fcp-indi / c-pac_templates Goto Github PK
View Code? Open in Web Editor NEWTemplates and atlases that aren't included in Neuroparc and are packaged in C-PAC
License: BSD 3-Clause "New" or "Revised" License
Templates and atlases that aren't included in Neuroparc and are packaged in C-PAC
License: BSD 3-Clause "New" or "Revised" License
The primary motivation of splitting this repo out of https://github.com/FCP-INDI/C-PAC is to clarify and document what the prepackaged templates are and where they are from.
At the time of opening this issue, the tables look like this:
Atlas Name # Regions Symmetrical? Hierarchical? Labelled? Generation Method Average Vol/Region Native coordinate space Description Reference Publication Year of Origin File Source/Download URL AAL ABIDE CC CSF EZ HarvardOxford ROIs Smith 10 10 well-matched maps from [β¦] 200-dimensional ICA, Resting-FMRI components [β¦] as shown in PNAS paperdoi:10.1073/pnas.0905267106 2009 https://www.fmrib.ox.ac.uk/datasets/brainmap+rsns/ https://www.fmrib.ox.ac.uk/datasets/brainmap+rsns/PNAS_Smith09_rsn10.nii.gz TalairachβTournoux
Atlas Name # Regions Symmetrical? Hierarchical? Labelled? Generation Method Average Vol/Region Native coordinate space Description Reference Publication Year of Origin File Source/Download URL MacaqueYerkes19
Fill in the empty cells of the tables
No response
When this issue is resolved, please reply to Atlases for timeseries extraction
Because of the kind of image file this is vs. all the other default templates, we have to do a different kind of timeseries analysis:
tse_roi_paths: /cpac_templates/CC400.nii.gz: Avg /cpac_templates/aal_mask_pad.nii.gz: Avg /cpac_templates/CC200.nii.gz: Avg /cpac_templates/tt_mask_pad.nii.gz: Avg /cpac_templates/PNAS_Smith09_rsn10.nii.gz: SpatialReg /cpac_templates/ho_mask_pad.nii.gz: Avg /cpac_templates/rois_3mm.nii.gz: Avg /ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/CAPRSC_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/DKT_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/DesikanKlein_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/MICCAI_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Schaefer1000_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Schaefer200_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Schaefer300_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Schaefer400_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Talairach_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Desikan_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Yeo-17-liberal_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-1x1x1.nii.gz: Avg /ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-1x1x1.nii.gz: Avg
β Configuration Without the GUI β C-PAC 1.8.1 Beta documentation
Create a binary mask at Z > 3, package that template, and use it with the same analysis as the other templates
No response
The original file is "10 well-matched maps from these, as shown in PNAS paper" from Correspondence between BrainMap and Resting-FMRI ICA components. Threshold is from Fig. 1 of Correspondence of the brain's functional architecture during activation and rest1
Smith, Stephen M et al. βCorrespondence of the brain's functional architecture during activation and rest.β Proceedings of the National Academy of Sciences of the United States of America vol. 106,31 (2009): 13040-5. doi:10.1073/pnas.0905267106 β©
Both of these templates (mni_icbm152_t1_tal_nlin_asym_09c.nii
packaged in C-PAC & tpl-MNI152NLin2009cAsym
from TemplateFlow) seem to be templates for space-MNI152NLin2009cAsym
but they aren't identical.
Templates are identical or have different names
v1.8.5-dev
They both have b'mnc2nii mni_icbm152_nlin_asym_09c/mni_icbm152_t1_tal_nlin_asym_09c.mnc mni_icbm'
as the description in the header, but mni_icbm152_t1_tal_nlin_asym_09c.nii
has
cal_max : 100.0
qoffset_x : 0.0
qoffset_y : 0.0
qoffset_z : 0.0
where tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz
from TemplateFlow has
cal_max : 10000.0
qoffset_x : -96.0
qoffset_y : -132.0
qoffset_z : -78.0
They look the same visually,
mni_icbm152_t1_tal_nlin_asym_09c |
tpl-MNI152NLin2009cAsym_res-01_T1w |
---|---|
![]() |
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but get_fdata()
shows roughly a 100Γ scaling between the data points (like the cal_max
in the headers, although less precisely):
count 8530021.00
mean 101.04
std 7.21
min -1844.27
25% 100.85
50% 100.92
75% 101.10
max 1029.66
Gist with files, headers, and images: https://gist.github.com/shnizzedy/03e8ba5ead9987b5a299e2501ec77ae0
The templates used in c-pac are currently pulled from a variety of sources, several of which are non-canonical. This should be resolved.
No response
All templates pulled from canonical sources into a common location, which is then pulled directly into C-PAC.
Clear provenance on where all templates/data sources reside and came from.
No response
No response
No response
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No response
Neuroparc has this image near the top of it's README:
It would be nice if this repository had a comparable visual
No response
The Neuroparc image looks manually curated to me. I don't know that it's worth it for this repository to do this manually.
