Comments (3)
Here's what I use but I have two magnitude images and a phase difference:
{
"dataType": "fmap",
"modalityLabel": "magnitude",
"criteria": {
"SidecarFilename": "*010*fieldmap1*"
}
},
{
"dataType": "fmap",
"modalityLabel": "phasediff",
"criteria": {
"SidecarFilename": "*011*fieldmap1*"
}
},
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@gladomat it sounds like you have a field map, e.g. for use with FUGUE. I think @dlevitas is using two acquisitions with reversed phase encoding directions, e.g. for use with TOPUP. If you have modern Siemens data, the phase encoding should be encoded in the PhaseEncodingDirection BIDS tag, e.g. "PhaseEncodingDirection": "j-"
. However, this information is not available for data from other vendors. At our center, we make the phase encoding explicit when we set up the protocol name on the scanner, e.g. so we will have "fMRI_ap" and "fMRI_pa" to distinguish anterior-posterior phase encoding. In this case, the this should be reported in the SidecarFilename (as long as dcm2niix was called with protocol name inserted in the filename -f %p) as well as in the BIDS ProtocolName tag, e.g. "ProtocolName": "fMRI_ap"
.
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I had forgotten about this, but wanted to post my solution before closing. For spin echo field maps, they should follow a format like this in the configuration file:
{
"dataType": "fmap",
"modalityLabel": "epi",
"IntendedFor": [
4,
6,
8,
10,
12,
14,
16,
18
],
"criteria": {
"SidecarFilename": "004*"
}
},
{
"dataType": "fmap",
"modalityLabel": "epi",
"IntendedFor": [
4,
6,
8,
10,
12,
14,
16,
18
],
"criteria": {
"SidecarFilename": "005*"
}
},
I have also come across field maps where there are two magnitudes and one phase difference. In these cases, the portion of the configuration file for the field maps is something like this:
{
"dataType": "fmap",
"modalityLabel": "magnitude1",
"IntendedFor": [
9,
10,
11
],
"criteria": {
"SidecarFilename": "011*",
"EchoTime": 0.00492
}
},
{
"dataType": "fmap",
"modalityLabel": "magnitude2",
"IntendedFor": [
9,
10,
11
],
"criteria": {
"SidecarFilename": "011*",
"EchoTime": 0.00738
}
},
{
"dataType": "fmap",
"modalityLabel": "phasediff",
"IntendedFor": [
9,
10,
11
],
"criteria": {
"SidecarFilename": "012*"
},
"sidecarChanges": {
"EchoTime1": 0.00492,
"EchoTime2": 0.00738
}
},
It should be noted that these examples require the most recent software versions of dcm2bids (2.1.4) and dcm2niix (v1.0.20190410).
from dcm2bids.
Related Issues (20)
- IntendedFor and Sources with only relative path to dataset root is now deprecated
- Two H1s in "How to use advanced configuration" prevent full TOC
- sidecar_changes doesn't support int / numerical objects
- Should this line be pointing to one of the sidecar files? HOT 2
- Typos in some files of the scaffold raise errors on the validator
- Creating several 3D images instead of a single 4D image. HOT 2
- New features or enh for next release
- post_op HOT 6
- Provide a Docker image that includes pydeface HOT 4
- [BUG] dcmbids binary
- Processing order issue ? ```"IntendedFor" No id found for 'IntendedFor' value 'XX'``` HOT 4
- KeyError: 'datatype' HOT 1
- TypeError in Acquisition.init() when running dcm2bids HOT 1
- `sidecar_changes` do not fetch all matches of the referenced description
- Error: Too many NIFTI images with the name HOT 1
- compKeys default for run numbering doesn't seem like a good one HOT 1
- Subprocess Error Assistance HOT 3
- Allowing for post_op command's output to be printed to stdout HOT 2
- Script removes task information from filenames. HOT 8
- bids validator not working properly HOT 8
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