AFNI2NIFTI which data

AFNI Message Board
1

Hi you all,

I’m trying to use the 3dAFNI2NIFTI command to convert my stats map (after analyses) in NIFTI format to be ready by a neuronavigation software. However I’m struggling with it cause I think the default are exporting the Fstats from the full model. How can I modify this so that it will convert only my contrast of interest?

I tried adding “idat X” (with X being the my contrast of interest) but I’m getting the same output that with the default. I do not see any of this in the help of 3dAFNI2NIFTI command.

Does someone has an idea?

Thank you in advance

2

Hello,

Note that 3dAFNI2NIFTI is not very special, most AFNI programs can read and write either format, and therefore could be used for the conversion.

It is not clear how you are using idat, I don’t think the program has such an option.

But programs will not generally separate a 4D dataset into subsets unless you tell them to. For that, it might be good to specify the volume indices of interest. For example (I will switch to 3dbucket, though 3dAFNI2NIFTI would work, too):

3dbucket -prefix full_fstat.nii stats+tlrc'[0]'
3dbucket -prefix all_betas1.nii stats+tlrc'[1,4,7,10,13,16,29,22,25,28]'
3dbucket -prefix all_betas2.nii stats+tlrc'[1..28(3)]'
3dbucket -prefix all_tstats.nii stats+tlrc'[2..29(3)]'

Here, all_betas1.nii and all_betas2.nii would be the same dataset.

Does that seem like what you want?

  • rick
3

Thank you very much

It works very well.