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  

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March 07, 2014 10:09AM
Dear AFNIs,
Hi,
I plan to use Human connectome data, which provides both in volumetric and surface (grayordinate) timeseries files. Both files have .nii suffix.
When I use afni codes such as 3dFourier as follows, I receive following error for the surface data:

3dFourier -lowpass .08 -retrend -prefix test.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii

++ 3dFourier: AFNI version=AFNI_2011_12_21_1014 (Jan 8 2014) [64-bit]
** ERROR: nifti_convert_nhdr2nim: bad datatype
** ERROR (nifti_image_read): cannot create nifti image from header 'rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii'
** FATAL ERROR: Can't open dataset 'rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii'
** Program compile date = Jan 8 2014

(I run it in the same directory as data, so I am sure it should be able to open the data, but it seems it cannot understand it is nifti(or it is not nifti though it has .nii suffix?)

And for the volumetric data , it seems it starts working but after a while it stops and just says

dFourier -lowpass .08 -retrend -prefix test.nii rfMRI_REST1_RL_hp2000_clean.nii
++ 3dFourier: AFNI version=AFNI_2011_12_21_1014 (Jan 8 2014) [64-bit]
Killed

though I do not stop it!

Would you please let me know how to fix above problems or if some steps should be applied to HCP data to make it ready for AFNI/SUMA?

Thanks in advance,
Mahshid
Subject Author Posted

Problem with using AFNI for Human Connectome data

Mahshid March 07, 2014 10:09AM

Re: Problem with using AFNI for Human Connectome data

Daniel Glen March 07, 2014 10:20AM

Re: Problem with using AFNI for Human Connectome data

Mahshid March 07, 2014 11:01AM

Re: Problem with using AFNI for Human Connectome data

rick reynolds March 07, 2014 01:16PM

Re: Problem with using AFNI for Human Connectome data

Mahshid March 07, 2014 01:39PM

Re: Problem with using AFNI for Human Connectome data

rick reynolds March 07, 2014 02:48PM

Re: Problem with using AFNI for Human Connectome data

Mahshid March 10, 2014 08:29AM

Re: Problem with using AFNI for Human Connectome data

Emperor Zhark March 07, 2014 04:41PM