Commit 26191147 authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

upgraded to new version of Filetree

parent 29c37353
......@@ -36,7 +36,7 @@ python run_template_construction.py [Options]
Show help message
#### `-i <dir>, --input <dir>`
Directory containing the defaced subjects/timepoints
Absolute path to directory that contains the defaced subjects/timepoints
#### `-t <path>, --tree <path>`
Path to FSL Filetree describing the subject-specific directory structure and selection of modalities.
......@@ -82,7 +82,7 @@ For a T1-only template this would look like:
- if the `--subids <path>` flag is not provided, the sub-directories of `--input <dir>` will be used
#### `-o <dir>, --output <dir>`
Output directory
Absolute path to output directory
#### `-s <path>, --subids <path>`
Path to .csv file containing one subject ID per row: subject IDs have to indentify the sub-directories of the
......@@ -113,9 +113,9 @@ A typical command for within-subject template construction given multiple timepo
```bash
export MMORFDIR=/path/to/mmorf.sif
python run_template_construction.py
-i /full/path/to/subject/containing/timepoint/directories/
-i /absolute/path/to/subject/containing/timepoint/directories/
-t ./config/MS_template.tree
-o /full/path/to/output/directory/
-o /absolute/path/to/output/directory/
-aff True
-nln True
-nres 6
......
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