mri_info will give you the voxel-to-RAS matrix and the number of cols, rows, slices. I don't think those commands are doing what you think. I don't understand where vol2surf or cor2label come in.

On 4/1/19 12:55 PM, JD Knotts wrote:

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Hi Dr. Greve,

Thanks very much for your reply! The lh.atlas.mgz file is a volumetric atlas (Kastner atlas https://www.ncbi.nlm.nih.gov/pubmed/25452571) generated for an individual subject as described here https://gizemaltan.com/get-rois-kastner-freesurfer-atlas/. And subject_t1.nii.gz is the subject's T1-weighted nifti file. Is there an easy way to check the respective geometries?

Thanks again, JD

On Mon, Apr 1, 2019 at 8:56 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:

Not sure what is going on here. What is lh.atlas.mgz? Is is a
surface overlay? What is subject_t1.nii.gz? If it is not the same
geometry of lh.atlas.mgz, then strange things will happen when you
do it a second time.

On 3/31/2019 12:28 PM, JD Knotts wrote:

...

        External Email - Use Caution

Hello experts,

As a sanity check in a pipeline I'm running I tried converting an
atlas file containing visual ROIs from .mgz to .nii.gz and then
immediately converting the resulting .nii.gz file back to .mgz:

mri_convert lh.atlas.mgz lh.atlas.nii.gz --reslice_like
subject_t1.nii.gz--resample_type nearest --out_data_type int
--no_scale 1

mri_convert lh.atlas.nii.gz lh.atlas_reconverted.mgz
--reslice_like subject_t1.nii.gz--resample_type nearest
--out_data_type int --no_scale 1
Something is getting lost in this conversion and reconversion,
because when I run the following two lines (to generate a label
for V1) on the two different .mgz files, the original file
correctly results in the identification of 1591 label voxels,
while the converted/reconverted file incorrectly results in the
identification of 111 label voxels, none of which overlap with
the 1591 correct voxels:
mri_vol2surf --src mri/lh.atlas.mgz \

--src_type FLOAT \

--srcreg mri/register.dat \

--hemi lh \

--surf white \

--o mri/lh.atlas.mgh


mri_cor2label --c mri/lh.atlas.mgh \

--id 1 \

--surf SubID lh \

--l label/lh.V1_ventral.label

Any feedback on where I'm going wrong here would be greatly
appreciated!
Thanks for your time,
JD Knotts
1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
2) Platform: Mac OSX 10.11.6
3) Darwin Jeffreys-MacBook-Pro.local 15.6.0 Darwin Kernel Version
15.6.0: Thu Jun 23 18:25:34 PDT 2016;
root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64

-- 
Doctoral Candidate, Cognitive Neuroscience
Department of Psychology
University of California, Los Angeles

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-- JD Knotts Doctoral Candidate, Cognitive Neuroscience Department of Psychology University of California, Los Angeles

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