[Freesurfer] extracting values from signifciant clusters

[Eszter Boros]

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Dear FreeSurfer Team,


We are doing a longitudinal analysis with Freesufer 7.1.1 (two-stage
longitudinal model), and  we would like to extract the Cortical
thickness values from the significant clusters (before and after
treatment changes) to visualize the individual values/changes.

I am wondering how I can do that?


Please let me know if you need any more information.

Thank you for your answer in advance!

All the best,
Eszter Boros
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[Freesurfer] Subcortical regions of Brainnetome Atlas

[Garrett Tan]

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Hi FreeSurfer Experts,

I am using Brainnetome Atlas in FreeSurfer to calculate the brain volume. The 
cortical regions are done smoothly by using 
mris_ca_label->mris_anatomical_stats with materials on 
https://secure-web.cisco.com/1p7TY1frW67uqViolqd97Sub3WUDGgPjPK0_YAEmmtEENBBjRqkxRhrM7lhQNbQoPTsnER7AEPASg0AMWvbh6ul9GG-VZIQL-qXWdva_lU2kvgeWbLOUKfHebFsSJi8SqqRlrWZCDXtotZtMgyb_wugL_-b6quUDqFpQbuKUrdh6fTEHlsGrK7IOqAVCheGDZi2YHdXybErdaYLFTq6vEoyF8XOTvbLUq_a_HWEiVy7Q6_Vy2TPb2tgjnMnSM5nNDLEAnuP2WUdlqvoKAyElf2GqlxaalTg_oxbGYfuT37Yaj9E0yuHwhq6samKGKSO-AbqTpoqjt5589vCtDhss-bQ/https%3A%2F%2Fatlas.brainnetome.org%2Fdownload.html
 However, when I was trying to get the volume of subcortical regions (the 
hippocampus, amygdala, thalamus, and basal ganglia), they are excluded since 
the ?h.cortex.label files do not include them. 

My plan was to use aseg.mgz to get each subcortical regions and do the same 
procedure as for the cortical regions. However, mri_ca_label did not allow me 
to create .annot from BN_Atlas_subcortex.gca from Brainnetome website. So I 
continued using mris_convert to convert .gca to label.mgz, and I am stuck here.
Is there any way to get the subcortical regions’ .gcs file, or even an easier 
way to calculate the volume of subcortical regions in brainnetome atlas from 
FreeSurfer?

Best,
Garrett

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Re: [Freesurfer] Hippocampal/amygdala subfields hemisphere error

[Iglesias Gonzalez, Juan E.]

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Dear Chris,
This is a pretty weird one!
Question: what files are there in the temporary directory 
subjectDir/subjectBase/tmp/hippoSF_T1_long.v22_left/ ?
Cheers,
/E

--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1FmaPIPrt8VADXFs3ezSt_rWHcBh_tWsK4JwiAlnAziRQsMYS29OTHG0OFvV76XsIIJ982XXhoaBTgJ-k7cqsqnAeop22V0Toxlf-AGxdw6j_QcPvw7CjtdXJYXG0o-D3oQauN4lyTq-irnQqX4dFWXu6ibNkmVkHRSNvmcLolEIp1GHPh7WU7Mp1PoxCFy8OTfnqbGwEqjKF6mLs-_A2rFMw9dwXFhFPXDaWtJMYhuVY7FfONo3YDVYU8npupSVE/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hemond, Christopher 

Date: Wednesday, April 19, 2023 at 18:47
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Hippocampal/amygdala subfields hemisphere error

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Dear experts,

I'm getting an error running the longitudinal hippocampal/amygdala subfields 
analysis and hoping for help.  I've been able to complete this analysis without 
problems for all but one of my subjects.  The issue is that only the left 
hemisphere will be processed (but successfully).  Cross-sectional 
hippocampal/amygdala subfield processing works fine, and the quality of the 
scans and recon-all output looks good.  I've tried several times to re-process 
the data but to no avail.  I get the following error message:

...
Wrote image to file image_tp_2.mgz
This file does not contain MRI parameters
Unable to perform assignment because the left and right sides have a different 
number of elements.
Error in SegmentSubfieldsT1Longitudinal (line 2136)
MATLAB:matrix:singleSubscriptNumelMismatch

Any ideas on what I might be doing wrong?  I couldn't find this specific error 
in the forums.

