[Freesurfer] mri_robust_register for 2D images

[Léorah Freeman]

Hi,

We are using mri_robust_register in one of our pipelines to register two 2D
T2 images from the same patient (2 different timepoints). We resample both
volumes into halfway space to then perform image subtraction.
Both T2 volumes are 2D images, each with 44 slices. However when volumes
are resampled into halfway space, each volume has over 130 slices. Without
going into too much details, I feel that this "oversampling" is posing some
problems in our subsequent subtraction scheme.

Is there a way to conserve the number of slices from the original volumes
into the one resampled to halfway space?

Thanks a lot,

Leorah Freeman, MD
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[Freesurfer] surface based analyses using PET

[Léorah Freeman]

Dear FreeSurfers,



I would like to perform surface based analyses using PET but I am not sure
I am doing things correctly. For each subject, I have reconstructed the
3DT1 MRI using recon-all –all.

Then I have coregistered the PETs with the anatomical using:

Bbregister  --s name  --mov pet.nii  --bold  --init-fsl  --reg
pet_2_T1_register.dat


Registration worked very well.

Now I  am trying to process the PET in order to do a surface based analysis
of the PET signal.

I was thinking of running:



1)  mris_preproc --target fsaverage --hemi lh  --iv
subject1/pet/subject1_pet.nii
 subject1/pet/pet_2_T1_register.dat  --iv  subject2/pet/subject2_pet.nii
subject2/pet/pet_2_T1_register.dat  --iv
subject3/pet/subject3_pet.nii  subject3/pet/pet_2_T1_register.dat
(…)  --projfrac 0.5  --out  lh.pet.mgh



I am not sure this is the right command line. I am especially concerned
with the registration file I should use. Here I used the PET àMRI
registration file. Is this the right one to use. Or should I use a
registration file from native space to fsaverage space. If so, how do I do
that?



2)  mri_surf2surf --hemi lh --s fsaverage --fwhm 10 --cortex
--sval  lh.pet.mgh
--tval lh.pet.sm10.mgh

Any advice on the fwhm I should use for smoothing the data to the surface?



3)  mri_glmfit  --y  lh.fmz.sm10.mgh  --fsgd  fsgd.txt  --C X.mtx  --surf
 fsaverage lh  --cortex  --glmdir lh.pet-age.glmdir



Can you please tell me if I got it right, especially regarding the
registration file I should use with mris_preproc?



Thank you so much,



Leorah Freeman, MD, MSc
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