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help > RE: Field Map Correction
Oct 25, 2021 03:10 PM | jblujus
RE: Field Map Correction
Hi Alfonso,
Thanks for your reply. In Setup, I imported the e1_real, e1_imag, e2_real, e2_imag files (in this order) as a secondary dataset named fmap. When setting up the preprocessing in the VDM create settings, I specified the following parameters, according to the information in the JSON files:
Feildmap location: secondary dataset #2 (fmap)
Fieldmap type: Real1, Imag1, Real2, Imag2 files
Short Echo Time (in ms) 2.3
Long Echo Time (in ms) 4.6
EPI Total Readout Time (in ms) 0.6638
Blip direction (+1 or -1) -1
When the job is submitted, I get the following error.
ERROR DESCRIPTION:
Error using vertcat
Dimensions of arrays being concatenated are not consistent.
Error in FieldMap (line 2110)
IP.fmagP = spm_imcalc(spm_vol([IP.P{1}.fname;IP.P{2}.fname]),IP.fmagP,'sqrt(i1.^2 + i2.^2)');
Error in FieldMap (line 1610)
IP.fmagP = FieldMap('Magnitude',IP);
Error in FieldMap_create (line 146)
IP.fm = FieldMap('CreateFieldMap',IP);
Error in conn_setup_preproc (line 2883)
VDM = FieldMap_create(char(fmap),{filename},pm_def); %[ET1,ET2,0,ERT,-1]
Error in conn (line 1143)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 121)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
Do you have any recommendations on what to do to circumvent the issue?
Thank you!
Jenna
Originally posted by Alfonso Nieto-Castanon:
Thanks for your reply. In Setup, I imported the e1_real, e1_imag, e2_real, e2_imag files (in this order) as a secondary dataset named fmap. When setting up the preprocessing in the VDM create settings, I specified the following parameters, according to the information in the JSON files:
Feildmap location: secondary dataset #2 (fmap)
Fieldmap type: Real1, Imag1, Real2, Imag2 files
Short Echo Time (in ms) 2.3
Long Echo Time (in ms) 4.6
EPI Total Readout Time (in ms) 0.6638
Blip direction (+1 or -1) -1
When the job is submitted, I get the following error.
ERROR DESCRIPTION:
Error using vertcat
Dimensions of arrays being concatenated are not consistent.
Error in FieldMap (line 2110)
IP.fmagP = spm_imcalc(spm_vol([IP.P{1}.fname;IP.P{2}.fname]),IP.fmagP,'sqrt(i1.^2 + i2.^2)');
Error in FieldMap (line 1610)
IP.fmagP = FieldMap('Magnitude',IP);
Error in FieldMap_create (line 146)
IP.fm = FieldMap('CreateFieldMap',IP);
Error in conn_setup_preproc (line 2883)
VDM = FieldMap_create(char(fmap),{filename},pm_def); %[ET1,ET2,0,ERT,-1]
Error in conn (line 1143)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 121)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
Do you have any recommendations on what to do to circumvent the issue?
Thank you!
Jenna
Originally posted by Alfonso Nieto-Castanon:
Hi
Jenna,
Yes, you may include the fieldmap images real_echo1+imag_echo1+real_echo2+imag_echo2 (in that order) directly into a secondary dataset labeled 'fmap' in your CONN project, and those will be used by the 'functional creation of voxel-displacement maps for Susceptibility Distortion Correction' step part of your pipeline
Best
Alfonso
Originally posted by jblujus:
Yes, you may include the fieldmap images real_echo1+imag_echo1+real_echo2+imag_echo2 (in that order) directly into a secondary dataset labeled 'fmap' in your CONN project, and those will be used by the 'functional creation of voxel-displacement maps for Susceptibility Distortion Correction' step part of your pipeline
Best
Alfonso
Originally posted by jblujus:
Hi all,
I am new to CONN and using field maps, so I apologize for the basic question. I am utilizing the ADNI dataset which provides four T1-weighted field map images (two sets of real/imag files) for select participants. I would like to use the "indirect normalization to MNI space when FieldMaps are available pipeline" for preprocessing. Following dcm2niix conversion of the field map images, can I feed the e1/e2 real/imag files directly into preprocessing or do these images need to be unwrapped?
Thank you in advance!
Jenna
I am new to CONN and using field maps, so I apologize for the basic question. I am utilizing the ADNI dataset which provides four T1-weighted field map images (two sets of real/imag files) for select participants. I would like to use the "indirect normalization to MNI space when FieldMaps are available pipeline" for preprocessing. Following dcm2niix conversion of the field map images, can I feed the e1/e2 real/imag files directly into preprocessing or do these images need to be unwrapped?
Thank you in advance!
Jenna
Threaded View
| Title | Author | Date |
|---|---|---|
| jblujus | Oct 22, 2021 | |
| Alfonso Nieto-Castanon | Oct 24, 2021 | |
| jblujus | Oct 25, 2021 | |