Thanks very much,
Chris

(running freesurfer-darwin-macOS-7.3.2-20220804-6354275)


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[Freesurfer] Hippocampal/amygdala subfields hemisphere error

[Hemond, Christopher]

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Dear experts,

I'm getting an error running the longitudinal hippocampal/amygdala subfields 
analysis and hoping for help.  I've been able to complete this analysis without 
problems for all but one of my subjects.  The issue is that only the left 
hemisphere will be processed (but successfully).  Cross-sectional 
hippocampal/amygdala subfield processing works fine, and the quality of the 
scans and recon-all output looks good.  I've tried several times to re-process 
the data but to no avail.  I get the following error message:

...
Wrote image to file image_tp_2.mgz
This file does not contain MRI parameters
Unable to perform assignment because the left and right sides have a different 
number of elements.
Error in SegmentSubfieldsT1Longitudinal (line 2136)
MATLAB:matrix:singleSubscriptNumelMismatch

Any ideas on what I might be doing wrong?  I couldn't find this specific error 
in the forums.

Thanks very much,
Chris

(running freesurfer-darwin-macOS-7.3.2-20220804-6354275)


The information transmitted is intended only for the person or entity to which 
it is addressed and may contain confidential and/or privileged material. Any 
review, transmission, re-transmission, dissemination or other use of, or taking 
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please contact the sender and delete the material from any computer.
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Re: [Freesurfer] TIV from manually corrected aseg+aparc.mgz

[Huang, Yujing]

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Hi Daniela,

On this page 
https://secure-web.cisco.com/1eUQpVvxrVeNEfeuknfSJu6n3plR5yKIy8iRlfATB5XV2S4Wq_68rpEnw4YyVZM9BjK4jMfItVUk3EBKG85JZGFeYB67XqxzUaW3sx_iQBKkuPpJnxHb70EvrWDP21B9zMFJAXpCVKvaAGxd2BG1YToPdu2TLDfqVo880z9p3OfdSus4qO0uJPBNy3Vb9DNri0QsNNhyuDL4_lqx9WtKk40t023R40UXi9hi5KGDYPp9HDW4NCQpoLsJFrL4ysUhX/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FeTIV,
 it explains how Freesurfer estimates TIV.  

Basically, total intracranial volume is found to correlate with the determinant 
of the transform matrix used to align an image with an atlas. The work 
demonstrates that a one-parameter scaling factor provides a reasonable TIV 
estimation (but biased). This method uses an atlas based spatial normalization 
procedure, and requires that the talairach.xfm be correct.

Best,

Yujing

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Daniela Vecchio
Sent: Wednesday, April 19, 2023 5:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TIV from manually corrected aseg+aparc.mgz

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Hi FreeSurfer Developers,

For our study we had to manually correct some recon-all outputs due to some 
ROIs underestimation. For the purpose we manually edited the aparc+aseg.mgz 
file using the "voxel edit” command from Freeview. Then we use the mri_segstats 
command to extract volumes from the corrected aparc+aseg.mgz file. However, 
from the MRI_segstats we didn’t obtain a new TIV value. I want to ask if the 
TIV value is computed using the parcellation files (like aseg+aparc one) or 
instead using the brain.mgz file. How can I check that the TIV value reported 
in aseg.stats was unaffected from the underestimation we had to correct?

Please find below the command we use to compute volumes from the corrected 
aseg+aparc file:

mri_segstats --seed 1234 --seg 
/Applications/freesurfer/7.1.1/subjects/CorrectedSegmentations/${subj_id}.mgz 
--sum /Applications/freesurfer/7.1.1/subjects/${subj_id}/stats/AllVolumes.stats 
--pv /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz --empty 
--brainmask 
/Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/brainmask.mgz 
--brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray 
--in /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/Applications/freesurfer/7.1.1/AreasList.txt  --subject ${subj_id}


Thank you for your support!

Daniela 


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[Freesurfer] creating average labels

[Carlos Alcocer]

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Good afternoon,

I would like to verify that the subcallosal cingulate cortex (SCC)
segmentation of my subjects are correct. I want to do this by creating an
average label of the left SCC and an average label of the right SCC which I
can then map onto each subject.

If I save these labels from each subject as a volume (.mgz) and then run
mri_concat on the left SCC labels (.mgz) and then on the right SCC labels
(.mgz), would this accomplish my desired goal?

Tks,

Carlos
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Re: [Freesurfer] is it possible to run a longitudinal study on 2 "-base" images?

[Huang, Yujing]

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You can run longitudinal analysis with 2 timepoints -  
https://secure-web.cisco.com/1jQQ0cVi7lI0yGhk44hY2J-io2CWVn1H8Pa0LTIgv7lJoY6DvAzdL-94yJFuUJgiTBTy90dccfUzUHS74CitHvEMQPm31joNosyoZGVcpO0GnFgFpHpm-PYiOjWcw_hH1AS_OZXMTT517S1fM6Ldxek4-QJbcuzYXEjTS-R732JLE0qhJmEjSCM9vSs9SNgadFwCKjstoQAknqe3BybCgxS4-OdJI2F8eKz2o3nwvxUZDkEcBJPIM_KA7AcelwhFM/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing

For base processing, the command will look like this
recon-all -base  -tp  -tp   -all

 needs to be an unique identifier in your SUBJECTS_DIR.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of KennethSPrice
Sent: Tuesday, April 18, 2023 7:08 PM
To: Freesurfer support list 
Subject: [Freesurfer] is it possible to run a longitudinal study on 2 "-base" 
images?


