Hi Anam
Sorry for the lag. mris_left_right_register takes as input surfaces, not the
overlays or thicknesses.
To flip an overlay file, here is what I would do. Maybe others can chime in on
weather this makes sense or if there is an easier way.
I'd start by running mris_left_right_register. Then, I would use read_surf.m
to load in the original, and registered surfaces, eg lh.right and
lh.sphere.left_right. Then, I would go through each vertex in lh.right and
find the corresponding (or closest) vertex in lh.sphere.left_right. This
correspondence will define a mapping you could then apply to the overlays.
-Paul
________________________________________
From: Anam Anzak <a.an...@qmul.ac.uk>
Sent: Wednesday, March 15, 2023 3:52 AM
To: Wighton, Paul; Freesurfer@nmr.mgh.harvard.edu
Cc: Bernardo Pimentel
Subject: Re: Flipping Thickness Matrices
External Email - Use Caution
Dear Paul,
Thank you for your reply! Just one thing we haven't really figured out... does
mris_left_right_register take as input the thickness (mgh) files or the
surfaces? I've been trying but can't really apply it to the thickness files. In
theory, we would really just like to flip the thickness matrix right->left...
is mris_left_right_register something we should apply upstream of the thickness
file generation?
Thank you and all the best,
Bernardo and Anam
--
Bernardo Pimentel
Neurology Resident
Department of Neurology - Christian-Doppler University Hospital
Paracelsus Medical University
Salzburg, Austria
Miss Anam Anzak MBBS PhD MRCS PGCCE
NIHR Clinical Lecturer (Neurosurgery)
Specialty Registrar in Neurosurgery, London deanery
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wighton, Paul
<pwigh...@mgh.harvard.edu>
Sent: 07 March 2023 21:31
To: Freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edu>
Cc: Bernardo Pimentel <bcpimente...@gmail.com>
Subject: Re: [Freesurfer] Flipping Thickness Matrices
Hi Anam,
Check out mris_left_right_register. It's not super well documented, but it
takes as input the right and left hemispheres, inflated onto a sphere, and
outputs the left hemisphere registered to the right and the right hemisphere
registered to the left, also inflated onto a sphere.
If you'd like to do this in matlab, perhaps looking at the code for
mris_left_right_regsiter would help
https://github.com/freesurfer/freesurfer/blob/dev/mris_left_right_register/mris_left_right_register.cpp<https://secure-web.cisco.com/1IwEg4Ngb-r-J1t-vbpx7YHZQj0wpI3pm8yDOxlEsVPbG9aHMjST1Zv4dmfGDlKw8xL5o8GYkytU3ISu0F5HlXjONh2LzdtmgzKFJ0WwnLXHfA18XsLx4iMYbDiteSBCazkrtdTg7f25v5HZ7xfz8XNdZ7ka2CRQQqGNvMDf2EEHXqV2DNYIAL6pRWufQVVNmDXI1YuhcaLz27rpi_1yWgrPozQc5QxAxSi4KOTMLWdE4wcAACPJhgG8TI2cXlEP0reXb7KKBFSpCJoJ1rb7NyeaNTztnK06U7f0rxM4ZY8ax2ZYJRPjygatZbyMQ4pvA/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fmris_left_right_register%2Fmris_left_right_register.cpp>
-Paul
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anam Anzak
<a.an...@qmul.ac.uk>
Sent: Tuesday, March 7, 2023 4:00 PM
To: Freesurfer@nmr.mgh.harvard.edu
Cc: Bernardo Pimentel
Subject: [Freesurfer] Flipping Thickness Matrices
External Email - Use Caution
Dear FreeSurfer Community,
Has anyone had any success with solving the below problem:
I am dealing with brain lesions which may present on the left or right
hemisphere of the brain.
1. I wish to 'FLIP' RIGHT sided hemispheres (which contain lesions) to the
LEFT side, so I ultimately can collate all my data and analyse brain
hemispheres that are IPSILATERAL or CONTRALATERAL to the side of the brain
lesion.
2. When I use the Flip function below, the matrix generated seems to be
correct, HOWEVER the subsequent IMAGE generated from the matrix, appears
incorrect (it is not at all a mirror image of the original image).
3. NOTE: My matrices include a Lesion Mask and a Medial Wall Mask (I am
interested in examining Cortical Thickness values of all the cortex EXCEPT the
lesion and medial wall (tentorium and ventricles etc).
Here are the commands used, for eg. 'subject 1':
%% 4b. Load the binary Lesion masks RIGHT
right_lesion_filelist = strcat(P, '/Oedema_masks_bin/', Imaging_Code,
'_rh_fsaverage5_bin.mgh');
% load RIGHT lesion masks into a matrix
right_lesions = SurfStatReadData([right_lesion_filelist]);
right_lesions = ~right_lesions;
% create a left hemisphere matrix filled with 1s
left_hemisphere = ones(17,10242)
% concatenate horizontally lesions masks (L) with right hemisphere matrix
fullbrain_with_right_lesions = horzcat(left_hemisphere, right_lesions)
% create medial wall mask for all subjects
r_whole_mask = repmat(mask, 17, 1)
% add the medial wall mask on the lesion masks
fullbrain_lesion_medialwall = fullbrain_with_right_lesions.*r_whole_mask
% apply matrix with lesion & medial wall to the thickness values
T_right = fullbrain_lesion_medialwall .* T_rightlesion
%% Flip the Right sided images to the left
% reverse the element in each row
subject1 = T_right(1,:)
SurfStatView(subject1, SP)
SP = SurfStatAvSurf({[P '/fsaverage5/surf/rh.pial'],[P
'/fsaverage5/surf/lh.pial']})
subject1_flipped = fliplr(subject1)
SurfStatView(subject1_flipped, SP)
mirror_image = fliplr(T_right)
SurfStatView(mirror_image(1,:), SP)
Any thoughts would be very much appreciated!
Kind regards
Anam
Miss Anam Anzak MBBS PhD MRCS PGCCE
NIHR Clinical Lecturer (Neurosurgery)
Specialty Registrar in Neurosurgery, London deanery
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