Re: [Freesurfer] creating. or replacing a label of choice in aseg atlas

2022-05-16 Thread Douglas N. Greve 
Adding ROIs in fsaverage will not cause them to appear in the aseg.mgz 
volume; fsaverage is not the atlas. If you have your ROIs in fsaverage 
space, you can map them to the individual via a linear or nonlinear 
mapping, but the accuracy will be debatable. You don't need to merge 
them with the aseg to do the volume calculation



On 5/16/2022 1:59 AM, Ramtilak Gattu wrote:


External Email - Use Caution

Thank you for the response,

Yes editing the aseg.mgz in the fsaverage directory with the custom 
roi's.


The purpose of doing it on the aseg.mgz in the fsaverage directory is- 
so that  we can use these roi's once for all for every subsequent 
subject we process from here on.


Would it be possible to replace certain existing labels with our own 
custom roi's and do the final volume calculations?


If so how?

Thanks

Regards
Tilak





*From:* Ramtilak Gattu
*Sent:* Sunday, May 15, 2022 5:01 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* creating. or replacing a label of choice in aseg atlas
Hi,

We are interested in replacing a couple of labels in aseg atlas with 
our own roi's already in the same space as of "aseg.mgz" atlas in the 
fsaverage folder.


What would be the best way to do this? Could someone help or guide me 
if anyone has done something similar to this query?


Can I just add the regions (in the form of 3d masks) to the aseg atlas 
and create aseg_modified.mgz and later replace the aseg.mgz with 
aseg_modified.gz and rename the aseg_modified.mgz back to aseg.mgz.


If I follow this procedure and run "recon-all" will the aseg_stats 
will give me volumes based on the new volumes?


--
Regards
Tilak


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Re: [Freesurfer] Integrating glmsingle with freesurfer and mri_glmfit

2022-05-16 Thread Douglas N. Greve 
No, I think that should work fine.

On 5/16/2022 3:49 PM, Lauri Tuominen wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I would like to use mri_glmfit to do 2nd level random effects analysis on 
> fMRI data I fit with GLMsingle: 
> https://secure-web.cisco.com/114IBmtjAcpPLMEdKHUFIkzufzyCZI6VANnXTx7RjQGYq5yErpvkas_-zypLXsmlhOEN4GD44L8NWAdWRkDPdDZ4SKnPxyGgqRnL5qni8GG5_Ha4Jb4byuo1vceieC8Wrfx-mrHKZQySW_vXva_0qO-1MBz6x1Lp-KgCwzfBDEJvpiI71cKZQ81upZuqclhaczlWroiNyF4GbRi_Iul8eV7cDCHp4RT1F5fEj6sSwG2Y6uapdzDoQADWgNw2aPmj2Ex-I3w4So9vE86L-ctw0u79MnPJCuovJrU9xISWGgTOPhG_p2MPMl1RstQZ_H7qMMLyzTcAo-FBSUBwIS-q_Hg/https%3A%2F%2Fdoi.org%2F10.1101%2F2022.01.31.478431
>
> >From GLMsingle I get standardized mean difference (SMD) for any given 
> >contrast, i.e. beta- difference map weighted by inverted square root of 
> >pooled variance. 
>
> I am wondering if can I just feed those SMD maps to mri_glmfit via mri_concat 
> or am I missing something elementary?
>
> Thank you again!
> Lauri Tuominen
>
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Re: [Freesurfer] Perform aseg in Freeview

2022-05-16 Thread Douglas N. Greve 
Nope, you have to use the command line. If you have a T1weighted image, 
you can just
recon-all -i t1w.mgz -s subject -all
The aseg will be in subject/mri/aseg.mgz
There are a few other options for this as well, like
samseg --i t1w.mgz --o samsegdir
The seg will be in samsegdir/seg.mgz
Or you can
synthseg --i t1w.mgz --o synthseg.mgz


On 5/16/2022 8:55 AM, R.J. Austerman wrote:
>  External Email - Use Caution
>
> Hello, brand new to this software and community so I apologize if this is a 
> dumb question or if I’m asking it through the wrong channels. I understand 
> that Freeview is just a visualizer for Freesurfer, but since I just want to 
> use it to automatically segment brain MRIs for 3D modeling, I wondered if 
> there was a way to do that within Freeview instead of working with it via the 
> command line. Thank you!
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Freesurfer Passcode

2022-05-16 Thread Utsav Shrestha (shrstha3) 
External Email - Use Caution

Hello all,

I would like to request for a passcode for 
FS_7_2_0_Ubuntu_18_04_06.ova.7z
 as being instructed in the wiki. Thank you for your time!

