[Freesurfer] Subcortical surfaces from volume features.

2024-05-10 Thread Sam Maddox (CMP - Postgraduate Researcher) 
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Dear Freesurfer Experts,

I am looking into generating subcortical surfaces from the subcortical volumes 
generated from recon-all. The reason for this is I am trying to create a vertex 
based Morphological Similarity Network generated from both cortical and 
subcortical regions. Ideally I would avoid Volume Based Statistics as, from 
what I can see, I am limited to just thickness features.

I have run recon-all for all of my participants, and ideally my set up for 
surface subcortical features would be done in freesurfer as well, although I am 
aware of other tools such as:
https://secure-web.cisco.com/1Naw6TVmVSgW4iHi_BvEcAItpkOmdAs3fMgTWn1abKwPfBB8rdZFU3uvsi4cPqx3S8bYQkyU527GS0tUWq5iTLIxi4h-neYTg3rRF4rm36g6ssGYvZTHYISx4xuiaDvdlgjLf00reXO6y4TRF6SOjlA2eclFajGQaaMj_WAPMydblg1WhHM3s49fAVOEYVpYz5DKxrM9HaIEbEhAUQfic1RPJW9C_WvN7qtqqxCGA2jBE5sAQ3gQdaiTi6ckB5Co2EaKd_919kOa34WJ6MXeQhIRrDU18ASd_y1u_AhvG__WBnPhcjqAzmFXgwtAXFQUeuXxMG33RICOWUxpS-QpFhg/https%3A%2F%2Fgithub.com%2FNIRALUser%2FSPHARM-PDM%3Ftab%3Dreadme-ov-file
https://secure-web.cisco.com/1u1Ru_EifdWYQsjg7F-GHFGBp-Vkvjk_3iHSqwgV0CTWKwS_FdITj126INHIN78MyDplkEgShMCUIlnKVgVAVeIL4pXXY0VzSExsLZPdSZzxjJkfX71D38cItZvMy0YpbKye--NNeT0bh3Tomd12EW1AAdNcOFsjDbbn_pa2ThIa_zYKV1RErGaiqR-uN33LV-JUKm-H6SrWEurQFUU9O-BLvIKrPcdGn_ZP7LhTJSQSzia576nMQtbhwz8k4uk9Tn3scHnFpNNJ-BdlV-VJmxSSTlz9c8vsy4woTK4TB-kkfz47AKxZg0RU8oilcgIikrfo_kO5HCoQwAMqTqxsJhA/https%3A%2F%2Fgithub.com%2Fthomas-vincent%2Fnipic%2Fwiki%2F%255BFreesurfer%255D-Get-surfaces-of-subcortical-structures
https://secure-web.cisco.com/1yhlZBs4CaRuE7OrwrGVtEsQL33d47WfL9Yu02tKHEzKqGis-VZ2QsUo3wc0I-F9Xl4CD42o42gUtGEvKCz8usWl7X-3fhwsXAu2DKmngoloe8OIoLcqBvxP7uX_nAUAOzJVhL1v1X1wGpSSCDx2i646Rrxd1R0iGBv28T3TEcEzQA7Mfpl98Tse0ab3SdW04eOZHbRzG0bqADUjE7WXLR3jQUj9GAT4IkULnuGhhv7CP9gF2IIOAaNcBqU8xsijZDxWuelDUPELsRrWlxOJ6HSBWWntUhP7GZF336sA8O4ErBZai7rjk2BwMvCxskkvPYYEduQ_YepFNicYE-rsWnA/https%3A%2F%2Fgithub.com%2Fkhanlab%2Fsurfmorph
https://secure-web.cisco.com/1SH8G6D-66tFkOVdkMhKlZU3DoZJWFrankZvFbDjhud520NPLJFMbPVEY3QEkx1Anjs_T-mOZ802DkO8IMAoKICsuHGbfGHzlCBpuLpBo3eG6xOMEBAvyPoDJp4Foco_c278n-AKuUSqWStoiyqybIWHuEDnEVXSCFHtEcCER3WFc7Y05QDcELHJxcVyfuqIM49409LcHzosBJuWF2rTNTteyik5rMYdclhak8oiyez2cmqdIO_JRAajAd0aadfNPhe0A7A41RkGowT8gzaCssM-DEIHPy8MjjNu8X8iL8dp0yAyktpa1nICSQP4S41QtHxJqzOkF7bZHOU6xFerjNA/https%3A%2F%2Fgsl.lab.asu.edu%2Fmtsms%2F
inaivu/aseg2srf at master * aestrivex/inaivu * 
GitHub

