[Freesurfer] Coordinates transformation from conformed space to the original FLAIR image

2020-02-13 Thread Xiaojiang Yang 
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Hi everyone,

I have used both T1 and (T2) Flair images as inputs to recon-all, and I
have generated some coordinates (ROI) that I can transform to the
original T1 images. Basically, I use the two matrixes obtained from the
mri_info -- vox2ras commands:

Sr = mri_info --vox2ras  $SUBJECTS_DIR/$subject/mri/orig/001.mgz
Sc = mri_info --vox2ras  $SUBJECTS_DIR/$subject/mri/T1.mgz

For a given point Coordinate=(x, y, z, 1) in the conformed space, I get the
coordinates in the original T1 space using the formula:

t1_Coordinate = inv(Sr) * Sc * Coordinate.

The above formula works fine. But I also want to get the transformed
coordinates in the Flair image space. I have used a similar way:

Srf = mri_info --vox2ras
 $SUBJECTS_DIR/$subject/mri/orig/FLAIRraw.mgz
Sc = mri_info --vox2ras  $SUBJECTS_DIR/$subject/mri/T1.mgz
flair_Coordinate = inv(Srf) * Sc * Coordinate.

But the above calculation is not correct. Does anyone have an idea of how
to get this flair coordinate?

Thank you!!!

Xiaojiang
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[Freesurfer] Systematically Navigating .sphere vertices

2020-02-13 Thread Mcnorgan, Christopher 
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I’m interested in working with data mapped to the .sphere icosohedrons. I 
understand from a response from Doug back in 2017 that:

   waveforms = fast_vol2mat(MRIread('waveform.nii.gz'));

will give me a v x time matrix of values from my functional values.
In the case of fsaverage, I believe I can expect somewhere around 160K rows, 1 
per vertex, for each hemisphere.
I was wondering how I might be able to determine the neighbors (i.e., vertices 
connected by an edge) for any vertex v?

Thanks,
Chris

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
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[Freesurfer] ROI Analysis in a given label with Functional Constraint in FSFAST

2020-02-13 Thread Star Xi 


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FS experts,Commonly, I can use mri_vol2vol -> mri_segstats to extract anatomical ROI from aparc or aseg template.However, now I want to extract the average percent signal change in the hV5+/MT by constrained  positive functional activation. The anatomical label is from other template.My question is, after using mri_vol2vol, which command can extract signals from a given label with constrained activation ?Thanks,Star







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[Freesurfer] study design flair T1

2020-02-13 Thread Renew Andrade 
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Dear FreeSurfer experts: 

I am dealing with a crossectional retrospective case control  study where I 
don't have all subjects with the same inaging protocols. I do have T1 for all 
of them although some have T2 others FLAIR others T2+FLAIR (besides T1 for all 
of them). My question is regarding VBM can I do inference on images with 
different characteristics? Or should them all have T1 + T2 or T1 + FLAIR. I 
guess this is the case that is all subjects should be processed with the same 
protocols.  This is in Multiple Sclerosis by the way just in case it matters. 

Sincerely,
Andrade. 

Sent from my iPhone


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