Add amygdala and hippocampus from HCP subcortical atlas #16

tsalo · 2023-10-16T19:07:57Z

Closes #14 and closes #7.

Ready to try out.

tsalo · 2023-10-30T21:40:39Z

Did it work?

mattcieslak · 2023-10-31T01:41:18Z

I'm having issues with my templateflow installation. We may have done ourselves a disservice by not using containers for this whole thing

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=== Do not change lines below === { "chain": [], "cmd": "jupyter nbconvert --to notebook --execute --allow-errors Volumetric4S.ipynb", "dsid": "9b64b8a0-c0b2-42c5-b65f-7f6aaf0b67f8", "exit": 0, "extra_inputs": [], "inputs": [ "subcortical_merged/tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-01_dseg.nii.gz", "subcortical_merged/tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.nii.gz", "subcortical_merged/tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.tsv", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-1000ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-100ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-200ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-300ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-400ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-500ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-600ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-700ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-800ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-900ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-1000ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-100ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-200ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-300ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-400ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-500ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-600ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-700ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-800ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-900ParcelsAllNetworks_dseg.nii.gz", "Schaefer/atlas-Schaefer2018v0143_desc-1000ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-100ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-200ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-300ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-400ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-500ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-600ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-700ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-800ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-900ParcelsAllNetworks_dseg.tsv", "atlas-4S1052Parcels_dseg.tsv", "atlas-4S152Parcels_dseg.tsv", "atlas-4S252Parcels_dseg.tsv", "atlas-4S352Parcels_dseg.tsv", "atlas-4S452Parcels_dseg.tsv", "atlas-4S552Parcels_dseg.tsv", "atlas-4S652Parcels_dseg.tsv", "atlas-4S752Parcels_dseg.tsv", "atlas-4S852Parcels_dseg.tsv", "atlas-4S952Parcels_dseg.tsv" ], "outputs": [ "tpl-MNI152NLin2009cAsym_atlas-4S1056Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz" ], "pwd": "." } ^^^ Do not change lines above ^^^

tsalo · 2023-10-31T23:52:38Z

Darn, the parcel counts in the dseg tsv and json filenames are wrong.

=== Do not change lines below === { "chain": [], "cmd": "jupyter nbconvert --to html --execute JointAtlas.ipynb", "dsid": "9b64b8a0-c0b2-42c5-b65f-7f6aaf0b67f8", "exit": 0, "extra_inputs": [], "inputs": [ "transforms/tpl-MNI152NLin2009cAsym_from-MNI152NLin2009aSym_mode-image_xfm.h5", "transforms/tpl-MNI152NLin6Asym_from-MNI152NLin2009aSym_mode-image_xfm.h5", "transforms/tpl-MNI152NLin6Asym_from-MNI152NLin2009cAsym_mode-image_xfm.h5", "transforms/tpl-MNI152NLin6Asym_from-MNI152NLin6Sym_mode-image_xfm.h5", "JointAtlas.ipynb", "Schaefer/Atlas_ROIs.2.nii.gz", "Schaefer/tpl-fsLR_hemi-L_den-32k_desc-nomedialwall_dparc.label.gii", "Schaefer/tpl-fsLR_hemi-R_den-32k_desc-nomedialwall_dparc.label.gii" ], "outputs": [ "JointAtlas.html", "tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.tsv", "tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-01_dseg.nii.gz", 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=== Do not change lines below === { "chain": [], "cmd": "jupyter nbconvert --to html --execute Volumetric4S.ipynb", "dsid": "9b64b8a0-c0b2-42c5-b65f-7f6aaf0b67f8", "exit": 0, "extra_inputs": [], "inputs": [ "subcortical_merged/tpl-MNI152NLin6Asym_atlas-SubcorticalMerged_res-01_dseg.nii.gz", "subcortical_merged/tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.nii.gz", "subcortical_merged/tpl-MNI152NLin2009cAsym_atlas-SubcorticalMerged_res-01_dseg.tsv", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-1000ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-100ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-200ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-300ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-400ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-500ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-600ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-700ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-800ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin6Asym_atlas-Schaefer2018v0143_res-01_desc-900ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-1000ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-100ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-200ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-300ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-400ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-500ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-600ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-700ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-800ParcelsAllNetworks_dseg.nii.gz", "Schaefer/tpl-MNI152NLin2009cAsym_atlas-Schaefer2018v0143_res-01_desc-900ParcelsAllNetworks_dseg.nii.gz", "Schaefer/atlas-Schaefer2018v0143_desc-1000ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-100ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-200ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-300ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-400ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-500ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-600ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-700ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-800ParcelsAllNetworks_dseg.tsv", "Schaefer/atlas-Schaefer2018v0143_desc-900ParcelsAllNetworks_dseg.tsv", "atlas-4S1056Parcels_dseg.tsv", "atlas-4S156Parcels_dseg.tsv", "atlas-4S256Parcels_dseg.tsv", "atlas-4S356Parcels_dseg.tsv", "atlas-4S456Parcels_dseg.tsv", "atlas-4S556Parcels_dseg.tsv", "atlas-4S656Parcels_dseg.tsv", "atlas-4S756Parcels_dseg.tsv", "atlas-4S856Parcels_dseg.tsv", "atlas-4S956Parcels_dseg.tsv" ], "outputs": [ "tpl-MNI152NLin2009cAsym_atlas-4S1056Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-4S156Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-4S256Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-4S356Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-4S456Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-4S556Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-4S656Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-4S756Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-4S856Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin2009cAsym_atlas-4S956Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz", "tpl-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz", "volumetric4S.html" ], "pwd": "." } ^^^ Do not change lines above ^^^

