On 2/6/18 5:26 PM, Michiko H. wrote:
Hi Doug,

That's very helpful, thank you! I have 2 follow-up questions though:

1. Is it possible to merge the cortical label (e.g. label 1001 ctx-lh-bankssts) with its corresponding label that extends into the WM (e.g. label 3001 wm-lh-bankssts)? I'm not completely sure but this may/may not give better results when tracking between labels as nodes.
You can use something like
mri_binarize --replaceonly 1001 3001 --i aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz

2. Is it possible to include the subcortical structures in the final masked image?
Yes, use mri_binarize --i aparc+aseg+2mm.nii.gz --match 10 11 12 ... --o aparc+aseg+2mm.subcort.nii.gz
where 10 11 12 is a list of the ids of the subcortical structures you want
Then
fscalc aparc+aseg+2mm.subcort.nii.gz add aparc+aseg+2mm.masked.nii.gz -o both.nii.gz


Thank you so much!
Michiko

On Mon, Feb 5, 2018 at 12:30 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:

    You mean you want to remove everything but the WM labels? You can
    do it in two steps:

    1. Create a mask of the wm labels:

    mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5
    --o wm.mask.nii.gz

    2. Mask the wmparc:

    mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz
    aparc+aseg+2mm.masked.nii.gz




    On 2/4/18 5:28 PM, Michiko H. wrote:
    Hi Freesurfer experts,

    I am wondering if it is possible to remove the original labels
    after extending the parcellation by 2mm into the WM for
    tractography? I don't wish to have tractography run on both sets
    of labels considering the algorithm would take into account the
    streamlines terminating at nodes defined by the labels so it
    doesn't quite make sense to count streamlines terminating at both
    the original label separately from the new label extending into
    the WM.

    I used the following command for growing the parcellation into WM:

    mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm
    --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz


    Would appreciate help and suggestions!


    Thanks,

    Michiko.



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