With Regards,

[UofM logo]

Utsav Shrestha
Biomedical Engineering
Class of 2024
Research Assistant
The University of Memphis
https://secure-web.cisco.com/1R7Pv-5gfP8NMbNFTlLNdukObQbEhW9E7Rd8vOYudaxHuVXQW0FNik32BFUg0mzliL5Vn4hLKQUgaxA_UrSC9mX9YZii8_QwtzDSoy70plhmgIFCCjsObWWbGESC4iHoX0P-zqEIVo16jYDgK7Or4KwbUBGEuECewUuQgDvQaYbgihzKgJdtoEm63NnDQbhFABhsXc_MFzfJetyn7m5Sm2eZlbud8E2pdW0ywsdpZLT11_MAm5E8NxMu8H05MGND665nfhirh5389warj4bsEJQifF8tmYOijNo7yXHcMd6jIoJVH11OWbYjWSl5X4clUXe6REvcBGUKEobwE_KYm6Ione_d_Fh093pDdnNui7DY/https%3A%2F%2Fwww.memphis.edu%2Fmrisl%2F

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Re: [Freesurfer] Permission denied error from -localGI

2022-05-16 Thread Billah, Tashrif 
Just closing this thread: we have solved it in 
https://forum.freesurfer.net/t/permission-denied-error-from-localgi/62

Thanks,
Tashrif
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[Freesurfer] Integrating glmsingle with freesurfer and mri_glmfit

2022-05-16 Thread Lauri Tuominen 
External Email - Use Caution

Dear FreeSurfer experts,

I would like to use mri_glmfit to do 2nd level random effects analysis on fMRI 
data I fit with GLMsingle: 
https://secure-web.cisco.com/114IBmtjAcpPLMEdKHUFIkzufzyCZI6VANnXTx7RjQGYq5yErpvkas_-zypLXsmlhOEN4GD44L8NWAdWRkDPdDZ4SKnPxyGgqRnL5qni8GG5_Ha4Jb4byuo1vceieC8Wrfx-mrHKZQySW_vXva_0qO-1MBz6x1Lp-KgCwzfBDEJvpiI71cKZQ81upZuqclhaczlWroiNyF4GbRi_Iul8eV7cDCHp4RT1F5fEj6sSwG2Y6uapdzDoQADWgNw2aPmj2Ex-I3w4So9vE86L-ctw0u79MnPJCuovJrU9xISWGgTOPhG_p2MPMl1RstQZ_H7qMMLyzTcAo-FBSUBwIS-q_Hg/https%3A%2F%2Fdoi.org%2F10.1101%2F2022.01.31.478431
 

>From GLMsingle I get standardized mean difference (SMD) for any given 
>contrast, i.e. beta- difference map weighted by inverted square root of pooled 
>variance. 

I am wondering if can I just feed those SMD maps to mri_glmfit via mri_concat 
or am I missing something elementary? 

Thank you again! 
Lauri Tuominen   

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[Freesurfer] Infant FreeSurfer: volumes extraction without surface

2022-05-16 Thread k3ops 
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Hi FreeSurfer team,

I've been using Infant FreeSurfer for several very young subjects and it works 
pretty well.
But after reviewing the generated surfaces, it looks like pial surface is not 
extended to fit the cortical grey matter as you can see here:
https://secure-web.cisco.com/1bVpNYbCiS9rSsh1DZzM2NKnotXc5MALdQxso7AZkTASVmPCclDCx7Dfrn5pcIruv4PyHkTc_b-TVOb67KcRe2v4KmxaMdotz5KLF1LNhUyZJ_Bl_wiEowBrKSPP6UTM0zi8eiZAiirAe4SQFTnDeSbgHX5cc9akhcwznNRTVk_mTqOfbAM817lsZ0T8YkW_-S5dlT8Yn_dMTqUFJgFGhXanWVuGvfU1fl0Re90nTpX_-PqEUM9KP3kW_g4MowWFmaGmBnghlpjfJSIViTeonFC_sjtu_uDBCHdMVvT8bHO5p5e-8SaCvQdXvqRothvx_DMEKyJCLhOo8EQYp9iJwgw/https%3A%2F%2Fibb.co%2FykCnZ5R
(By the way, did you already observed such surface error for infants using 
Infant FreeSurfer?)


