AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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sud8233
January 13, 2023 08:04AM
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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How to deal with oblique fMRI scans? Attachments

sud8233 January 13, 2023 08:04AM

Re: How to deal with oblique fMRI scans?

Daniel Glen January 13, 2023 05:04PM