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

History of AFNI updates  

|
September 29, 2021 04:02PM
Hi Rick,

Below are the outputs of each command:

nifti_tool -disp_hdr -field pixdim -infiles sub01.nii.gz
N-1 header file 'sub-002_S_0295_task-rest_run-01_bold.nii.gz', num_fields = 1
  name                offset  nvals  values
  ------------------- ------  -----  ------
  pixdim                76      8    -1.0 3.3125 3.3125 3.3125 6.021583 0.0 0.0 0.0

3dinfo -tr sub01.nii.gz
6.021583

So, the TRs match between those two commands. However, when I grep the information from the dicom_hdr, it differs:
dicom_hdr $file | grep "Repetition Time"
ACQ Repetition Time//3000

The TR of 3000ms matches the protocol information for this participant. I'm not sure how or why it is getting changed in the conversion from dcm2niix. Should I change the TR information in the NIFTI header to match that of the dicom?

Thanks,
Jenna
Subject Author Posted

Discrepancy of repetition time between dicom and nifti header

jkblujus September 27, 2021 06:34PM

Re: Discrepancy of repetition time between dicom and nifti header

Daniel Glen September 28, 2021 12:46PM

Re: Discrepancy of repetition time between dicom and nifti header

jkblujus September 28, 2021 05:55PM

Re: Discrepancy of repetition time between dicom and nifti header

rick reynolds September 28, 2021 06:48PM

Re: Discrepancy of repetition time between dicom and nifti header

jkblujus September 29, 2021 12:10PM

Re: Discrepancy of repetition time between dicom and nifti header

rick reynolds September 29, 2021 03:50PM

Re: Discrepancy of repetition time between dicom and nifti header

jkblujus September 29, 2021 04:02PM

Re: Discrepancy of repetition time between dicom and nifti header

Daniel Glen October 04, 2021 01:59PM

Re: Discrepancy of repetition time between dicom and nifti header

Daniel Glen October 05, 2021 10:20AM