Open kousu opened 2 years ago
If our acq-b0 files are really fieldmaps
no they are not. It is quite confusing. These are not B0 fieldmap (where B0 refers to the static magnetic field) but b=0 images (where b refers to the diffusion-encoding b-value).
this additional image is acquired in order to improve SNR when computing diffusion tensor metrics.
i'm not sure how we can make BIDS happy with this special image type...
Single-Band Reference | sbref | Single-band reference for one or more multi-band dwi images. |
---|
so then
git mv ./sub-vallHebron06/dwi/sub-vallHebron06_acq-b0_dwi.nii.gz ./sub-vallHebron06/dwi/sub-vallHebron06_sbref.nii.gz
?
But maybe it's fine like it is. That spec page is pretty vague, only mentioning
The OPTIONAL
acq-<label>
key/value pair corresponds to a custom label the user may use to distinguish different sets of parameters.
which is also appropriate since the scanner set the different parameter set b=0
!
Do you think the spec is implying or just suggesting that _dwi.nii.gz
implies _dwi.bval
and _dwi.bvec
here?
sub-<label>/ [ses-<label>/] dwi/ sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.bval sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.bvec sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.json sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.nii[.gz] sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_sbref.json sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_sbref.nii[.gz]
Single-Band Reference
no it's not that (for the record: SB reference refers to images acquired with SMS factor of >1)
But maybe it's fine like it is.
i can sleep at night with this status quo
Do you think the spec is implying or just suggesting that _dwi.nii.gz implies _dwi.bval and _dwi.bvec here?
dwi data definitely need a bval and a bvec in order to be able to compute DTI metrics
Do you think the spec is implying or just suggesting that _dwi.nii.gz implies _dwi.bval and _dwi.bvec here?
dwi data definitely need a bval and a bvec in order to be able to compute DTI metrics
Okay well, stupid question then: doesn't the BIDS naming scheme would seem to mean there's missing files here? The existence of
./sub-vallHebron03/dwi/sub-vallHebron03_acq-b0_dwi.json
should imply
./sub-vallHebron03/dwi/sub-vallHebron03_acq-b0_dwi.bval
./sub-vallHebron03/dwi/sub-vallHebron03_acq-b0_dwi.bvec
but if that's wrong then _dwi
is the wrong suffix for these files isn't it?
Do you think the spec is implying or just suggesting that _dwi.nii.gz implies _dwi.bval and _dwi.bvec here?
dwi data definitely need a bval and a bvec in order to be able to compute DTI metrics
Okay well, stupid question then: doesn't the BIDS naming scheme would seem to mean there's missing files here? The existence of
./sub-vallHebron03/dwi/sub-vallHebron03_acq-b0_dwi.json
should imply
./sub-vallHebron03/dwi/sub-vallHebron03_acq-b0_dwi.bval ./sub-vallHebron03/dwi/sub-vallHebron03_acq-b0_dwi.bvec
but if that's wrong then
_dwi
is the wrong suffix for these files isn't it?
ah! sorry i misunderstand your point above-- a b=0 image has (by definition) no bvec/bval associated with it.
that being said, we could also make the point that a very low b-value would be considered b=0 and labeled as is (and in this case a bvec/bval should be needed)-- so, i'm not sure what to advise here 🤷♂️
Maybe we can bring it up on the BIDS bug tracker when we get a free moment?
A bunch of files are tagged
acq-b0
The files affected are all DWI images:The only mention I can find of b0 in BIDS is about using the
fmap/
datatype/subfolder, and it recommends four schemas depending on how many files you have:sub-*/{ses-*/,}anat/*_{magnitude{1,2}, phasediff}.nii.gz
sub-*/{ses-*/,}anat/_{magnitude{1,2},phase{1,2}}.nii.gz
sub-*/{ses-*/,}anat/_{magnitude,fieldmap}.nii.gz
sub-*/{ses-*/,}anat/_epi.nii.gz
If our
acq-b0
files are really fieldmaps, they only slot they fit into is the_epi
case. But again, they're underdwi/
right now so I don't know what to make of the situation.