data-raw/HarvardOxford/README.md

In neuroconductor-devel-releases/ggsegExtra: Plotting tool for brain atlases

Converting the Harvard-Oxford cortical atlas to ggseg

The Harvard-Oxford atlas is available with FSL. Here is a process for converting the cortical parts, via FreeSurfer, to a ggseg format.

Prerequisites

FSL, FreeSurfer, connectome workbench, parallel, ImageMagick, R.

Converting to FreeSurfer and fixing

1. Take a copy of the fsaverage folder, and set up SUBJECTS_DIR to point to the folder containing the fsaverage copy.

2. Import the atlas as a surface ```bash cd ${SUBJECTS_DIR}/fsaverage/mri mri_vol2surf --sd $(pwd)/../.. --src ${FSLDIR}/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr25-1mm.nii.gz --mni152reg --out harvard_oxford_surf_rh.mgh --hemi rh --projfrac 0.5

   mri_vol2surf --sd $(pwd)/../.. --src ${FSLDIR}/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr25-1mm.nii.gz --mni152reg --out harvard_oxford_surf_lh.mgh --hemi lh --projfrac 0.5

   ```

3. Create a color table. Run an R session in ${SUBJECTS_DIR}/fsaverage/mri r source("ho_ctab.R")

4. Create a series of individual label files ``` mkdir Labels seq 1 48 | parallel mri_vol2label --c harvard_oxford_surf_rh.mgh --id {} --surf fsaverage rh --l ./Labels/rh_HO_{}.label seq 1 48 | parallel mri_vol2label --c harvard_oxford_surf_lh.mgh --id {} --surf fsaverage lh --l ./Labels/lh_HO_{}.label

   1. Create annotation files bash LABS=$(seq 1 48 | parallel echo -n '\ --l ./Labels/lh_HO_{}.label\ ') mris_label2annot --sd ${SUBJECTS_DIR} --s fsaverage --ctab ../label/ho.annot.ctab ${LABS} --h lh --a ho

   LABS=$(seq 1 48 | parallel echo -n '\ --l ./Labels/rh_HO_{}.label\ ')

   mris_label2annot --sd ${SUBJECTS_DIR} --s fsaverage --ctab ../label/ho.annot.ctab ${LABS} --h rh --a ho ```

5. Check how the surface looks - note lots of holes etc. Using the 0 prob threshold leads to more bleed to neighboring sulci, which I think is harder to fix. ```bash vglrun freeview --surface ../surf/rh.inflated:annot=../label/rh.ho.annot --surface ../surf/lh.inflated:annot=../label/lh.ho.annot

   1. Fill and smooth bash

   convert to gifti

   mris_convert --annot ../label/rh.ho.annot ../surf/rh.inflated ./fsaverage_rh.label.gii mris_convert --annot ../label/lh.ho.annot ../surf/lh.inflated ./fsaverage_lh.label.gii

   mris_convert --annot ../label/rh.aparc.annot ../surf/rh.inflated ./fsaverage_aparc_rh.label.gii mris_convert --annot ../label/lh.aparc.annot ../surf/lh.inflated ./fsaverage_aparc_lh.label.gii

   ./smooth_labels.sh fsaverage_lh_10.label.gii inflated_lh.surf.gii fsaverage_lh_10.smooth.label.gii ./smooth_labels.sh fsaverage_rh_10.label.gii inflated_rh.surf.gii fsaverage_rh_10.smooth.label.gii

   Back to viewing with freesurfer

   for hemi in lh rh ; do mris_convert --annot fsaverage_${hemi}10.smooth.label.gii inflated${hemi}.surf.gii ./${hemi}.ho.smooth.annot done ```

6. Screengrabs with tksurfer. This can be reun somewhere other than fsaverage.

   bash ./mkPics.sh

7. Rename the unknowns to medial wall ```bash mv PicsHarvardOxford/lh_\?\?\?med.tif PicsHarvardOxford/lh_medialwall_med.tif mv PicsHarvardOxford/rh\?\?\?_med.tif PicsHarvardOxford/rh_medialwall_med.tif

   rm PicsHarvardOxford/_\? ```

8. Finally, let the R spatial tools work their magic... R source("mkHO.R")

   This creates ho_atlas.Rda which contains a couple of data frames, almost ready for inclusion in ggsegExtra.

Comments

I suspect something similar will be possible with tkedit, or other viewers that are able to look at the subcortical structures. Otherwise maximal projections after thresholding will probably suffice.

neuroconductor-devel-releases/ggsegExtra documentation built on Oct. 22, 2020, 4:47 p.m.