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Helloo,

I have 2 sets clinical scans on a single subject that I put through Synth_SR. 
The Synth_SR tutorial suggests that if you have T1, T2, and FLAIR scans, you 
might want to average the number of voxels when doing ROI analysis. I want to 
apply this logic to cortical analysis.

My idea is to "average" the cortex of T1, T2, and FLAIR scans from year 1 and 
year 2 using the longitudinal pipeline. Then I'd like to compare the "-base" 
images from both sets. Previously, when I've tried using the "-base" images in 
a study, I get the error that says something to the effect of "It appears that 
this subject ID is an existing base/template from longitudinal processing 
(-base): . If you are trying to re-run a -base template you need to pass 
the -base and all -tp flags:"

So, is it possible to do a longitudinal analysis on 2 "-base" images, or is 
there a different method you might suggest?

Thank you all.
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[Freesurfer] License key

[Mohammad Amin Khodadadegan]

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Hello
could you please guide me where I should copy the license.txt file in Linux
Ubuntu
There is no installation demo video for Linux and I am totally confused
I couldn't install freesurfer, not only the DEB file but also tar.gz .
Unfortunately, all the instructions are for MacOS.
Please guide me to follow your lead.
-- 
*Kind regards,*
*Khodadadegan M.A,*
*Medical Doctor*
*Mashhad University Of Medical Sciences*
*Mashhad*

*Iran*
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[Freesurfer] Fw: freesurfer download zip password

[Parmaksiz, Deniz]

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Hi I reached out previously but haven't heard back -- can you please provide me 
with the password for the zip file? Thanks!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Parmaksiz, Deniz 

Sent: Tuesday, April 18, 2023 1:26 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freesurfer download zip password


Attention: This email originated outside of Penn State Health. Use caution when 
clicking links or opening attachments.


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Hi,

I'm trying to download FreeSurfer and run it on VirtualBox but can't expand the 
7zip file on WinRAR because I don't have a password. I saw 'brain2009' 
suggested online but WinRAR gives an error message saying the file is either 
corrupted or it's the wrong password when I try that.  The wiki says to contact 
you & I would really appreciate help with this -- thanks!

Best,
Deniz
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[Freesurfer] TIV from manually corrected aseg+aparc.mgz

[Daniela Vecchio]

External Email - Use Caution

Hi FreeSurfer Developers,

For our study we had to manually correct some recon-all outputs due to some 
ROIs underestimation. For the purpose we manually edited the aparc+aseg.mgz 
file using the "voxel edit” command from Freeview. Then we use the mri_segstats 
command to extract volumes from the corrected aparc+aseg.mgz file. However, 
from the MRI_segstats we didn’t obtain a new TIV value. I want to ask if the 
TIV value is computed using the parcellation files (like aseg+aparc one) or 
instead using the brain.mgz file. How can I check that the TIV value reported 
in aseg.stats was unaffected from the underestimation we had to correct?

Please find below the command we use to compute volumes from the corrected 
aseg+aparc file:

mri_segstats --seed 1234 --seg 
/Applications/freesurfer/7.1.1/subjects/CorrectedSegmentations/${subj_id}.mgz 
--sum /Applications/freesurfer/7.1.1/subjects/${subj_id}/stats/AllVolumes.stats 
--pv /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz --empty 
--brainmask 
/Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/brainmask.mgz 
--brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray 
--in /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/Applications/freesurfer/7.1.1/AreasList.txt  --subject ${subj_id}


Thank you for your support!

Daniela 


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[Freesurfer] Fwd: Password to VirtualMachine request

[Gromki Hados]

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Hi,

I would like to kindly ask you for the password for FreeSurfer 7.2.0
Virtual Machine.

I tried using old password (brain.map), but that doesn't work anymore.

Also, is there a possiblity of getting sudo password? It was quite annoying
to work on previous version without it.

Thank you in advance!

Best regards,
Jakub Wojciechowski
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[Freesurfer] Extracting statistical values from significant ROIs after running GLM

[Akansha Mahesh Naraindas]

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Hi
I have run a GLM using cortical thickness and a behavioural measure on specific 
ROIs, 
I have a query about extracting the statistical values, specifically the test 
statistic from the significant regions after running the GLM but prior to 
multiple comparison correction. Is there any way to extract the test statistic 
of each vertex of the significant regions?

Thanks
Akansha

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