The above tools may be able to generate subcortical surfaces, but I would then 
need to convert them back to freesurfer formats to run mris_anatomical_stats, 
which I am lost with. If anyone has any advice for this, this would be great!

Within freesurfer, I am aware of tools such as mri_vol2surf, as well as other 
such as mris_sample_parc - Free Surfer Wiki 
(harvard.edu).
 I am a bit lost as to how to use these tools, as the documentation is limited, 
and threads are more looking at generating these surfaces for visualizations 
rather than anatomical statistics.

I am also wondering if there are any additional processing steps, perhaps 
normalization, that may be required before creating the MSN.

If anyone has tried this before or has any advice, I would love to hear. I am 
relatively new to this area, using freesurfer past recon-all, so any help is 
appreciated!

Many thanks,
Sam
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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

2024-05-10 Thread Liliana Wu 
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Thank you Douglas. That’s much clearer. I do however,  have a subject without a 
gender disclosure. Would I set up my class and contrasts as:

5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa


then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]?



Best,
Liliana

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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

2024-05-10 Thread Douglas N. Greve 
The first one will test for a difference between group offset/intercept 
accounting for age, gender, episodes, and residuals. By setting a 
regressor contrast element to 0, one accounts for that variable because 
the variable appears in the model that is fit to the data (and so its 
effects already removed from other variables). One more thing: I would 
recommend incorporating gender in the class structure not as a 
continuous variable. So you would have 4 classes: PatentientsMale, 
PatientsFemale, HCMale, HCFemale then use contrast [0.5 0.5 -0.5 -0.5 0 
0 0 0 0 ...]


On 5/9/2024 3:26 PM, Liliana Wu wrote:


External Email - Use Caution

Hello!

I am having trouble with creating my contrast files. I did go over 
FsfdExamples (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples 
). 
However, I am unsure how should I create my contrast files if I want 
do a 2 group comparison while controlling 4 covariates:


Class:

Patients, healthy control

variables are:

Age,gender,episodes,residuals,

Here is how I set up my contrast files:

1 -1 0 0 0 0 0 0 0 0  - Contrast1 (measure group differences)

1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 
(measure group differences while accounting for covariates)


For some reason I think I am setting up those contrast files wrong… 
Any help is appreciated.


Best,

Liliana


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[Freesurfer] mri_segment_hypothalamic_subunits 7.4.1 issue

2024-05-10 Thread Antonio Di Renzo 
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Dear FreeSurfer developers,

I have just tested the Segmentation of hypothalamic subunits, but unfortunately 
it does not work.
I simply wrote:

mri_segment_hypothalamic_subunits --s subject_folder

or

mri_segment_hypothalamic_subunits --s subject_folder/T1.nii

or

mri_segment_hypothalamic_subunits --s recon_all_processed_folder

Every time the message is: Illegal instruction (core dumped).

Moreover when I asked the help option:

mri_segment_hypothalamic_subunits -h

I obtained again: Illegal instruction (core dumped).

I installed tensorflow as answered using:

fspython -m pip install tensorflow

 but these libraries are installed already because the messages are: 
Requirement already satisfied written on every row.

How can I use this function?

Thank you in advance,

Antonio



ps. I used the following softwares

Freesurfer version 7.4.1

Ubuntu 22.04.4 LTS

Oracle virtual box for Windows 10 pro
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