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Download resources from osf #277

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8 changes: 0 additions & 8 deletions hippunfold/config/nnunet_model_urls.yml

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92 changes: 55 additions & 37 deletions hippunfold/config/snakebids.yml
Original file line number Diff line number Diff line change
Expand Up @@ -337,43 +337,40 @@ cifti_metric_types:
singularity:
autotop: 'docker://khanlab/hippunfold_deps:v0.5.0'

xfm_identity: resources/identity_xfm.txt
template: CITI168
xfm_identity: resources/etc/identity_xfm.txt

template_files:
CITI168:
T1w: resources/CITI168/T1w_head_700um.nii.gz
T2w: resources/CITI168/T2w_head_700um.nii.gz
xfm_corobl: resources/CITI168/CoronalOblique_rigid.txt
crop_ref: resources/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
crop_refT1w: resources/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
Mask_crop: resources/CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
T1w: T1w_head_700um.nii.gz
T2w: T2w_head_700um.nii.gz
xfm_corobl: CoronalOblique_rigid.txt
crop_ref: T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
crop_refT1w: T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
Mask_crop: Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
dHCP:
T1w: resources/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_res-1_T1w.nii.gz
T2w: resources/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_res-1_T2w.nii.gz
xfm_corobl: resources/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_to-corobl_affine.txt
crop_ref: resources/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
crop_refT1w: resources/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
Mask_crop: resources/CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz

atlas:
- multihist7
T1w: tpl-dHCP_cohort-1_res-1_T1w.nii.gz
T2w: tpl-dHCP_cohort-1_res-1_T2w.nii.gz
xfm_corobl: tpl-dHCP_cohort-1_to-corobl_affine.txt
crop_ref: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_T2w.nii.gz
crop_refT1w: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_T1w.nii.gz
Mask_crop: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_desc-hipp_mask.nii.gz

atlas_files:
multihist7:
label_nii: resources/multihist7/sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
label_list: resources/multihist7/labellist.txt
thick: resources/multihist7/thickness.nii.gz
curv: resources/multihist7/curvature.nii.gz
gyr: resources/multihist7/gyrification.nii.gz
label_nii: sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
label_list: labellist.txt
thickness: thickness.nii.gz
curvature: curvature.nii.gz
gyrification: gyrification.nii.gz
bigbrain:
label_nii: resources/bigbrain/sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
label_list: resources/bigbrain/sub-bigbrain_labellist.txt
label_nii: sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
label_list: sub-bigbrain_labellist.txt
magdeburg:
label_nii: resources/magdeburg/sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
label_list: resources/magdeburg/magdeburg_labellist.txt
label_nii: sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
label_list: magdeburg_labellist.txt
freesurfer:
label_nii: resources/freesurfer/sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
label_list: resources/freesurfer/freesurfer_labellist.txt
label_nii: sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
label_list: freesurfer_labellist.txt


#values to use for re-mapping tissue labels when combining with subfields.
Expand Down Expand Up @@ -407,18 +404,39 @@ no_reg_template: False

modality: T2w

template: CITI168

atlas:
- multihist7



#these will be downloaded to ~/.cache/hippunfold
nnunet_model:
T1w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar'
T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task102_hcp1200_T2w.nnUNetTrainerV2.model_best.tar'
hippb500: 'zenodo.org/record/5732291/files/trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar'
neonateT1w: 'zenodo.org/record/5733556/files/trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar'
neonateT1w_v2: 'zenodo.org/record/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar'
T1T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task103_hcp1200_T1T2w.nnUNetTrainerV2.model_best.tar'
synthseg_v0.1: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task102_synsegGenDetailed.nnUNetTrainerV2.model_best.tar'
synthseg_v0.2: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task203_synthseg.nnUNetTrainerV2.model_best.tar'
resource_urls:
nnunet_model:
T1w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar'
T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task102_hcp1200_T2w.nnUNetTrainerV2.model_best.tar'
hippb500: 'zenodo.org/record/5732291/files/trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar'
neonateT1w: 'zenodo.org/record/5733556/files/trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar'
neonateT1w_v2: 'zenodo.org/record/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar'
T1T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task103_hcp1200_T1T2w.nnUNetTrainerV2.model_best.tar'
synthseg_v0.1: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task102_synsegGenDetailed.nnUNetTrainerV2.model_best.tar'
synthseg_v0.2: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task203_synthseg.nnUNetTrainerV2.model_best.tar'
atlas:
multihist7: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b782827451220b86dd8/?zip='
bigbrain: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8b13d27b123094c96f/?zip='
magdeburg: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8013d27b122f94c938/?zip='
freesurfer: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8513d27b123094c96a/?zip='
template:
CITI168: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf0282745121fb86a93/?zip='
dHCP: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bff13d27b123094c9b4/?zip='
MBMv2: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0887852d133ca597dd/?zip='
MBMv3: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0e8a28b11240ffc6e9/?zip='
upenn: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c1613d27b122a94ca09/?zip='
#to get hash, see https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911




crop_native_box: '256x256x256vox'
crop_native_res: '0.2x0.2x0.2mm'
Expand Down
84 changes: 0 additions & 84 deletions hippunfold/download_models.py

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5 changes: 0 additions & 5 deletions hippunfold/resources/CITI168/CoronalOblique_rigid.txt

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36 changes: 0 additions & 36 deletions hippunfold/resources/Training_Instructions.md

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24 changes: 0 additions & 24 deletions hippunfold/resources/bigbrain/bigbrain_snaplabels.txt

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10 changes: 0 additions & 10 deletions hippunfold/resources/bigbrain/sub-bigbrain_labellist.txt

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5 changes: 0 additions & 5 deletions hippunfold/resources/desc-flipLR_type-itk_xfm.txt

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13 changes: 0 additions & 13 deletions hippunfold/resources/example_sbatch.sh

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46 changes: 0 additions & 46 deletions hippunfold/resources/fineTune_UNet.sh

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6 changes: 0 additions & 6 deletions hippunfold/resources/freesurfer/README.md

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