[Freesurfer] Applying Wang Atlas to Group Analysis Results in FreeSurfer

[Sujeevini Sujanthan]

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Hi,

I would like to apply the wang atlas over the group activation maps produced 
from Freesurfer analysis. I would appreciate any guidance/instructions you can 
offer for how I can do that.

Thank you for your time!
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Re: [Freesurfer] Issue with mri_brainvol_stats for only some participants

[Huang, Yujing]

mri_brainvol_stats reads the following files:

mri/aseg.mgz
surf/lh.white
surf/rh.white
surf/lh.pial
surf/rh.pial
mri/brainmask.mgz
mri/transforms/talairach.xfm
$FREESURFER_HOME/ASegStatsLUT.txt

Can you check if they all exist for your subjects?

Any errors if you run 'mri_brainvol_stats ' at prompt?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carly McIntyre-Wood
Sent: Tuesday, January 16, 2024 4:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants


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Hi there,

I've come across a strange issue while running some new participants through 
Freesurfer 7.3.

A portion of participants (30%) are missing their stats files, although I have 
visually inspected the segmentation using Freeview and they look great. I have 
rerun autorecon3 and it only fixes the problem for select subjects. The exact 
error is below:


mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness

   Update not needed

\n mri_brainvol_stats 1096 \n

Segmentation fault

I found one instance of this in the archives where someone recommended running:

recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc 
-balabels

However, this command exits at the same point with the same error.

Thanks so much,
Carly
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Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

[Heese, E. van (Eva)]

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Hi all,

Thanks again for your help.

We fixed the issue by adding user write permissions for the owner-user in the 
installation folder (note that the owner of the file in the installation folder 
is different from the users that we used for testing). :
-rw-r--r--. 1 admin admin 366711 Sep 21  2017 
/installationfolder/7.3.2-centos8_x86_64/average/HippoSF/atlas/AtlasDump.mgz

The fix was necessary for the other AtlasDump.mgz files.

Best,
Eva
__
AmsterdamUMC disclaimer : 
http://secure-web.cisco.com/1wlx9tXYYUIMj_Rg1KZxU9HYTynqYvQ9dJZEYbomVrvzBlzLm4andwpgnk2hTvQ6sA5B0ovH8jwCcDYSOIp5QcQniU7m2rRmoVyOEf5SuFmQLQTkMiIkXVI5Ufn709QMSJlnqUOb0uek2u2OdfWDeoAKEovgYopS1qG6kZ08XpN9Zay5vCrrP4NKAPg9-YxaZ4_tg2SMukEwGynglaripw4Zmx0VLIzyHLp07VRLfvIjZiSJoqL9HsqLue_VKyPhaH4hYByp4al2MAR6fYy7hpeiI1G-Uuvlnc6VViHWc6R1Eg-IXhxcmB3vIzVsKXR5h8-0iPqyW3IfhmRcKDRnOkQ/http%3A%2F%2Fwww.amsterdamumc.org%2Fdisclaimers
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Re: [Freesurfer] Ex-vivo adult brain MRI segmentation and surface analysis

[Douglas N. Greve]

That does not look like it is a problem with the input image. Do you 
have a normal, invivo MRI that you can run samseg on to see if it is 
just a problem with your platform?


On 1/18/2024 3:57 AM, K Eswar wrote:


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Dear FS community

I have an ex-vivo human adult brain MRI, both in T1 MPRAGE and Fiesta. 
I have recently come across a paper on MRI segmentation using a 
function called- samseg. From the webpage( *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon 
) 
I realized that there is a different approach altogether to processing 
these fixative brains. However, as a first step, when I tried the 
samseg function, I noticed that the function exited with errors.


The steps where it fails are:
Read mesh collection: 
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz

Transforming points
Transforming points
Read mesh collection: 
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Read mesh collection: 
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz

Killed

I am using the Ubuntu 22.04 version with RAM 32GB
Freesurver version: 
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275


I would greatly appreciate it if you could help me with MRI 
segmentation and cortical surface analysis on these brains.


Thanks for your time and consideration.

Regards
K Eswar
Project Scientist
Sudha Gopalakrishnan Brain Centre
IIT Madras, India

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Re: [Freesurfer] T1map processing error

[Douglas N. Greve]

The way I have done this was do compute T1w images (MPRAGE) through 
simulations, then run recon-all on that.


On 1/17/2024 11:55 AM, Maksim Slivka wrote:


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Dear FS community,


Recently our lab started collecting 3D-QALAS (Cho et al., 2023). Using 
this method, a quantitative T1map was constructed.



Trying to process this map, FS (v7.1.0) recon-all would output the 
following error:


mri_cc: no WM voxels found with norm > 40 -- check skull stripping


I would like to ask if anyone here has experience in processing 
quantitative T1maps with FS? Did you also run into that error? Were 
you able to solve it?



I am looking forward to hearing from you.


Best regards,

Maksim Slivka

Head engineer

Center for Lifespan Changes in Brain and Cognition (LCBC)

Department of Psychology

University of Oslo

POB 1094 Blindern

0317 Oslo

Norway


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[Freesurfer] Ex-vivo adult brain MRI segmentation and surface analysis

[K Eswar]

External Email - Use Caution

Dear FS community

I have an ex-vivo human adult brain MRI, both in T1 MPRAGE and Fiesta. I
have recently come across a paper on MRI segmentation using a function
called- samseg. From the webpage(
https://secure-web.cisco.com/1AJdw_iZ93Ctl2bXUM-tS9sQoJ_9a6-0RHBNEGqz7c8Pz8GSVQSAS9NvPicCtOfOlcCk2usfSQaphR2x5O9OtMVeO3byxBTtWanL1Lo6pkUBbO7WBqlr0s2GXTavc8OsJmxaGyjxPXbpYGjyC-R9lbgqfpPqvPSFBqUm2C1CcpmZtpG68WfRTj09GXjjGFDeJvf9e1rMz7DTEq_IjhzeX_ueSNnY8PVK6WlzPVLcJT-wzuUaplRF9gMRJevnnNwDO9_ahhh74NOapQ6VO_0eaM8Vbsa9FN4_n6ghVPXg-ptwtkfgZtPfaTd8CDM1lEKjcGz9EsuNtBKF8XpvLnJQS3g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FExvivoRecon)
 I realized that
there is a different approach altogether to processing these fixative
brains. However, as a first step, when I tried the samseg function, I
noticed that the function exited with errors.

The steps where it fails are:
Read mesh collection:
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Transforming points
Transforming points
Read mesh collection:
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Read mesh collection:
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Killed

I am using the Ubuntu 22.04 version with RAM 32GB
Freesurver version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275

I would greatly appreciate it if you could help me with MRI segmentation
and cortical surface analysis on these brains.

Thanks for your time and consideration.

Regards
K Eswar
Project Scientist
Sudha Gopalakrishnan Brain Centre
IIT Madras, India
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