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help > RE: Field mapping correction
Feb 27, 2019 12:02 PM | Alfonso Nieto-Castanon - Boston University
RE: Field mapping correction
Dear Juan,
Yes, the issue is perhaps that you need to import these magnitude&phase maps into your secondary dataset called "fmap" (or create one new secondary dataset if that does not exist yet). If, when selecting your "fmap" secondary dataset, you are not seeing the option to load/select the data there, simply change in the option in the menu (right below the "secondary dataset" title) that currently is probably reading something like "secondary dataset is derived from primary dataset: ..." to "secondary dataset is independent of primary dataset: explicitly select functional files". That will allow you to explicitly select your magnitude and phasedifference maps and enter them into the fmap secondary dataset, and then proceed normally from there. Also remember to enter into your "primary dataset" your actual functional BOLD timeseries before proceeding to create your vdm files (this is actually needed by the vdm_create procedure because the fieldmap files will be coregistered to your functional data to make sure they are all in the same space)
Hope this helps
Alfonso
Originally posted by Juan Dominguez:
Yes, the issue is perhaps that you need to import these magnitude&phase maps into your secondary dataset called "fmap" (or create one new secondary dataset if that does not exist yet). If, when selecting your "fmap" secondary dataset, you are not seeing the option to load/select the data there, simply change in the option in the menu (right below the "secondary dataset" title) that currently is probably reading something like "secondary dataset is derived from primary dataset: ..." to "secondary dataset is independent of primary dataset: explicitly select functional files". That will allow you to explicitly select your magnitude and phasedifference maps and enter them into the fmap secondary dataset, and then proceed normally from there. Also remember to enter into your "primary dataset" your actual functional BOLD timeseries before proceeding to create your vdm files (this is actually needed by the vdm_create procedure because the fieldmap files will be coregistered to your functional data to make sure they are all in the same space)
Hope this helps
Alfonso
Originally posted by Juan Dominguez:
Dear Alfonso,
I am using the latest version of CONN (18b) and want to do field mapping correction with resting state data. Data were acquired on a Siemens scanner and I have one phase diff and two magnitude images. I have imported the images together with the functional images in the conn gui (see screenshot). I have tried to run preprocessing importing the short echo magnitude and phase images only (together with the resting state file) and importing the two magnitude and phase images (together with the resting state file). I have also tried "Fieldmap type: automatically detect" and "Fieldmap type:magnitude, phase diff files." Finally. I have tried to import all the files in the different orders; i.e., fmri, mag1, mag2, phase and mag1, mag2, phase, fmri.
This is the error I am getting when trying any of the above (reported in previous posts):
One thing is that I can only import the field map images when the primary dataset is selected in functional.setup. When I change to secondary dataset #2 (fmap), there is no option to import data, and I wonder if this has anything to do with the issue.
Finally, I also tried using the patch you provided in your previous reply in this thread, but got the same error message.
Thanks for your help with this.
Best,
Juan
I am using the latest version of CONN (18b) and want to do field mapping correction with resting state data. Data were acquired on a Siemens scanner and I have one phase diff and two magnitude images. I have imported the images together with the functional images in the conn gui (see screenshot). I have tried to run preprocessing importing the short echo magnitude and phase images only (together with the resting state file) and importing the two magnitude and phase images (together with the resting state file). I have also tried "Fieldmap type: automatically detect" and "Fieldmap type:magnitude, phase diff files." Finally. I have tried to import all the files in the different orders; i.e., fmri, mag1, mag2, phase and mag1, mag2, phase, fmri.
This is the error I am getting when trying any of the above (reported in previous posts):
ERROR DESCRIPTION:
Error using FieldMap_create (line 139)
Funny number of input fieldmap images
Funny number of input fieldmap images
Error in conn_setup_preproc (line
2489)
VDM = FieldMap_create(char(fmap),{filename},pm_def); %[ET1,ET2,0,ERT,-1]
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});
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 + ALI Anatomy DEM FieldMap MEEGtools Masking com conn
Matlab v.2017b
project: CONN18.b
storage: 26.5Gb available
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN18.b
SPM12 + ALI Anatomy DEM FieldMap MEEGtools Masking com conn
Matlab v.2017b
project: CONN18.b
storage: 26.5Gb available
spm @ /usr/local/spm12
conn @ /usr/local/spm12/toolbox/conn
conn @ /usr/local/spm12/toolbox/conn
One thing is that I can only import the field map images when the primary dataset is selected in functional.setup. When I change to secondary dataset #2 (fmap), there is no option to import data, and I wonder if this has anything to do with the issue.
Finally, I also tried using the patch you provided in your previous reply in this thread, but got the same error message.
Thanks for your help with this.
Best,
Juan
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| Title | Author | Date |
|---|---|---|
| Dayana Hayek | Feb 13, 2019 | |
| jothini | Mar 1, 2024 | |
| Yi Ding | Nov 20, 2020 | |
| Dayana Hayek | Mar 6, 2019 | |
| boris | Feb 22, 2019 | |
| Alfonso Nieto-Castanon | Feb 27, 2019 | |
| boris | Feb 27, 2019 | |
| Zhaoxia Qin | Feb 22, 2019 | |
| Alfonso Nieto-Castanon | Feb 14, 2019 | |
| Dayana Hayek | Feb 15, 2019 | |
| Alfonso Nieto-Castanon | Feb 15, 2019 | |
| Juan Dominguez | Feb 27, 2019 | |
| Alfonso Nieto-Castanon | Feb 27, 2019 | |
| Dayana Hayek | Feb 20, 2019 | |
| Alfonso Nieto-Castanon | Feb 20, 2019 | |
| Dayana Hayek | Feb 20, 2019 | |
| Victoria Okuneye | Feb 15, 2019 | |
| Alfonso Nieto-Castanon | Feb 15, 2019 | |
| madeleine | Oct 15, 2020 | |
| Alfonso Nieto-Castanon | Oct 15, 2020 | |
| madeleine | Oct 16, 2020 | |
| madeleine | Oct 19, 2020 | |