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Expand file tree Collapse file tree Original file line number Diff line number Diff line change @@ -97,29 +97,12 @@ Processing time depends on:
9797
9898## Step 5: View Results
9999
100- After processing completes, find your results in the output directory:
101-
102- ```
103- output/spimquant/
104- ├── sub-01/
105- │ ├── micr/
106- │ │ ├── sub-01_sample-brain_acq-4x_stain-YOPRO_space-ABAv3_SPIM.nii.gz
107- │ │ └── sub-01_sample-brain_acq-4x_mask.nii.gz
108- │ ├── seg/
109- │ │ └── sub-01_sample-brain_acq-4x_stain-Abeta_SPIM.ome.zarr
110- │ ├── parc/
111- │ │ └── sub-01_sample-brain_acq-4x_seg-ABAv3_from-ABAv3_dseg.nii.gz
112- │ └── tabular/
113- │ └── sub-01_sample-brain_acq-4x_seg-ABAv3_from-ABAv3_stain-Abeta_segstats.tsv
114- └── group/
115- ├── *_groupstats.tsv
116- └── *_groupstats.png
117- ```
100+ After processing completes, find your results in the output directory.
118101
119102Key output files:
120103
121104- ` micr/*_space-{template}_SPIM.nii.gz ` : Registered SPIM data in template space
122- - ` seg/*_SPIM.ome.zarr ` : Full-resolution segmentation results
105+ - ` seg/*_mask.ozx ` : Full-resolution segmentation results
123106- ` parc/*_from-{template}_dseg.nii.gz ` : Atlas-based parcellation maps
124107- ` tabular/*_segstats.tsv ` : Quantitative statistics by brain region
125108- ` group/*_groupstats.tsv ` : Group-level statistical results
@@ -211,4 +194,4 @@ pixi run spimquant ./bids ./output group \
211194 --contrast_column treatment \
212195 --contrast_values control drug \
213196 --cores all
214- ```
197+ ```
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