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Enhanced dicom fixes #45

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Enhanced dicom fixes #45

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37679c0
update cfmm_base to accept 'NONE' in addition to 'ND'
akhanf Nov 18, 2024
4f871d9
fix parsing for more generic StudyID tag in filename
akhanf Nov 18, 2024
4fc9830
update to latest dcm2niix
akhanf Nov 18, 2024
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7 changes: 4 additions & 3 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,11 @@ FROM debian:bullseye
LABEL maintainer="<[email protected]>"

# dcm2niix version
ENV DCM2NIIXTAG v1.0.20230411
ENV DCM2NIIXTAG v1.0.20240202

#heudiconv version:
ENV HEUDICONVTAG unstacked_dcm
ENV HEUDICONVOWNER akhanf
ENV HEUDICONVTAG v1.3.2+enhdicom.0

#bids validator version:
ENV BIDSTAG 1.9.7
Expand Down Expand Up @@ -44,7 +45,7 @@ RUN apt-get update -qq \
git \
python3-setuptools \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& git clone https://github.com/AlanKuurstra/heudiconv.git /src/heudiconv \
&& git clone https://github.com/${HEUDICONVOWNER}/heudiconv.git /src/heudiconv \
&& git -C /src/heudiconv checkout ${HEUDICONVTAG}
WORKDIR /src/heudiconv
RUN python3 -m pip install --no-cache-dir -r /src/heudiconv/requirements.txt \
Expand Down
52 changes: 26 additions & 26 deletions heuristics/cfmm_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -322,17 +322,17 @@ def infotodict(seqinfo):
info[DIS2D_inv1_mp2rage].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_inv1_mp2rage].append({'item': s.series_id})
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[inv1_mp2rage].append({'item': s.series_id})
if ('T1_Images' in (s.series_description).strip()):
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_t1map].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_t1map].append({'item': s.series_id})
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[t1map].append({'item': s.series_id})
if ('UNI-DEN' in (s.series_description).strip()):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[t1w].append({'item': s.series_id})
elif ('DIS2D' in (s.image_type[4].strip())):
info[DIS2D_t1w].append({'item': s.series_id})
Expand All @@ -343,14 +343,14 @@ def infotodict(seqinfo):
info[DIS2D_uni_mp2rage].append({'item': s.series_id})
if ('DIS3D' in s.image_type):
info[DIS3D_uni_mp2rage].append({'item': s.series_id})
if ('ND' in s.image_type):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[uni_mp2rage].append({'item': s.series_id})
if ('_INV2' in (s.series_description).strip()):
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_inv2_mp2rage].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_inv2_mp2rage].append({'item': s.series_id})
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[inv2_mp2rage].append({'item': s.series_id})


Expand All @@ -359,7 +359,7 @@ def infotodict(seqinfo):
info[DIS2D_t1w_mprage].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_t1w_mprage].append({'item': s.series_id})
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[t1w_mprage].append({'item': s.series_id})


Expand All @@ -375,7 +375,7 @@ def infotodict(seqinfo):

#sa2rage
if ('sa2rage' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
if ('invContrast1' in s.series_description or 'INV1' in s.series_description):
info[inv_1_sa2rage] = [s.series_id]
if ('invContrast2' in s.series_description or 'INV2' in s.series_description):
Expand Down Expand Up @@ -403,7 +403,7 @@ def infotodict(seqinfo):


if ('pd_t2_tse_tra' in s.series_description or 'pd+t2_tse_tra' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[pd_t2_tse_tra].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_pd_t2_tse_tra].append({'item': s.series_id})
Expand All @@ -413,15 +413,15 @@ def infotodict(seqinfo):

#tse cor T2w
elif ('pd_t2_tse_cor' in s.series_description or 'pd+t2_tse_cor' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[pd_t2_tse_cor].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_pd_t2_tse_cor].append({'item': s.series_id})
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_pd_t2_tse_cor].append({'item': s.series_id})

elif ('pd_t2_tse' in s.series_description or 'pd+t2_tse' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[pd_t2_tse].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_pd_t2_tse].append({'item': s.series_id})
Expand All @@ -431,7 +431,7 @@ def infotodict(seqinfo):


elif ('t2_tse_tra' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[t2_tse_tra].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_t2_tse_tra].append({'item': s.series_id})
Expand All @@ -441,7 +441,7 @@ def infotodict(seqinfo):

#tse cor T2w
elif ('t2_tse_cor' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[t2_tse_cor].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_t2_tse_cor].append({'item': s.series_id})
Expand All @@ -450,15 +450,15 @@ def infotodict(seqinfo):


elif ('t2_tse' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[t2_tse].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_t2_tse].append({'item': s.series_id})
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_t2_tse].append({'item': s.series_id})

if ('pd_tse_tra' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[pd_tse_tra].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_pd_tse_tra].append({'item': s.series_id})
Expand All @@ -468,7 +468,7 @@ def infotodict(seqinfo):

