General instructions

Create a project folder (only once)
For each subject, create a folder
For each study, create a folder "Study 1 ...", "Study 2..." with the date of the study
- Update from 2015-08: if the project has more than one type of data collection, add "[[MRI]]", "[[WHH]]" or "[[Physiology]]" at end of folder name, after date.
Inside the study folder, create a folder "MRI" for the MRI files, and "physiology" for physiology files.

Copy the raw DICOM or PARREC or nifti files into the MRI folder. You can also create a "raw" folder, and move a copy of the DICOM/PARREC/nifti files there.

You will create the series subfolders later.

Once those sub-folders are created, you will delete the raw files from the MRI folder, after you have put a copy in the "raw images" subfolder. (This means you don't view potentially thousands of files every time you navigate to the "MRI" folder.)

MRI Siemens Prisma, BMC scans

The Siemens Prisma scans from the BMC arrive as a series of folders. the CSPM "DICOM convert" has an option for subfolders:

This will convert each subfolder independently, and create "series 03 (...)" sub-sub-folders. We actually want these "series..." folders to be moved to the MRI folder, and to de-clutter the MRI folder. There are 4 steps:

Copy the DICOM folders from the scanner into the study ...\MRI\ folder.
Run CSPM's DICOM convert with the Subfolders option; make sure you set the Protocol id.
Move the "series ..." sub-folders to the ...\MRI\ folder; in Windows Explorer, search for "series" to show the newly-created folders, which you can select and move to ...\MRI\.
Create a "raw" folder in ...\MRI\, and move the DICOM folders into that.

Examples are below.

Step 1 example

Step 2 example

Step 3 example

Step 4 example - final organization

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