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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jjarcho
July 17, 2019 12:34PM
Hi All,

We just started collecting fMRI data on a new (to us) scanner and are having some trouble converting our T1 DICOM images to AFNI format. There appears to be aliasing and dropped slices (see attached). These artifacts are not present when the data are converted to NIfTI format in FSL, ruling out acquisition or data transfer issues.

Here's what we've done thus far:
1) to3d -assume_dicom_mosaic -prefix $subj'_anat'$anat/DICOM/*dcm
-resulted in attached image

2) to3d -anatparent -prefix $subj'_anat'$anat/DICOM/*dcm
-resulted in the script not working

3) to3d -prefix $subj'_anat'$anat/DICOM/*dcm
-resulted in attached image

Any suggestions about how we might resolve this? We are trying to process this data quickly for an upcoming grant deadline - any help is very much appreciated!

Johanna
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open | download - Screen Shot 2019-07-16 at 6.00.10 PM.png (656.4 KB)
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Aliasing and dropped slices from anatomical scan Attachments

jjarcho July 17, 2019 12:34PM

Re: Aliasing and dropped slices from anatomical scan

ptaylor July 17, 2019 01:35PM

Re: Aliasing and dropped slices from anatomical scan

rick reynolds July 18, 2019 09:14AM