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Update based on Mike's changes to enable a subject-wise folder structure for the data authored by Mike Cichonski's avatar Mike Cichonski
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directories.md
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......@@ -28,12 +28,13 @@ This is where you can store all the data files for all stages of the pipeline. T
2. Copy your subject folders into this directory (assumes that each subject's files for all steps will be stored within its own subject folder).
3. When running a job through the File->Batch->Run History Template Batch menu, replace the values for [in_path] (and [out_path], if exists),
3. When running a job through the File->Batch->Run History Template Batch menu, replace the values for '[in_path]' and '[out_path]' (if it exists),
located in the "replace_string" field of each batch config file, with analysis/data (or [batch_dfp]) if this is what you enter into the "path:" field).
located in the "replace_string" field of each batch config file, with analysis/data.
*Example:* [in_path],analysis/data/1_init ----- change to -----> [in_path],analysis/data
*Example:*
[in_path],analysis/data/1_init ----- change to -----> [in_path],analysis/data
[out_path],analysis/data/2_preproc ----- change to -----> [out_path],analysis/data
4. For now, the path to the folder containing the subject folders must be manually typed/pasted into the "path:" field. This will usually be analysis/data if that's
......@@ -42,9 +43,15 @@ This is where you can store all the data files for all stages of the pipeline. T
of the subject folder in the name.
*Example:* subj001/subj001_init.set (this should work regardless of how many folders deep the init file is stored)
*Example:*
5. If you are running your jobs remotely, remember to also change the folder structure on the remote end in the same way as in steps 1-4 above.
subj001/subj001_init.set
subj002/subj002_init.set
subj003/subj003_init.set
This should work regardless of how many folders deep the init file is stored.
5. If you are running your jobs remotely, repeat steps 1-4 on the remote end.
# Log
Log is automatically populated with scripts when you execute the pipeline. You will see a folder generated for every script identified by the script that was run followed by the date and time of the scripts execution. These folders contain:
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