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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Daniel Glen
November 20, 2009 03:45PM
To get around the numbering order, you can do something like this:
to3d -time:zt 34 67 3.0s alt+z -xFOV 120R-L -yFOV 120A-P -zFOV 75I-S 3D:-1:0:64:64:1:`cat dimon.files.run.003`

adding a command to output the order produced by Dimon. Note this to3d command does not include a prefix. Consequently, to3d will bring up its GUI. There you will be able to verify orientation, voxel size and view the data. Once you figure out all the correct parameters, you can supply a complete to3d command in the future.

For Siemens mosaic data with volumes stored in each DICOM file, you can use the -gert_nz option with Dimon to set the number of slices stored in a DICOM file, e.g. -gert_nz 28. Also check this previous link on a problem with Siemens DICOM data that was solved by using -use_last_elem option with Dimon or to3d.
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Subject Author Posted

not recognizing single dicom file

Rob Hester November 18, 2009 09:16PM

Re: not recognizing single dicom file

Daniel Glen November 18, 2009 11:15PM

Re: not recognizing single dicom file

Rob Hester November 20, 2009 05:13AM

Re: not recognizing single dicom file

Rob Hester November 20, 2009 03:18PM

Re: not recognizing single dicom file

Daniel Glen November 20, 2009 03:45PM