, Malte,PhD
Sent: Wednesday, October 9, 2024 03:22
To: Freesurfer support list
Subject: Re: [Freesurfer
06
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from.lta
file
External Email - Use Caution
Thanks You for the response!
Another issue I encountered was with the .lta file that is being generated
using mri_synthmorph.
I want to use the .lta
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Tuesday, October 1, 2024 17:12
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file
You don't often get email fro
External Email - Use Caution
Hello Raj,
Sometimes when OS’s update to a new major revision, the system libraries change
such that software installed under the old OS version is not backwards
compatible with the new OS version. I think we may have already mentioned
on the list t
External Email - Use Caution
Dear Developers
I installed Freesurfer 7.4.1 when using Ubuntu 22 in an Oracle VM on
Windows 10 as a host OS. However, I recently updated to Ubuntu 24.04.1 LTS
(I still regret it), and after that, Freesurfer stopped working. It shows
"bash: /usr/local/f
?
Thanks again,
Noga
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, September 30, 2024 17:02
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file
You don't
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, September 30, 2024 17:02
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] FreeSurfer - extract rigid parameters from
.lta
on in the |.lta| file?
Freesurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
Thank you,
Noga
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kef>
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Joshua K Lee
Inviato: Sunday, September 29, 2024 5:53:01 PM
A: Freesurfer support list
Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error
External Email - Use Caution
I just want
...@ucdavis.edu
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce R.,PHD
Sent: Sunday, September 29, 2024 1:20 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer - skull stripping error
You could try synthstrip, it might work
Outlook per iOS<https://aka.ms/o0ukef>
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Fischl, Bruce R.,PHD
Inviato: Sunday, September 29, 2024 4:20:00 AM
A: Freesurfer support list
Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error
You
rd.edu
per conto di Fischl, Bruce R.,PHD
Inviato: Sunday, September 29, 2024 4:20:00 AM
A: Freesurfer support list
Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error
You could try synthstrip, it might work
Cheers
Bruce
On Sep 29, 2024, at 7:38 AM, William Baare wrote:
Ex
External Email - Use Caution
Hello FreeSurfer Developers,
I am using mri_robust_register to register a moving volume to a fixed one. The
algorithm outputs the rigid transformation in a .lta file. I need to extract
the rigid parameters (3 rotation angles in degrees and 3 translati
te over unencrypted e-mail.
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External Email - Use Caution
Hi Sara,
You need to denoise the background.
Here are some links that might be of help. Always check the quality of the
output :-)
https://secure-web.cisco.com/11TUQn3ZMjB9gy2mI09erMcLASzJWGpSLFMUxf9tT-XFEDmLfZKdF-O_LIYc_Nlr6rt_zg2mZoh6G-ql4JyDGF9_GK
ace
and thought that I had obtained it correctly.
Best,
John___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi all,
I've downloaded Freesurfer version 5.3 and signed up for a license. However,
when I try to run the example:
mri_convert sample-001.mgz sample-001.nii.gz
I get the following error:
ERROR: Invalid FreeSurfer license key found in license file
ume is CuDNN version 8, and may not be compatible with CUDA
> 12.6?
>
> Is there a way I can get freesurfer's script to use the CuDNN 9.4.0 that
> are installed globally on the WSL system? Any other suggestions on what
> m
surfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only
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Hello,
My name is Alisha Davis, and I have been using Freesurfer over the past few
weeks for an MRI project but have encountered a few issues due to the version
of my computer. Is there a plan to release a newer version of Freesurfer
compatible with
Hi all,
Could it be a problem in FreeSurfer longitudinal analysis if I use two
different sequences (T1 MP2RAGE and T1 MPRAGE) for different time
points/follow-ups?
Thanks for the support,
Sara
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Is there a way to install freesurfer6 on Debian? I see only CentOS packages
available for freesurfer6.
Or, is there a way to build from source on Debian?
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Subject: Re: [Freesurfer] FreeSurfer in fmriprep
The log file says that recon-all finished without error. The command (robust
register) was not called during recon-all. It must be called by fmriprep at
some point. I don't understand what they are trying to d
bject:* Re: [Freesurfer] FreeSurfer in fmriprep
You don't often get email from dgr...@mgh.harvard.edu. Learn why this
is important <https://aka.ms/LearnAboutSenderIdentification>
please send the recon-all.log file in the scripts folder
On 7/23/2024 2:14
Douglas N. Greve
Sent: Monday, July 29, 2024 12:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer in fmriprep
You don't often get email from dgr...@mgh.harvard.edu. Learn why this is
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please sen
Best,
Selena
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return self._accessor.open(self, mode, buffering,
encoding, errors,
FileNotFoundError: [Errno 2] No such file or directory:
'/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta'
Best,
Tengwen
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Hi,
I hope you are doing well, I subscribed to your mailing list to ask my question!
I was wondering if you knew the reason as to why my extraction code in
FreeSurfer listed regions such as "Whole_hippocampal_body" amongst other brain
regions twice
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Dear FreeSurfer Developers,
I hope this email finds you well!
I am using fMRIprep to do pre-processing. The fMRIprep combines methodology
from AFNI, ANTs, Freesurfer, FSL, and Mindboggle to do preprocessing.
An error was reported while running the
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Thank you very much!
From: fsbuild
Sent: Tuesday, July 2, 2024 11:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freesurfer as module
My understanding is that it is up to the sysadmins who run
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My understanding is that it is up to the sysadmins who run a cluster to
choose how to present and configure the apps they host whether it be thru
modules, spack, or other tools. We don't track how cluster admins do
that, but you could ask the helpd
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Hi Freesurfer Developers,
If Freesurfer is available as a module on a computer cluster, is it still
necessary to source/configure the freesurfer module in a .bashrc script on
Linux?
Sincerely,
Yilei
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Subject: Re: [Freesurfer] FreeSurfer atlases
Try looking at it in freeview first. Some of the regions may be small, so you
may have to hunt to get them. FYI you can specify nii as the output of
mri_binarize
On 6/28/2024 5:30 AM, Savoia, Alice (Stud. FPN) wrote:
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have suggestions?
Thanks,
Alice
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, June 27, 2024 12:36 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] FreeSurfer atlases
I'm not sure wha
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