Hi al, Just wondering if anyone has any suggestionsto my previous question as to why the volume from mni152 space would be rotated, even though the MNI152 to subject T1 alignment looks good?

As a recap, here are my commands:

mni152reg --s ${subject} --1

tkregister2 --mov ${subj_dir}/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz --reg ${reg_file}

mri_vol2vol --mov ${subj_dir}/mri/orig.mgz --targ /home/Documents/thalamus/AtlasMNI152/left-vols-1mm/global.nii.gz --reg ${reg_file} --inv --o ${out_dir}/lh_global.nii.gz

tkmedit -f subject/mri/orig.mgz -aux ${out_dir}/lh_global.nii.gz -ov ${out_dir}/lh_global.nii.gz -fminmax .5 1

On Thu, Apr 20, 2017 at 2:31 PM, Corinna Bauer corinnab83@gmail.com wrote:

Great, thank you!

There seems to be a registration error getting the label from MNI into subject space, even though the MNI152 1mm and the subject line up well in tkregister2. Attached are two images, the first is the MNI152_1mm brain with the label overlaid, and the second is a sample subject with the same label overlaid. After running the following commands:

mni152reg --s ${subject} --1

tkregister2 --mov ${subj_dir}/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz --reg ${reg_file}

mri_vol2vol --mov ${subj_dir}/mri/orig.mgz --targ /home/Documents/thalamus/AtlasMNI152/left-vols-1mm/global.nii.gz --reg ${reg_file} --inv --o ${out_dir}/lh_global.nii.gz

tkmedit -f subject/mri/orig.mgz -aux ${out_dir}/lh_global.nii.gz -ov ${out_dir}/lh_global.nii.gz -fminmax .5 1

[image: Inline image 4][image: Inline image 3]

On Thu, Apr 20, 2017 at 11:09 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:

...

You can use mri_segstats passing newoutputfile as the --seg

On 04/19/2017 06:47 PM, Corinna Bauer wrote:

...

Dear all,

I have a series of .vtk files in MNI152 1mm space from an external thalamus atlas outlining specific thalamic nuclei. I would like to put these into native subject space and calculate the volume from each

nuclei.

...

I would imagine that I would do the following:

1. run mni152reg --s --1 on each subject
2. mri_vol2vol --mov mni152space_atlas_file.nii.gz -- targ

subject/mri/orig.mgz --reg subject/mri/mni152.orig.mgz.reg --inv --o newoutputfile_subject_space

But then I am not certain how to calculate the volume of the new output file.

Suggestions?

Thanks!

Corinna

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