3dClusterize on a .nii image without subbricks ?

AFNI Message Board
1

Hello you all,

I was wondering if there was an equivalent of 3dClusterize that would work for .nii files that do not have multiple sub bricks and therefore don’t have an -idat and -ithr?

Thanks!

2

Hi, Lysianne-

You can make idat and ithr just both point to that [0]th volume:


3dClusterize -idat 0 -ithr 0 ...

–pt

3

but it says:
++ Looks like clustering is not being performed on a stat value; won’t worry about sidedness, then.
** FATAL ERROR: Thresholding volume does not appear to be a stat so you can’t use the ‘p=…’ internal conversion to stat

Even though my .nii is coming from a stat image

4

Hi Lysianne,

Does that NIFTI image have a proper intent_code?

nifti_tool -disp_hdr -field intent_code -infiles MY_IMAGE.nii

If it does not, and so 3dClusterize cannot convert form p to an appropriate threshold, you can always provide a raw threshold yourself.

  • rick
5

Hi, Lysianne-

Indeed, the “p= …” convenience comes about only from AFNI-program-produced stats, which stick the conversion information into the header.

What is the 3dClusterize command you are using, and where did the stats dataset come from?

–pt

6

the stats comes from APP, registered in Talairach space ,
then I use 3dAllineate to bring it back to native space, and keep only the t-stats from my contrast of interest in .nii format so I can use it with my neuronavigation software.

I was just being lazy and trying to find a way to extract the peak on my .nii file; I guess I can just switch the order of my steps and get the peak before converting to .nii

7

this command gives me: Intent_code offset: 68, nvals 1 and values 0

8

You could use p2dsetstat to get the desired threshold for volume AAA in the original DSET_WITH_INFO, for a given pvalue PVAL, say for a bisided stat:


p2dsetstat \
  -bisided  \
   -inset DSET_WITH_INFO"[AAA]" \
   -pval PVAL

… and then you could use that threshold value directly within your warped dset.

–pt

9

hmm ok let me try that !

10

oh ok that works well

Thanks

1 Like
11

Cool, glad that sorted things.

–pt