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Hi Lilla,
1. Many thanks for the assurance.
2. My structural data was preprocessed in FS while my functional data was
preprocessed in FSL. As far as I can tell, the difference lies in the MNI152
standard brain size:
* In FSL, the MNI152 1mm brain’s SForm code is MNI152 and its dimensions
are anisotropic at 182x218x182.
* In FS, the SForm code for the T1 brain in the cvs_avg35 folder (as
well as the output from the registration to the MNI152) is Aligned anatomical
and its dimensions are isotropic at 256^3.
I want to use FS as I need a more accurate segmentation of the amygdala. Is
there a reason the two MNI152 brains would have different numbers of voxels and
is there a way to reconcile this so that my structural and functional have the
same voxel dimensions?
Many thanks,
Liz
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Zollei,
Lilla,Ph.D." <lzol...@mgh.harvard.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 2 July 2020 at 1:07 am
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bounding box dimensions for mri_cvs_register (MNI
space)
Hi Liz,
(1) Given that the included MNI template lives in the 1mm isotropic space, the
output will also live there. Your two commands seem to be the right for to
achieve what you intend to do.
(2) I suspect there was a dimensionality difference between your fMRI and sMRI
images even before the CVS registration was run. You will need to register
those two spaces in order to accurately align them. (I am not exactly sure what
steps are involved in your FSL preprocessing)
Lilla
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Elizabeth Haris
<e.ha...@unsw.edu.au>
Sent: Wednesday, July 1, 2020 3:20 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Bounding box dimensions for mri_cvs_register (MNI space)
External Email - Use Caution
Hi guys,
I have a couple of queries regarding the output dimensions for mri_cvs_register.
1. If I am registering my images to MNI space, can the command give me a 2mm
image, or will I only get a 1mm image which I then need to convert into a 2mm?
I am currently getting a 1mm image and resampling it to a 2mm image afterwards
(for fMRI analysis), using the following commands, and wanted to double check
the procedure:
* CVS command: mri_cvs_register --mov <subjID> --mni
* FSL command:
flirt -in <final_CVSmorphed_tocvs_avg35_inMNI152_norm.nii> \
-ref < final_CVSmorphed_tocvs_avg35_inMNI152_norm.nii > -applyisoxfm 2.0
-nosearch \
-out <subject_MNI_2mm.nii>
1. I also noticed that when I resample the image this way, though its
dimensions are 2mm^3 the voxels in the bounding box are different to the voxels
in my 2mm^3 functional image preprocessed in FSL (FS: 128^3 vs FSL: 109 91 109).
* Is this a problem?
* If so, is there a way to rectify this?
Many thanks!
Liz
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