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

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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MGH-NMR Center
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