Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add F-T2 and F-S0 maps to verbose outputs #893

Merged
merged 4 commits into from
Nov 11, 2022
Merged

Add F-T2 and F-S0 maps to verbose outputs #893

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
d42bb34
Add F-T2 and F-S0 maps to verbose outputs.
tsalo Nov 4, 2022
8ca7f5a
Add new outputs to outputs list.
tsalo Nov 4, 2022
4dee339
Fix keys.
tsalo Nov 4, 2022
ca25678
Didn't realize four-echo was verbose.
tsalo Nov 4, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions docs/outputs.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,8 @@ echo-[echo]_desc-[PCA|ICA]S0ModelPredictions_components.nii.gz Component- and v
separated by echo.
desc-[PCA|ICA]AveragingWeights_components.nii.gz Component-wise averaging weights for metric
calculation.
desc-[PCA|ICA]S0_stat-F_statmap.nii.gz F-statistic map for each component, for the S0 model.
desc-[PCA|ICA]T2_stat-F_statmap.nii.gz F-statistic map for each component, for the T2 model.
desc-optcomPCAReduced_bold.nii.gz Optimally combined data after dimensionality
reduction with PCA. This is the input to the ICA.
echo-[echo]_desc-Accepted_bold.nii.gz High-Kappa time series for echo number ``echo``
Expand Down
10 changes: 10 additions & 0 deletions tedana/metrics/collect.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -160,6 +160,16 @@ def generate_metrics(
metric_maps["map predicted T2"] = p_m_T2
metric_maps["map predicted S0"] = p_m_S0

if io_generator.verbose:
io_generator.save_file(
utils.unmask(metric_maps["map FT2"], mask),
label + " component F-T2 img",
)
io_generator.save_file(
utils.unmask(metric_maps["map FS0"], mask),
label + " component F-S0 img",
)

if "map Z clusterized" in required_metrics:
LGR.info("Thresholding z-statistic maps")
z_thresh = 1.95
Expand Down
16 changes: 16 additions & 0 deletions tedana/resources/config/outputs.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,14 @@
"orig": "pca_weights",
"bidsv1.5.0": "desc-PCAAveragingWeights_components"
},
"PCA component F-T2 img": {
"orig": "pca_FT2",
"bidsv1.5.0": "desc-PCAT2_stat-F_statmap"
},
"PCA component F-S0 img": {
"orig": "pca_FS0",
"bidsv1.5.0": "desc-PCAS0_stat-F_statmap"
},
"PCA reduced img": {
"orig": "oc_reduced",
"bidsv1.5.0": "desc-optcomPCAReduced_bold"
Expand All @@ -95,6 +103,14 @@
"orig": "ica_weights",
"bidsv1.5.0": "desc-ICAAveragingWeights_components"
},
"ICA component F-T2 img": {
"orig": "ica_FT2",
"bidsv1.5.0": "desc-ICAT2_stat-F_statmap"
},
"ICA component F-S0 img": {
"orig": "ica_FS0",
"bidsv1.5.0": "desc-ICAS0_stat-F_statmap"
},
"high kappa ts split img": {
"orig": "hik_ts_e{echo}",
"bidsv1.5.0": "echo-{echo}_desc-Accepted_bold"
Expand Down
4 changes: 4 additions & 0 deletions tedana/tests/data/fiu_four_echo_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,13 @@ desc-ICA_components.nii.gz
desc-ICA_decomposition.json
desc-tedana_metrics.json
desc-tedana_metrics.tsv
desc-ICAS0_stat-F_statmap.nii.gz
desc-ICAT2_stat-F_statmap.nii.gz
desc-ICA_mixing.tsv
desc-ICA_stat-z_components.nii.gz
desc-PCAAveragingWeights_components.nii.gz
desc-PCAS0_stat-F_statmap.nii.gz
desc-PCAT2_stat-F_statmap.nii.gz
desc-PCA_decomposition.json
desc-PCA_metrics.json
desc-PCA_metrics.tsv
Expand Down
4 changes: 4 additions & 0 deletions tedana/tests/data/nih_five_echo_outputs_verbose.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,13 @@ desc-ICA_components.nii.gz
desc-ICA_decomposition.json
desc-tedana_metrics.json
desc-tedana_metrics.tsv
desc-ICAS0_stat-F_statmap.nii.gz
desc-ICAT2_stat-F_statmap.nii.gz
desc-ICA_mixing.tsv
desc-ICA_stat-z_components.nii.gz
desc-PCAAveragingWeights_components.nii.gz
desc-PCAS0_stat-F_statmap.nii.gz
desc-PCAT2_stat-F_statmap.nii.gz
desc-PCA_decomposition.json
desc-PCA_metrics.json
desc-PCA_metrics.tsv
Expand Down