C-PAC installs a bunch of templates in a bunch of places:
https://github.com/FCP-INDI/C-PAC/blob/ecf297738117b09a3534543c16629066767ca098/Dockerfile#L143-L144
https://github.com/FCP-INDI/C-PAC/blob/ecf297738117b09a3534543c16629066767ca098/Dockerfile#L191
https://github.com/FCP-INDI/C-PAC/blob/ecf297738117b09a3534543c16629066767ca098/Dockerfile#L238-L239
https://github.com/FCP-INDI/C-PAC/blob/ecf297738117b09a3534543c16629066767ca098/Dockerfile#L246
Instead of importing each of these sets of templates separately,
path in container source /ants_template/oasis
ANTs/ANTsR Brain Templates: OASIS.zip /ndmg_atlases
Neuroparc v1.0: Baseline /opt/dcan-tools/pipeline/global/templates
DCAN-HCP Pipelines: global/templates /usr/share/data/fsl-mni152-templates
fsl-mni152-templates β MNI152 stereotaxic brain templates for FSL /usr/share/fsl/5.0/data/atlases
fsl-atlases β FSLβs MNI152 standard space stereotaxic brain atlases http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz /usr/share/fsl/5.0/data/standard
http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz
use this repository's Dockerfile to collect them all, then just copy them from ghcr.io/fcp-indi/c-pac_templates
into C-PAC
ghcr.io/fcp-indi/c-pac_templates
into C-PAC in each C-PAC DockerfileNo response
Related: #3
This repo uses git-lfs but doesn't tell developers that or how to use it.
Add documentation for how git-lfs is / should be used for this repository
git-lfs
here (#21)I'm pretty sure #11 was a git-lfs configuration issue and could be reverted after this issue is resolved
Add surface based Schaefer2018_{}_Parcels_17Networks_order labels to the CPAC human templates folder.
The CPAC templates folder should contain the surface based Schaefer templates from the CBIG repo to the CPAC human templates folder.
cp the required files from the CBIG repo to the templates over here.
The docker image should be created without errors and the required surface based labels should be available in the CPAC templates folder.
No response
No response
Currently template-space files derived from C-PAC are labeled space-template
which does not differentiate different-template-spaced files from one another.
Use standard template identifiers like space-MNI152NLin2009
space-
entitySpatialReference
included in JSON sidecarNo response
Related:
In addition to the templates already moved here and the externally-sourced templates described in https://github.com/FCP-INDI/fcp-indi.github.io/blob/bb9aac4/docs/_sources/user/templates.rst, (
C-PAC images include the following templates:
path in container source /ants_template/oasis
ANTs/ANTsR Brain Templates: OASIS.zip /cpac_templates
C-PAC Templates /ndmg_atlases
Neuroparc v1.0: Baseline /opt/dcan-tools/pipeline/global/templates
DCAN-HCP Pipelines: global/templates /usr/share/data/fsl-mni152-templates
fsl-mni152-templates β MNI152 stereotaxic brain templates for FSL /usr/share/fsl/5.0/data/atlases
fsl-atlases β FSLβs MNI152 standard space stereotaxic brain atlases http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz /usr/share/fsl/5.0/data/standard
http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz
) C-PAC also includes templates from http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz:
https://github.com/FCP-INDI/C-PAC/blob/07d59f63ad716485ab0cf96e84f5d9a531312e9e/Dockerfile#L157-L164
Move or copy the templates from http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz into this repository
cpac_image_resources/install_resources.sh
in that archive (cpac_resources.tar.gz
) with $FSLDIR
set to /usr/share/fsl/5.0
(like https://github.com/FCP-INDI/C-PAC/blob/07d59f63ad716485ab0cf96e84f5d9a531312e9e/Dockerfile#L147)No response
No response
The filenames are currently not following any consistent pattern (the macaque files are nearly in BIDS):
atlases/label
βββ Human
βΒ Β βββ aal_mask_pad.nii.gz
βΒ Β βββ CC200.nii.gz
βΒ Β βββ CC400.nii.gz
βΒ Β βββ csf_mask_xtedit.nii.gz
βΒ Β βββ ez_mask_pad.nii.gz
βΒ Β βββ ho_mask_pad.nii.gz
βΒ Β βββ Mask_ABIDE_85Percent_GM.nii.gz
βΒ Β βββ PNAS_Smith09_rsn10.nii.gz
βΒ Β βββ rois_3mm.nii.gz
βΒ Β βββ tt_mask_pad.nii.gz
βββ Macaque
βββ MacaqueYerkes19_T1w_0.5mm_brain_mask.nii.gz
βββ MacaqueYerkes19_T1w_0.5mm_brain.nii.gz
βββ MacaqueYerkes19_T1w_0.5mm.nii.gz
βββ MacaqueYerkes19_T1w_1.0mm_brain_mask.nii.gz
βββ MacaqueYerkes19_T1w_1.0mm_brain.nii.gz
βββ MacaqueYerkes19_T1w_1.0mm.nii.gz
βββ MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz
βββ MacaqueYerkes19_T1w_2mm_brain.nii.gz
βββ MacaqueYerkes19_T1w_2mm.nii.gz
Rename all these images following the BIDS specification
No response
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