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Merge pull request #685 from grlee77/parrec_adc_fix
FIX: Read .PAR files corresponding to ADC maps
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‎nibabel/parrec.py

+7-1
Original file line numberDiff line numberDiff line change
@@ -784,7 +784,13 @@ def get_bvals_bvecs(self):
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if self.general_info['diffusion'] == 0:
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return None, None
786786
reorder = self.get_sorted_slice_indices()
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n_slices, n_vols = self.get_data_shape()[-2:]
787+
if len(self.get_data_shape()) == 3:
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# Any original diffusion scans will have >=2 volumes. However, a
789+
# single dynamic is possible for a post-processed diffusion volume
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# such as an ADC map. The b-values are unavailable in this case.
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return None, None
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else:
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n_slices, n_vols = self.get_data_shape()[-2:]
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bvals = self.image_defs['diffusion_b_factor'][reorder].reshape(
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(n_slices, n_vols), order='F')
790796
# All bvals within volume should be the same

‎nibabel/tests/data/ADC_Map.PAR

+124
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,124 @@
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# === DATA DESCRIPTION FILE ======================================================
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#
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# CAUTION - Investigational device.
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# Limited by Federal Law to investigational use.
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#
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# Dataset name: e:\dicom\\ADC_Map
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#
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# CLINICAL TRYOUT Research image export tool V4.2
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#
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# === GENERAL INFORMATION ========================================================
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#
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. Patient name : ADC_Map
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. Examination name : ADC_Map
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. Protocol name : ADC_Map
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. Examination date/time : 2018.01.01 / 01:01:01
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. Series Type : Image MRSeries
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. Acquisition nr : 8
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. Reconstruction nr : 3
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. Scan Duration [sec] : 276
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. Max. number of cardiac phases : 1
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. Max. number of echoes : 1
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. Max. number of slices/locations : 22
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. Max. number of dynamics : 1
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. Max. number of mixes : 1
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. Patient position : Feet First Supine
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. Preparation direction : Anterior-Posterior
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. Technique : DwiSE
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. Scan resolution (x, y) : 132 134
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. Scan mode : MS
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. Repetition time [ms] : 4600.000
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. FOV (ap,fh,rl) [mm] : 80.000 78.500 80.000
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. Water Fat shift [pixels] : 63.247
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. Angulation midslice(ap,fh,rl)[degr]: 0.109 -18.122 13.705
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. Off Centre midslice(ap,fh,rl) [mm] : 25.981 -8.163 16.342
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. Flow compensation <0=no 1=yes> ? : 0
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. Presaturation <0=no 1=yes> ? : 0
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. Phase encoding velocity [cm/sec] : 0.000000 0.000000 0.000000
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. MTC <0=no 1=yes> ? : 0
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. SPIR <0=no 1=yes> ? : 1
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. EPI factor <0,1=no EPI> : 151
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. Dynamic scan <0=no 1=yes> ? : 0
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. Diffusion <0=no 1=yes> ? : 1
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. Diffusion echo time [ms] : 0.0000
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. Max. number of diffusion values : 3
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. Max. number of gradient orients : 4
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. Number of label types <0=no ASL> : 0
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#
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# === PIXEL VALUES =============================================================
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# PV = pixel value in REC file, FP = floating point value, DV = displayed value on console
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# RS = rescale slope, RI = rescale intercept, SS = scale slope
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# DV = PV * RS + RI FP = DV / (RS * SS)
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#
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# === IMAGE INFORMATION DEFINITION =============================================
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# The rest of this file contains ONE line per image, this line contains the following information:
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#
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# slice number (integer)
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# echo number (integer)
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# dynamic scan number (integer)
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# cardiac phase number (integer)
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# image_type_mr (integer)
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# scanning sequence (integer)
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# index in REC file (in images) (integer)
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# image pixel size (in bits) (integer)
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# scan percentage (integer)
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# recon resolution (x y) (2*integer)
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# rescale intercept (float)
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# rescale slope (float)
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# scale slope (float)
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# window center (integer)
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# window width (integer)
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# image angulation (ap,fh,rl in degrees ) (3*float)
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# image offcentre (ap,fh,rl in mm ) (3*float)
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# slice thickness (in mm ) (float)
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# slice gap (in mm ) (float)
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# image_display_orientation (integer)
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# slice orientation ( TRA/SAG/COR ) (integer)
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# fmri_status_indication (integer)
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# image_type_ed_es (end diast/end syst) (integer)
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# pixel spacing (x,y) (in mm) (2*float)
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# echo_time (float)
81+
# dyn_scan_begin_time (float)
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# trigger_time (float)
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# diffusion_b_factor (float)
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# number of averages (integer)
85+
# image_flip_angle (in degrees) (float)
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# cardiac frequency (bpm) (integer)
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# minimum RR-interval (in ms) (integer)
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# maximum RR-interval (in ms) (integer)
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# TURBO factor <0=no turbo> (integer)
90+
# Inversion delay (in ms) (float)
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# diffusion b value number (imagekey!) (integer)
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# gradient orientation number (imagekey!) (integer)
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# contrast type (string)
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# diffusion anisotropy type (string)
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# diffusion (ap, fh, rl) (3*float)
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# label type (ASL) (imagekey!) (integer)
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#
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# === IMAGE INFORMATION ==========================================================
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# sl ec dyn ph ty idx pix scan% rec size (re)scale window angulation offcentre thick gap info spacing echo dtime ttime diff avg flip freq RR-int turbo delay b grad cont anis diffusion L.ty
100+
101+
1 1 1 1 11 5 0 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 34.69 -43.87 16.27 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
102+
2 1 1 1 11 5 1 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 33.86 -40.47 16.28 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
103+
3 1 1 1 11 5 2 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 33.03 -37.07 16.29 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
104+
4 1 1 1 11 5 3 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 32.20 -33.67 16.29 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
105+
5 1 1 1 11 5 4 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 31.37 -30.27 16.30 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
106+
6 1 1 1 11 5 5 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 30.54 -26.86 16.31 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
107+
7 1 1 1 11 5 6 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 29.71 -23.46 16.31 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
108+
8 1 1 1 11 5 7 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 28.88 -20.06 16.32 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
109+
9 1 1 1 11 5 8 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 28.05 -16.66 16.33 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
110+
10 1 1 1 11 5 9 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 27.22 -13.26 16.33 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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11 1 1 1 11 5 10 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 26.40 -9.86 16.34 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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12 1 1 1 11 5 11 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 25.57 -6.46 16.35 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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13 1 1 1 11 5 12 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 24.74 -3.06 16.35 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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14 1 1 1 11 5 13 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 23.91 0.34 16.36 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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15 1 1 1 11 5 14 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 23.08 3.74 16.37 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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16 1 1 1 11 5 15 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 22.25 7.14 16.37 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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17 1 1 1 11 5 16 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 21.42 10.54 16.38 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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18 1 1 1 11 5 17 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 20.59 13.94 16.39 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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19 1 1 1 11 5 18 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 19.76 17.34 16.39 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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20 1 1 1 11 5 19 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 18.93 20.74 16.40 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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21 1 1 1 11 5 20 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 18.10 24.14 16.41 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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22 1 1 1 11 5 21 16 101 144 144 0.00000 0.00067 1.46578e-001 1 1 0.11 -18.12 13.70 17.27 27.54 16.41 5.000 -1.500 0 1 0 2 0.556 0.556 134.09 0.00 0.00 0.00 1 90.00 0 0 0 151 0.0 1 4 0 0 0.000 0.000 0.000 1
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# === END OF DATA DESCRIPTION FILE ===============================================