I was using this command line to generate the volumes of the brain structures:
mri_segstats --seg mri/aseg_CCseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz 
--empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 
--excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name 
norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray 
--euler --ctab $FREESURFER_HOME/InfantASegStatsLUT.txt --subject $subjectId

So now, I would like to generate the volumes of the brain structres whithout 
any surface information, to avoid any missleading estimates, is this command 
line appropriate then?
mri_segstats --seg mri/aseg_CCseg.mgz --sum stats/aseg-nosurf.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --subcortgray --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --etiv --euler --ctab 
$FREESURFER_HOME/InfantASegStatsLUT.txt --subject $subjectId

>From what I see, most of the structures volume are identical, except that 
>cerebral grey and white is now provided by the labels and not the surface, and 
>supratentorial/totalgray regions are now missing because only provided by 
>surfaces.

Is there another way to generate statistical values only based on labels?
Do you recommend a more classic approach like counting voxels from each 
structure of interest and then multiplying by pixel resolution? (which is very 
tedious and error prone in my opinion)

Thanks a lot for your feedback.
Florent

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[Freesurfer] Perform aseg in Freeview

2022-05-16 Thread R.J. Austerman 
External Email - Use Caution

Hello, brand new to this software and community so I apologize if this is a 
dumb question or if I’m asking it through the wrong channels. I understand that 
Freeview is just a visualizer for Freesurfer, but since I just want to use it 
to automatically segment brain MRIs for 3D modeling, I wondered if there was a 
way to do that within Freeview instead of working with it via the command line. 
Thank you!


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[Freesurfer] Passcode for FreeSurfer VM

2022-05-16 Thread Aleksandra Petrovskaia 
External Email - Use Caution

Dear all,

I hope you are doing well. I am an intern at the University of Gothenburg,
Sweden,  could you please provide me with a passcode for FreeSurfer VM
image? I would like to use this version:
https://secure-web.cisco.com/1yZkS0R8VnbO1QWzTX29VVIIW4VCNsXbflY7tg4lYbLNqcPYGKMIrmThj-1QirUGispLS3vkkcWHFUnOY28bLGvIOZ586ZTD5mpo5yz6IonHmj-pTmu8xOQ8joYd_ETnYS_sxAMS_0Qnbl29cFa_-ntLlaD78F1dCp7Kx3uPS1ngd2TWPnJ_sqiD4XzTnuV_ZQvR5EUOJl154ZcquhmKibpbjiO7NCTnoOsWl-JhGk9PInWjj4UMfeH_ZGcSwIQCtFJOoYNNNOnHAhaQSKdoMfSzQk1lywcLHj3XFYNAL8t3K5wrpkiQHbaTPH5tneZHTh36OIwoB07bhNmFwTnT78Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2FFS_7_2_0_ubuntu_18_04_06.ova.7z

Best wishes,
Alexandra


Без
вирусов. 
http://secure-web.cisco.com/1Qc214ZMYtI0RLObvR0XBJdDSK2mgbyIuNC7SSyx5EDNCrneAoGwj_rJHlDK2csQJV3ijyOY-IN9GkGEPPek7OtNHD6WjwloqeV22og8tcCWLLbqHu7fhgc5c5M1tuSZqStgndqNfl9nfAKXsW6rHj4rdeRQunpI-YexS9I54CglWh-XXC3R10QAfbVxd1C145Xq13kSD5OnBGBXQyQx2JnvOYJnWJdKoVIMl5eaki0kXWB8vkvE5C4wk3Q9kjgiEImz99Yg0vFYhafzffxVpLmyy0Hlft9pzfDdtW7MdtToPurLSXftmq2j5qFTErX5YFSUBI-95UCKzpjT_ykfPKQ/http%3A%2F%2Fwww.avast.ru

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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Re: [Freesurfer] creating. or replacing a label of choice in aseg atlas

2022-05-16 Thread Ramtilak Gattu 
External Email - Use Caution

Thank you for the response,

Yes editing the aseg.mgz in the fsaverage directory with the custom roi's.

The purpose of doing it on the aseg.mgz in the fsaverage directory is- so that  
we can use these roi's once for all for every subsequent subject we process 
from here on.

Would it be possible to replace certain existing labels with our own custom 
roi's and do the final volume calculations?

If so how?

Thanks

Regards
Tilak





From: Ramtilak Gattu
Sent: Sunday, May 15, 2022 5:01 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: creating. or replacing a label of choice in aseg atlas

Hi,

We are interested in replacing a couple of labels in aseg atlas with our own 
roi's already in the same space as of "aseg.mgz" atlas in the fsaverage folder.

What would be the best way to do this? Could someone help or guide me if anyone 
has done something similar to this query?

Can I just add the regions (in the form of 3d masks) to the aseg atlas and 
create aseg_modified.mgz and later replace the aseg.mgz with aseg_modified.gz 
and rename the aseg_modified.mgz back to aseg.mgz.

If I follow this procedure and run "recon-all" will the aseg_stats will give me 
volumes based on the new volumes?

--
Regards
Tilak

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