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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B
June 25, 2014 03:23PM
Hey Everyone!

I'm (very!) new to MRI and analysis, so forgive me if this is a silly problem. I'm supposed to examine the Human Connectome data, using the FATCAToolbox and I've been trying to follow the pipeline suggested in their paper.

When trying to use 3dDWItoDT I constantly get an error "dataset must have number of sub-briks equal to one more than number of gradient vectors (B0+Bi)!"

The supplied HCP files are: 
    T1w_acpc_dc_restore_1.25.nii.gz
    bvals
    bvecs
    data.nii.gz
    nodif_brain_mask.nii.gz
    grad_dev.nii.gz
    GRADS_30.dat (created by 1dDW_Grad_o_Mat in the previous step*)


I run commands options as: 
3dDWItoDT -prefix DTI/DT -mask nodif_brain_mask.nii.gz -eigs -sep_dsets -nonlinear GRADS_30.dat T1w_acpc_dc_restore_1.25.nii.gz


* creates the GRADS file, the tutorial uses a range of the data bvecs[0..32]/ bvals[2..32], which I also tried, in various combinations, to no avail.

I've been stuck here for a quite a while, and I'm just not sure what I'm missing. I was looking into 3dcopy to format it to an AFNI dataset, but I couldn't figure how (or if I needed) to create the BRIK/HEAD files. Any help, or pointers where to look would be much appreciated!
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Subject Author Posted

3dDWItoDT with Human Connectome Data

B June 25, 2014 03:23PM

Re: 3dDWItoDT with Human Connectome Data

Daniel Glen June 25, 2014 03:33PM

Re: 3dDWItoDT with Human Connectome Data

B June 25, 2014 04:06PM

Re: 3dDWItoDT with Human Connectome Data

Daniel Glen June 25, 2014 04:26PM

Re: 3dDWItoDT with Human Connectome Data

B June 25, 2014 05:19PM

Re: 3dDWItoDT with Human Connectome Data

Daniel Glen June 25, 2014 05:31PM

Re: 3dDWItoDT with Human Connectome Data

ptaylor June 25, 2014 05:42PM

Re: 3dDWItoDT with Human Connectome Data

ptaylor June 25, 2014 04:31PM

Re: 3dDWItoDT with Human Connectome Data

B June 25, 2014 05:25PM