rawmapper - Man Page
Synopsis
rawmapper [-h] [-s SESSION [SESSION ...]] [-f NAME [NAME ...]] [-w PATTERN] [-o FOLDER] [-r] [-c] [-n PREFIX] [-m [PREFIX]] [-d] FOLDER
Description
Maps out the values of a DICOM attribute of all subjects in the sourcefolder, saves the result in a mapper-file and, optionally, uses the DICOM values to rename the sub-/ses-id's of the subfolders. This latter option can be used, e.g. when an alternative subject id was entered in the [Additional info] field during subject registration at the scanner console (i.e. this data is stored in the DICOM attribute named 'PatientComments')
- FOLDER
The source folder with the raw data in sub-#/ses-#/series organization
Options
- -s SESSION [SESSION ...], --sessions SESSION [SESSION ...]
Space separated list of selected sub-#/ses-# names/folders to be processed. Otherwise all sessions in the bidsfolder will be processed
- -f NAME [NAME ...], --field NAME [NAME ...]
The fieldname(s) of the DICOM attribute(s) used to rename or map the subid/sesid foldernames
- -w PATTERN, --wildcard PATTERN
The Unix style pathname pattern expansion that is used to select the series folders from which the dicomfield is being mapped (can contain wildcards)
- -o FOLDER, --outfolder FOLDER
The mapper-file is normally saved in sourcefolder or, when using this option, in outfolder
- -r, --rename
Rename sub-subid/ses-sesid directories in the sourcefolder to sub-dcmval/ses-dcmval
- -c, --clobber
Rename the sub/ses directories, even if the target-directory already exists
- -n PREFIX, --subprefix PREFIX
The prefix common for all the source subject-folders. Use a '*' wildcard if there is no prefix
- -m [PREFIX], --sesprefix [PREFIX]
The prefix common for all the source session-folders. Use a '*' wildcard if there is no prefix or an empty value if there are no sessions
- -d, --dryrun
Dryrun (test) the mapping or renaming of the sub-subid/ses-sesid directories (i.e. nothing is stored on disk and directory names are not actually changed))
Comments
examples:
rawmapper myproject/raw
rawmapper myproject/raw -f AcquisitionDate
rawmapper myproject/raw -s sub-100/ses-mri01 sub-126/ses-mri01
rawmapper myproject/raw -r -f ManufacturerModelName AcquisitionDate --dryrun
rawmapper myproject/raw -r -s sub-1*/* sub-2*/ses-mri01 --dryrun
rawmapper -f EchoTime -w *fMRI* myproject/raw
Author
Marcel Zwiers <m.zwiers@donders.ru.nl>