Dear experts,
Years later, the same problem still persists in our pipeline. We are currently trying to figure out which option is best for EPI distortions at 7T, FUGUE or TOPUP, but applytopup gives an immediate "segmentaion fault (core dumped)" message. We acquired 1 volume in both A>>P and P>>A direction, with exactly the same parameters as the BOLD sequence.
This is the command I run:
applytopup \
--imain=mc.func.nii.gz \
--inindex=1 \
--datain=acqparams.txt \
--topup=topup_b0_fieldcoef \
--out=my_topup_results \
--method=jac \
--verbose
Where imain is a motion corrected T2*-weighted timeseries acquired in A>>P direction (hence, inindex=1), datain is a textfile with 2 lines with parameters based from the mcverter output (please see attachments). Since it's not a memory issue (we can specify up to hundreds of RAM on the cluster), I suspect it might have something to do with the specification of the fourth column of the acqparams.txt file: I assumed we should take the "total readout time (FSL definition)" parameter, but maybe we should take a different one? The (effective) echo-spacing, perhaps?
Your help would be kindly appreciated.
Best regards,
Jurjen Heij
Berlin Ultrahigh Field Facility
Max Delbruck Center for Molecular Medicine
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Series UID: 1.3.12.2.1107.5.2.34.18923.2019061811162260215540730.0.0.0
Study date: 20190618
Study time: 090332.796000
Series date: 20190618
Series time: 111722.921000
Subject: MDC-0153,NMCImp002
Subject birth date: 19870101
Series description: fieldmap_bold_AP
Image type: ORIGINAL\PRIMARY\M\MB\ND\MOSAIC
Manufacturer: SIEMENS
Model name: Investigational_Device_7T
Software version: syngo MR B17
Study id: 1
Series number: 21
Repetition time (ms): 2200
Echo time[1] (ms): 28.2
Flip angle: 66
Number of averages: 1
Slice thickness (mm): 1.5
Slice spacing (mm): 1.499999970533
Image columns: 1440
Image rows: 1440
Phase encoding direction: COL
Voxel size x (mm): 1.5
Voxel size y (mm): 1.5
Number of volumes: 2
Number of slices: 80
Number of files: 2
Number of frames: 0
Slice duration (ms) : 26.5506
Volume interval (s): 0
Orientation: tra
PixelBandwidth: 1157
Acceleration factor: 2
BandwidthPerPixelPhaseEncode: 12.273
Echo spacing (ms): 0.97
Effective echo spacing (ms): 0.51
Total readout time (FSL definition) (ms): 80.97
Total readout time (SPM definition) (ms): 81.48
Mosaic rows: 160
Mosaic columns: 160
Acquisition order: Interleaved Even
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Series UID: 1.3.12.2.1107.5.2.34.18923.2019061811172585651041381.0.0.0
Study date: 20190618
Study time: 090332.796000
Series date: 20190618
Series time: 111818.625000
Subject: MDC-0153,NMCImp002
Subject birth date: 19870101
Series description: fieldmap_bold_PA
Image type: ORIGINAL\PRIMARY\M\MB\ND\MOSAIC
Manufacturer: SIEMENS
Model name: Investigational_Device_7T
Software version: syngo MR B17
Study id: 1
Series number: 22
Repetition time (ms): 2200
Echo time[1] (ms): 28.2
Flip angle: 66
Number of averages: 1
Slice thickness (mm): 1.5
Slice spacing (mm): 1.499999970533
Image columns: 1440
Image rows: 1440
Phase encoding direction: COL
Voxel size x (mm): 1.5
Voxel size y (mm): 1.5
Number of volumes: 2
Number of slices: 80
Number of files: 2
Number of frames: 0
Slice duration (ms) : 26.5506
Volume interval (s): 0
Orientation: tra
PixelBandwidth: 1157
Acceleration factor: 2
BandwidthPerPixelPhaseEncode: 12.273
Echo spacing (ms): 0.97
Effective echo spacing (ms): 0.51
Total readout time (FSL definition) (ms): 80.97
Total readout time (SPM definition) (ms): 81.48
Mosaic rows: 160
Mosaic columns: 160
Acquisition order: Interleaved Even
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0 -1 0 0.08097
0 1 0 0.8097
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