Harmonizing sequence/contrast names

[tsalo]

https://groups.google.com/d/msgid/bids-discussion/BCC1A813-0207-4D16-B095-4311B50F090D%40gmail.com?utm_medium=email&utm_source=footer

Rationale: In trying to apply the BIDS format to our MR database, we noticed that the current modality labeling schemes of BIDS 1.0 raises some confusion for some of our scans. Particularly, a consensus of many anatomical MR output was missing or not consequent across different sequences. Looking into the BIDS mailing list, it turns out that we were not the only one having these issues. To our opinion, most of the confusion stems from the intermixed use of sequence-, contrasts- and signal- labels.

To prevent confusion while still being able to fit a format to all possible scan types, we propose the following changes for BIDS 2.0 and where possible for backwards compatibility with BIDS 1.0:

1. All text in lowercase.
2. Punctuation marks:
   1. underscore (_) : before each prefix
   2. dash (-): after a prefix, to add labels, but not numbers!
3. ‘parent’ labels
   1. _out: referring to scanner output: in terms of volumes (regardless of how these are generated).
   2. _seq: referring to the MR sequence that generated the volumes (with the possibility to add modifier labels)
   3. _gen: referring to the result image that is generated/calculated with the output volumes
4. To prevent confusion we suggest to discard labelling for the specific ‘signal’ as modality (e.g. T1w, T2w, T2star). Often, scans are not purely t1w or t2w. Also, they might differ multiple output volumes for a specific sequence, resulting in messy and unclear labeling.
   • format:
     • sub01_… _out-(out-label1)-(out-label2)_seq-(seq-label)-(seq-modifier)gen-(gen-label) … nii.gz

Label specs

format:
- sub01_… _out-{out-label1}--{out-label}_seq-{seq-label}-{seq-modifier}gen-{gen-label} … nii.gz

_out

• output files, directly after reconstruction of K-space, referring to the volume-source.
• _out-labels:
  • inv# output volume for #th inversion time
  • echo# output volume for #th echo
  • fa# output volume for the #th flip angle
  • coil# output volume of coil element #
  • dyns# output volume(s) # of fMRI series
  • phs phase output volume
  • mag magnitude output volume

_seq

• sequence, arbitrary as these are brand specific.
• _seq-labels: [-- not exhaustive, add/edit where needed--]
  • 3dffe
  • flash
  • mp2rage
  • memp2rage
  • mprage
  • memprage
  • epi
  • tse
  • flair
  • pasl
  • SPGR
  • mef
• Optionally, one can add sequence modifiers to specify the sequence.
• _seq-modifiers:
  • bold
  • dwi
  • swi
  • t1w
  • t2w
  • t2starw
  • b0
  • b1
  • mt0
  • mt1

_gen

• generated / calculated images
• gen-labels:
  • uni unified image if first and second inversion MP2RAGE volumes
  • t1map
  • t2map
  • t2starmap
  • qsmap quantitative susceptibility map
  • mtr
  • mtsat

Examples

1. MP2RAGEME

• /anat/
  • sub-01_ses-1_out-inv1-mag_seq-memp2rage.nii.gz
  • sub-01_ses-1_out-inv1-phs_seq-memp2rage.nii.gz
  • sub-01_ses-1_out-inv2-echo1_mag_seq-memp2rage.nii.gz
  • sub-01_ses-1_out-inv2-echo1_phs_seq-memp2rage.nii.gz
  • sub-01_ses-1_out-inv2-echo2_mag_seq-memp2rage.nii.gz
  • sub-01_ses-1_out-inv2-echo2_phs_seq-memp2rage.nii.gz
  • sub-01_ses-1_seq-memp2rage_gen-uni.nii.gz [note that _out is discarded in this _gen image]

2. functional EPI

• /func/
  • sub-01_ses-1_out-dyns100_seq-epi-bold.nii.gz

3. diffusion EPI

• /dwi/
  • sub-01_ses-1_out-dyns64_seq-epi-dwi.nii.gz

Original authors: Martijn Mulder

[tsalo]

Simon Jones wrote:

_seq

• sequence, arbitrary as these are brand specific.

sequencefmod