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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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estee
November 25, 2014 12:53PM
We have recently encountered errors when reconstructing our dicom images into .HEAD/BRIK using the following command:

Dimon -infile_prefix (dicom data) -dicom_org -use_last_elem -sort_by_acq_time -GERT_Reco -save_file_list dimon.list -quit

Error:
-- run 801: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 - zoffset outside volume range of 58.696945 to 58.696945
- banishing image 1.2.840.113745.101000.1111000.41940.5967.16832173-801-42-1b9l5mk.dcm to FAILED state
--> will try to continue...

** bad image state: ind 833, errs 0, state -2 (FSTATE_FAILED), file 1.2.840.113745.101000.1111000.41940.5967.16832173-801-42-1b9l5mk.dcm
. . .

final run statistics:
volume info :
slices : 1
z_first : 58.7
z_last : 58.7
z_delta : 4
oblique : yes
mos_nslices : 0

run # 801 : volumes = 41, first file (#0) = 1.2.840.113745.101000.1111000.41940.5967.16832173-801-1-1b9jvip.dcm

++ writing dimon file list to dimon.files.run.801
-- writing file list to dimon.list...

** have 1434 unprocessed image(s)

Any idea about why this error is occurring?

Because of this reconstruction problem, we have been using MRIConvert to create NIFTI files, and then converting them to HEAD/BRIK files. When we were previously converting from DICOM files, the orientation of our images was RAI. The orientation for BRIK files converted from NIFTI format is now AIL. Do we need to re-orient these new files so that they are in RAI orientation before preprocessing and statistics are run?

Thanks!
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Subject Author Posted

Data reconstruction and image orientation

estee November 25, 2014 12:53PM

Re: Data reconstruction and image orientation

Daniel Glen November 25, 2014 02:11PM

Re: Data reconstruction and image orientation

rick reynolds November 25, 2014 03:58PM

Re: Data reconstruction and image orientation

rick reynolds December 04, 2014 12:37PM