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help > RE: Bands of low-to-no % of variance explained in BOLD signal
Jun 22, 2022 11:06 PM | Alfonso Nieto-Castanon - Boston University
RE: Bands of low-to-no % of variance explained in BOLD signal
Hi Hannah,
That is curious. I think this could be either an issue with the FieldMaps (e.g. if the fieldmap image generated from topup or equivalent had the "wrong" scaling, i.e. it is not in Hz units), or an issue with SPM's default masking during realignment. I would probably suggest to try realigning the data for this subject without the susceptibility distortion correction to see if the issue persists, and if it does then try the fix suggested in the following thread https://www.nitrc.org/forum/message.php?msg_id=35269, and if it does not then try figuring out what might have caused a wrong scale in the fieldmap files entered in CONN's fmap dataset (perhaps see the following thread for details https://www.nitrc.org/forum/message.php?msg_id=35243 )
Hope this helps
Alfonso
Originally posted by Hannah Lindsey:
That is curious. I think this could be either an issue with the FieldMaps (e.g. if the fieldmap image generated from topup or equivalent had the "wrong" scaling, i.e. it is not in Hz units), or an issue with SPM's default masking during realignment. I would probably suggest to try realigning the data for this subject without the susceptibility distortion correction to see if the issue persists, and if it does then try the fix suggested in the following thread https://www.nitrc.org/forum/message.php?msg_id=35269, and if it does not then try figuring out what might have caused a wrong scale in the fieldmap files entered in CONN's fmap dataset (perhaps see the following thread for details https://www.nitrc.org/forum/message.php?msg_id=35243 )
Hope this helps
Alfonso
Originally posted by Hannah Lindsey:
Alfonso,
Thanks so much for getting back to me. I checked the functional normalization plots, like you suggested, and I do see the problem there (see attached screenshots for the same two subjects I shared photos of in my first message). What do you recommend as the best way to fix this??
As a reminder, we used the preprocessing pipeline for volume-based analyses (indirect normalization to MNI-space) when FieldMaps are available, and our field maps were calculated from two separate acquisitions with opposite phase encoding directions.
Thanks again for your help!
Hannah
Thanks so much for getting back to me. I checked the functional normalization plots, like you suggested, and I do see the problem there (see attached screenshots for the same two subjects I shared photos of in my first message). What do you recommend as the best way to fix this??
As a reminder, we used the preprocessing pipeline for volume-based analyses (indirect normalization to MNI-space) when FieldMaps are available, and our field maps were calculated from two separate acquisitions with opposite phase encoding directions.
Thanks again for your help!
Hannah
Threaded View
| Title | Author | Date |
|---|---|---|
| Hannah Lindsey | Jun 17, 2022 | |
| Hannah Lindsey | Jul 12, 2022 | |
| Hannah Lindsey | Jun 24, 2022 | |
| Alfonso Nieto-Castanon | Jun 17, 2022 | |
| Hannah Lindsey | Jun 21, 2022 | |
| Alfonso Nieto-Castanon | Jun 22, 2022 | |
| Hannah Lindsey | Jun 29, 2022 | |