#tse cor T2w
elif ('pd_tse_cor' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[pd_tse_cor].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_pd_tse_cor].append({'item': s.series_id})
Expand All @@ -477,7 +477,7 @@ def infotodict(seqinfo):


elif ('pd_tse' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[pd_tse].append({'item': s.series_id})
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_pd_tse].append({'item': s.series_id})
Expand Down Expand Up @@ -509,15 +509,15 @@ def infotodict(seqinfo):
#susceptibility ND multiecho
if ('susc' in s.series_description or 'gre3d' in s.series_description or 't1_fl3d_p4_iso' in s.series_description ):
if ('M' in (s.image_type[2].strip())):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[mag_echo_GRE] = [s.series_id]
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_mag_echo_GRE] = [s.series_id]
if ('DIS3D' in (s.image_type[3].strip())):
info[DIS3D_mag_echo_GRE] = [s.series_id]

if ('P' in (s.image_type[2].strip())):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[phase_echo_GRE] = [s.series_id]
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_phase_echo_GRE] = [s.series_id]
Expand All @@ -544,19 +544,19 @@ def infotodict(seqinfo):
#multi-echo GRE with compressed sensing
if ('gre_CS_C41' in s.series_description):
if ('M' in (s.image_type[2].strip())):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[mag_echo_CS_GRE] = [s.series_id]


if ('P' in (s.image_type[2].strip())):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[phase_echo_CS_GRE] = [s.series_id]


# MTon GRE (excludes phase image since not needed)
if ('gre_ptx_MT_On' in s.series_description ):
if ('M' in (s.image_type[2].strip())):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[mag_MT_on_GRE].append({'item': s.series_id})
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_mag_MT_on_GRE].append({'item': s.series_id})
Expand All @@ -565,7 +565,7 @@ def infotodict(seqinfo):
#MToff GRE
if ('gre_ptx_MT_Off' in s.series_description ):
if ('M' in (s.image_type[2].strip())):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[mag_MT_off_GRE].append({'item': s.series_id})
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_mag_MT_off_GRE].append({'item': s.series_id})
Expand All @@ -576,7 +576,7 @@ def infotodict(seqinfo):

#T2star
if ('T2Star' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[T2_star].append({'item': s.series_id})
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_T2_star].append({'item': s.series_id})
Expand All @@ -586,7 +586,7 @@ def infotodict(seqinfo):
#spc T2w
if ('spc_T2' in s.series_description or 'T2w_SPC' in s.series_description or 'T2w_space' in s.series_description or 't2_space' in s.series_description or 't2_spc' in s.series_description or 'T2_spc' in s.series_description.strip() ):
if ('dark-fluid' not in s.series_description ):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[spc_T2w].append({'item': s.series_id})
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_spc_T2w].append({'item': s.series_id})
Expand All @@ -595,7 +595,7 @@ def infotodict(seqinfo):

#spc FLAIR
if ('spc_flair' in s.series_description or 'flair_spc' in s.series_description or 'dark-fluid' in s.series_description):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[spc_FLAIR].append({'item': s.series_id})
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_spc_FLAIR].append({'item': s.series_id})
Expand All @@ -605,7 +605,7 @@ def infotodict(seqinfo):
#TOF angio
if ('3D_TOF' in s.series_description or 'tof_fl3d' in s.series_description):
if (s.dim3>1):
if ('ND' in (s.image_type[3].strip())):
if ('ND' in (s.image_type[3].strip()) or 'NONE' in (s.image_type[3].strip())):
info[TOF_angio] = [s.series_id]
if ('DIS2D' in (s.image_type[3].strip())):
info[DIS2D_TOF_angio] = [s.series_id]
Expand Down
11 changes: 9 additions & 2 deletions tar2bids
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Original file line number Diff line number Diff line change
Expand Up @@ -213,13 +213,20 @@ do
# x is studyID, for instance 1
if [[ $patient_etc == *_[0-9].*.* ]]; then
patient=${patient_etc%_[0-9].*.*}
fi

#PI_project_studydate_PatientName_StudyDate_xy.hashcode.tar
# StudyDate: for instance, 20190101
# xy is StudyID, for instance, 01
if [[ $patient_etc == *_[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]_[0-9][0-9].*.* ]]; then
elif [[ $patient_etc == *_[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]_[0-9][0-9].*.* ]]; then
patient=${patient_etc%_[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]_[0-9][0-9].*.*}

#PI_project_studydate_PatientName_StudyID.hashcode.tar
# x is studyID, for instance 1
else
studyid_etc=`echo $patient_etc | awk -F '_' '{print $NF}'`
patient=${patient_etc%_${studyid_etc}}
echo "studyid_etc: ${studyid_etc}"
echo "patient: ${patient}"
fi

# if $patient is empty, skip it.
Expand Down
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