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help > RE: Field mapping correction
Feb 27, 2019 01:02 PM | Alfonso Nieto-Castanon - Boston University
RE: Field mapping correction
Dear Boris,
Sorry I was not too clear in my previous post. The "functional_vdm_create" step is just one preprocessing step in CONN. To run that step in isolation, simply click on the button labeled "preprocessing" (in the Setup tab lower left corner). That will launch a gui for applying any sequence of preprocessing steps to your data. In that GUI simply select/add the preprocessing step labeled as "functional creation of voxel-displacement map (VDM) for distortion correction", and then click on 'Start'. It should look something like the attached image (top figure).
More often, though, rather that running that step in isolation, you may prefer to simply include the vdm_create step as part of a longer preprocessing pipeline. For example, if you select any of the default CONN pipelines that reads "... when FieldMaps are available" CONN will simply include the vdm_create step as part of your preprocessing pipeline automatically (it will look something like the bottom figure in the attached image). When you run a whole pipeline like this each preprocessing step listed there is applied in sequence, so, for example, the vdm-files will be created at some point in the pipeline and then later used by other steps below in the pipeline (e.g. the realign&unwarp&distortion correction) automatically.
Hope this helps
Alfonso
Originally posted by Boris Rauchmann:
Sorry I was not too clear in my previous post. The "functional_vdm_create" step is just one preprocessing step in CONN. To run that step in isolation, simply click on the button labeled "preprocessing" (in the Setup tab lower left corner). That will launch a gui for applying any sequence of preprocessing steps to your data. In that GUI simply select/add the preprocessing step labeled as "functional creation of voxel-displacement map (VDM) for distortion correction", and then click on 'Start'. It should look something like the attached image (top figure).
More often, though, rather that running that step in isolation, you may prefer to simply include the vdm_create step as part of a longer preprocessing pipeline. For example, if you select any of the default CONN pipelines that reads "... when FieldMaps are available" CONN will simply include the vdm_create step as part of your preprocessing pipeline automatically (it will look something like the bottom figure in the attached image). When you run a whole pipeline like this each preprocessing step listed there is applied in sequence, so, for example, the vdm-files will be created at some point in the pipeline and then later used by other steps below in the pipeline (e.g. the realign&unwarp&distortion correction) automatically.
Hope this helps
Alfonso
Originally posted by Boris Rauchmann:
Dear Alfonso,
I was struggling finding your third step "functional_vdm_create". How does it work? I successfully selected the magnitude and the phasediff image but I was wondering how to go on. could You please help me?
Best regards,
Boris R.
I was struggling finding your third step "functional_vdm_create". How does it work? I successfully selected the magnitude and the phasediff image but I was wondering how to go on. could You please help me?
Best regards,
Boris R.
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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 | |
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| Alfonso Nieto-Castanon | Feb 14, 2019 | |
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| Juan Dominguez | Feb 27, 2019 | |
| Alfonso Nieto-Castanon | Feb 27, 2019 | |
| Dayana Hayek | Feb 20, 2019 | |
| Alfonso Nieto-Castanon | Feb 20, 2019 | |
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