How to deal with oblique fMRI scans?

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1

Hi,

I have recorded some resting state scans from Siemens 3T scanner. When I am running Dimon command to convert scan volumes with .IMA extension to afni compatible .BRIK formats I am getting the following warnings.

First, Slice-based center is different from mosaic center.
Second, Origin computation of obliquity may be incorrect

An image is attached for more details.

I am new in fMRI processing. I am not able to make much out of this error. For example, how bad this warning could be, how it could accumulate with every step of further processing and at what stage of processing “ignoring the warning about center mismatch” could introduce a major problem?

Please give me some expert suggestions.
My command is: Dimon -infile_prefix prefix -gert_create_dataset -gert_to3d_prefix {entry}fMRI${FA} or Dimon -infile_prefix prefix -gert_create_dataset -assume_dicom_mosaic -gert_to3d_prefix {entry}fMRI${FA}

Thanks,
Sudhakar

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2

That shows a disagreement between the DICOM header fields that sometimes seen in Siemens mosaic files. It usually won’t be too important if you align the EPI and anatomical data. You can always use the oblique information from the mosaic with the “-use_obl_origin” for Dimon.

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