mattcieslak · 2023-11-01T01:17:03Z

This PR got complicated, but I think we're there!

tsalo added 11 commits October 12, 2023 10:24

Reorganize folders.

04ff653

Reorganize files.

7d387f5

Keep reorganizing.

406253b

Keep working on code.

ee15758

Run black.

913630b

Keep going.

f9383cd

Keep going.

09604db

Keep going.

68e814a

Use utils.py.

4118e66

Keep going.

3736a6f

Update JointAtlas.ipynb

7c26f26

tsalo added the breaking-change label Oct 16, 2023

tsalo self-assigned this Oct 16, 2023

tsalo and others added 9 commits October 16, 2023 16:08

Call the CIFTI generation code in the notebook.

78fbd36

Remove old files.

865888f

Remove empty lines.

cfff64b

Add requirements.

dda0392

Update README.md

a6882b6

Improve docs.

83bf589

actually download schaefer

0b9228d

convert to html instead of notebook

07966aa

change wget

bf7ae44

mattcieslak added 3 commits October 30, 2023 20:21

rename "name" to label

174ed7a

Update some naming

9cb30d9

update jointAtlas.ipynb

6d94f81

mattcieslak added 3 commits October 30, 2023 21:55

handle templateflow_home being a datalad dataset

9b87e4b

remove directory

aef7270

mattcieslak added 5 commits October 31, 2023 13:20

cleanup

7ad44e4

mattcieslak added 4 commits October 31, 2023 20:41

52 -> 56

66d1136

remove 52s

dbe81fb

mattcieslak marked this pull request as ready for review November 1, 2023 01:16

tsalo merged commit 92a2677 into main Nov 1, 2023
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tsalo deleted the amygdala-and-hippocampus branch November 1, 2023 13:51

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Add amygdala and hippocampus from HCP subcortical atlas #16

Add amygdala and hippocampus from HCP subcortical atlas #16

tsalo commented Oct 16, 2023 •

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tsalo commented Oct 30, 2023

mattcieslak commented Oct 31, 2023

tsalo commented Oct 31, 2023

mattcieslak commented Nov 1, 2023

Add amygdala and hippocampus from HCP subcortical atlas #16

Add amygdala and hippocampus from HCP subcortical atlas #16

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tsalo commented Oct 16, 2023 • edited Loading

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mattcieslak commented Oct 31, 2023

tsalo commented Oct 31, 2023

mattcieslak commented Nov 1, 2023

tsalo commented Oct 16, 2023 •

edited

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