‎nibabel/tests/test_parrec.py

+22-1
Original file line numberDiff line numberDiff line change
@@ -38,6 +38,8 @@
3838
# Fake truncated
3939
TRUNC_PAR = pjoin(DATA_PATH, 'phantom_truncated.PAR')
4040
TRUNC_REC = pjoin(DATA_PATH, 'phantom_truncated.REC')
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# Post-processed diffusion: ADC Map
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ADC_PAR = pjoin(DATA_PATH, 'ADC_Map.PAR')
4143
# Fake V4
4244
V4_PAR = pjoin(DATA_PATH, 'phantom_fake_v4.PAR')
4345
# Fake V4.1
@@ -530,7 +532,7 @@ def test_diffusion_parameters_v4():
530532
def test_null_diffusion_params():
531533
# Test non-diffusion PARs return None for diffusion params
532534
for par, fobj in gen_par_fobj():
533-
if basename(par) in ('DTI.PAR', 'DTIv40.PAR', 'NA.PAR'):
535+
if basename(par) in ('DTI.PAR', 'DTIv40.PAR', 'NA.PAR', 'ADC_Map.PAR'):
534536
continue
535537
gen_info, slice_info = parse_PAR_header(fobj)
536538
with suppress_warnings():
@@ -833,6 +835,25 @@ def test_dualTR():
833835
assert_equal(dualTR_hdr.get_zooms()[3], expected_TRs[0]/1000)
834836

835837

838+
def test_ADC_map():
839+
# test reading an apparent diffusion coefficient map
840+
with open(ADC_PAR, 'rt') as fobj:
841+
842+
# two truncation warnings expected because general_info indicates:
843+
# 1.) multiple directions
844+
# 2.) multiple b-values
845+
# but neither of these exist in the post-processed ADC volume.
846+
with clear_and_catch_warnings(modules=[parrec], record=True) as wlist:
847+
adc_hdr = PARRECHeader.from_fileobj(fobj, permit_truncated=True)
848+
assert_equal(len(wlist), 2)
849+
850+
# general_info indicates it is a diffusion scan, but because it is
851+
# a post-processed image, the bvals and bvecs aren't available
852+
bvals, bvecs = adc_hdr.get_bvals_bvecs()
853+
assert_equal(bvals, None)
854+
assert_equal(bvecs, None)
855+
856+
836857
def test_alternative_header_field_names():
837858
# some V4.2 files had variant spellings for some of the fields in the
838859
# header. This test reads one such file and verifies that the fields with

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