Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

3db0map #741

Merged
merged 3 commits into from
Aug 12, 2023
Merged

3db0map #741

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
4f8499c
Segment GE 3dbomap that includesboth fieldmap and magnitude images
neurolabusc Aug 12, 2023
b11855f
Handle 3db0map and B0map
neurolabusc Aug 12, 2023
f7c3e3f
Clean up code
neurolabusc Aug 12, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 1 addition & 3 deletions console/nii_dicom.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5911,7 +5911,7 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
} else if (strstr( d.pulseSequenceName, "epi") != NULL) {
d.epiVersionGE = kGE_EPI_EPI; //-1 = not epi, 0 = epi, 1 = epiRT
}
if (strcmp( d.pulseSequenceName, "3db0map") == 0) {
if (strstr( d.pulseSequenceName, "b0map")) {
isGEfieldMap = true; //issue501
}
break;
Expand Down Expand Up @@ -7993,8 +7993,6 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
//avoid false positives: non-EPI GE scans can report b-value = 0
if ((d.isDiffusion) && (d.manufacturer == kMANUFACTURER_GE))
d.isDiffusion = ((d.internalepiVersionGE == kGE_EPI_EPI2) || (d.epiVersionGE == kGE_EPI_EPI2));
if ((d.manufacturer == kMANUFACTURER_GE) && (strstr( d.pulseSequenceName, "3db0map")) && strstr(d.imageType, "OTHER"))
d.isRealIsPhaseMapHz = true;
//detect pepolar https://github.com/nipy/heudiconv/issues/479
if ((d.epiVersionGE == kGE_EPI_PEPOLAR_FWD) && (userData12GE == 1))
d.epiVersionGE = kGE_EPI_PEPOLAR_REV;
Expand Down
11 changes: 4 additions & 7 deletions console/nii_dicom_batch.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6873,16 +6873,13 @@ void setBidsGE(struct TDICOMdata *d, int nConvert, int isVerbose, const char *fi
strcpy(dataTypeBIDS, "discard");
strcpy(modalityBIDS, "localizer");
isReportEcho = false;
} else if (d->isRealIsPhaseMapHz) {
isReportEcho = false;
//isAddSeriesToRun = false;
strcpy(dataTypeBIDS, "fmap");
strcpy(modalityBIDS, "fieldmap");
} else if (strstr( d->pulseSequenceName, "3db0map")) {
} else if ((d->isRealIsPhaseMapHz) || (strstr(seqName, "B0map")) || (strstr( d->pulseSequenceName, "3db0map"))) {
//case sensitivity: B0Map vs 3db0map
isReportEcho = false;
isAddSeriesToRun = false;
strcpy(dataTypeBIDS, "fmap");
strcpy(modalityBIDS, "magnitude");
if (strstr( d->imageType, "OTHER")) //NOT magnitude
if (d->isRealIsPhaseMapHz)
strcpy(modalityBIDS, "fieldmap");
} else if ((d->isMultiEcho) && (!isEPGR) && (isGR)) {
//detect EFGRE3D "STAGE 24" sequence, see 7T 29.1 example
Expand Down