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help > Error at vdm file generation
Jan 29, 2020 06:01 PM | Ariana Familiar
Error at vdm file generation
Hello,
I receive this error during VDM file generation for fieldmap distortion correction. I have separate files for the two magnitude and one phase images, and I used "read double-echo timing from BIDS / .json files" and "automatically determine" fieldmap type during setup. Please let me know how I can fix this - any insight would be appreciated!
ERROR DESCRIPTION:
Error using *
Arguments must be 2-D, or at least one argument must be scalar. Use TIMES (.*) for elementwise multiplication.
Error in FieldMap (line 1659)
IP.vdm.vdm = IP.blipdir*IP.tert*1e-3*IP.fm.fpm;
Error in FieldMap_create (line 159)
[IP.vdm, IP.vdmP]=FieldMap('FM2VDM',IP);
Error in conn_setup_preproc (line 2463)
VDM = FieldMap_create(char(fmap),{filename},pm_def); %[ET1,ET2,0,ERT,-1]
Error in conn (line 1081)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN18.b
SPM12 + DEM FieldMap MEEGtools
Matlab v.2019a
project: CONN18.b
storage: 411.9Gb available
ADDITIONAL INFO:
Preparing functional Creation of voxel-displacement map (VDM) for distortion correction
units of FieldMap /Users/ariana/Documents/face_value/data/session2/02_AS2/ref_run1.nii not found, assuming Hz
Creating vdm file for subject 2 session 1...
FieldMap : /Users/ariana/Documents/face_value/data/session2/02_AS2/B0_mag1.nii
ref : /Users/ariana/Documents/face_value/data/session2/02_AS2/ref_run1.nii
options.INPUT_DATA_FORMAT = PM
options.SHORT_ECHO_TIME = 10
options.LONG_ECHO_TIME = 12.46
options.MASKBRAIN = 1
options.UNWRAPPING_METHOD = Mark3D
options.FWHM = 10
options.PAD = 0
options.WS = 1
options.MFLAGS.TEMPLATE = /Users/ariana/Documents/MATLAB/spm12/toolbox/FieldMap/T1.nii
options.MFLAGS.FWHM = 5
options.MFLAGS.NERODE = 2
options.MFLAGS.NDILATE = 4
options.MFLAGS.THRESH = 0.5
options.MFLAGS.REG = 0.02
options.MFLAGS.GRAPHICS = 0
options.EPI_BASED_FIELDMAPS = 0
options.TOTAL_EPI_READOUT_TIME = 57.0004
options.DO_JACOBIAN_MODULATION = 0
options.sessname = session
options.match_vdm = 1
options.pedir = 2
options.defaultsfilename = /Users/ariana/Documents/MATLAB/spm12/toolbox/FieldMap/pm_defaults.m
I receive this error during VDM file generation for fieldmap distortion correction. I have separate files for the two magnitude and one phase images, and I used "read double-echo timing from BIDS / .json files" and "automatically determine" fieldmap type during setup. Please let me know how I can fix this - any insight would be appreciated!
ERROR DESCRIPTION:
Error using *
Arguments must be 2-D, or at least one argument must be scalar. Use TIMES (.*) for elementwise multiplication.
Error in FieldMap (line 1659)
IP.vdm.vdm = IP.blipdir*IP.tert*1e-3*IP.fm.fpm;
Error in FieldMap_create (line 159)
[IP.vdm, IP.vdmP]=FieldMap('FM2VDM',IP);
Error in conn_setup_preproc (line 2463)
VDM = FieldMap_create(char(fmap),{filename},pm_def); %[ET1,ET2,0,ERT,-1]
Error in conn (line 1081)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN18.b
SPM12 + DEM FieldMap MEEGtools
Matlab v.2019a
project: CONN18.b
storage: 411.9Gb available
ADDITIONAL INFO:
Preparing functional Creation of voxel-displacement map (VDM) for distortion correction
units of FieldMap /Users/ariana/Documents/face_value/data/session2/02_AS2/ref_run1.nii not found, assuming Hz
Creating vdm file for subject 2 session 1...
FieldMap : /Users/ariana/Documents/face_value/data/session2/02_AS2/B0_mag1.nii
ref : /Users/ariana/Documents/face_value/data/session2/02_AS2/ref_run1.nii
options.INPUT_DATA_FORMAT = PM
options.SHORT_ECHO_TIME = 10
options.LONG_ECHO_TIME = 12.46
options.MASKBRAIN = 1
options.UNWRAPPING_METHOD = Mark3D
options.FWHM = 10
options.PAD = 0
options.WS = 1
options.MFLAGS.TEMPLATE = /Users/ariana/Documents/MATLAB/spm12/toolbox/FieldMap/T1.nii
options.MFLAGS.FWHM = 5
options.MFLAGS.NERODE = 2
options.MFLAGS.NDILATE = 4
options.MFLAGS.THRESH = 0.5
options.MFLAGS.REG = 0.02
options.MFLAGS.GRAPHICS = 0
options.EPI_BASED_FIELDMAPS = 0
options.TOTAL_EPI_READOUT_TIME = 57.0004
options.DO_JACOBIAN_MODULATION = 0
options.sessname = session
options.match_vdm = 1
options.pedir = 2
options.defaultsfilename = /Users/ariana/Documents/MATLAB/spm12/toolbox/FieldMap/pm_defaults.m
Threaded View
Title | Author | Date |
---|---|---|
Ariana Familiar | Jan 29, 2020 | |
Alfonso Nieto-Castanon | Feb 5, 2020 | |
tali weiss | Mar 2, 2020 | |
Ariana Familiar | Jan 29, 2020 | |