Naming acquisitions

Once you've gotten your project approved, you will have to set up a scanning protocol that your project's scanning sessions will follow. An important part of this is how you name your acquisitions, since adequate naming will ensure an easy transition to BIDS (see the Data Export page).

Naming convention for exam cards

To enable correct file naming and conversion, exam card names should adhere to the following convention:

<researchgroup>_<project>_<extra info if need be>

E.g. Dumoulin_SDVICI, Zwaag_Cerebellum, or SC-develop_VASO etc.

Naming convention for subjects

To enable correct dicom naming, subject IDs should adhere to one these four formats: <subjectID>, <subjectID>_<sessionID> E.g. sub01, sub01_ses01 etc.

Do not use:

<projectID>_<subjectID> as this will lead to problems with subsequent automatic conversions.

Also, make sure that you use a new subjectID / sessionID for each subject in the project.

Naming convention for sequences (optional, only needed for automatic conversion)

Functional MRI with topup

func-bold_task-<taskname>_run-01 This is run 01 of the task

fmap-epi_acq-<taskname>_run-01 This is the topup sequence that goes with run 01

func-bold_task-<taskname>_run-02 This is run 02 of the task

fmap-epi_acq-<taskname>_run-02 This is the topup sequence that goes with run 02

Make sure that your runs are consecutively named _run-XX, where XX is the index of the run.

Functional MRI with B0

func-bold_task-<taskname>_run-03 This is run 03 of the task

fmap-B0_acq-<taskname> This is the B0 sequence that goes with run 03. Note that phase-difference B0 maps are usually applied to multiple bold runs in a session.

Standard Anatomy

run-01_anat-T1w This is the first T1 weighted anatomical

run-02_anat-T1w This is the second T1 weighted anatomical

anat-T2w This is the only T2 weighted anatomical

anat-T2starw This is the only T2* weighted anatomical

Fancy anatomy -- tentative (BIDS specification has changed and ReproIn is unclear)

anat-T1map_acq-MEMP2RAGE This is the only T1 map

anat-T2*map_acq-MEMP2RAGE This is the only T2* map

anat-MEMP2RAGE_[_echo-<index>]inv-1_part-mag This is the magnitude map of the first inversion in an MP2RAGE

anat-MEMP2RAGE_[_echo-<index>]inv-1_part-phase This is the phase map of the first inversion in an MP2RAGE

anat-MEMP2RAGE_[_echo-<index>]inv-2_part-mag This is the magnitude map of the second inversion in an MP2RAGE

anat-MEMP2RAGE_[_echo-<index>]inv-2_part-phase This is the phase map of the second inversion in an MP2RAGE