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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December 11, 2018 11:53PM
Hi, Rujing-

Re. Q1:
The following is a working example produced by the suma GUI when hitting the "clst" button to clusterize. I basically just loaded a dset (./std.60.lh.thickness.niml.dset, which is the dset that is thresholded (here at 3.58) + clusterized (here with NN=1, from '-rmm -1')), which is overlaid on the "underlay" data set (std.60.lh.smoothwm.gii):
SurfClust \
-i      ./std.60.lh.smoothwm.gii \
-input  ./std.60.lh.thickness.niml.dset 0 \
-rmm    -1.000000 \
-thresh_col 0 \
-athresh 3.580000 \
-amm2 50.000000 \
-sort_area \
-no_cent
The rest of the options are explained in the help file.

In your program call, you did not put two arguments after "-input ..."; see the helpfile here for that entry:
-input inData.dset dcol_index: The input dataset
                                  and the index of the
                                  datacolumn to use
                                  (index 0 for 1st column).
                                  Values of 0 indicate 
                                  inactive nodes.
I think that is the specific error you are getting, and why it is pointing to the "-input ..." opt for help.

I also don't think you can have both a "-spec ..." and "-i ..." surface file input; the helpfile seems to say one *or* the other:
Surface Input can be done with:
     -spec SpecFile: The surface spec file.
     -surf_A insurf: The input surface name.
    or with:
     -i insurf: With insurf being the full name of the surface.

Re. Q2: <<how to add more subjects' data such as a group data? >>
What kind of group statistic do you want? You can run that group-stat program and get a stats *.niml.dset, and then use that as your "-input ..." file, and threshold+clusterize that. For example, if you ran 3dtest++ on your data sets, then you could use the output from that.

--pt
Subject Author Posted

surfclust questions

charujing123 December 07, 2018 10:57AM

Re: surfclust questions

charujing123 December 11, 2018 09:26PM

Re: surfclust questions

ptaylor December 11, 2018 11:53PM

Re: surfclust questions

charujing123 December 12, 2018 01:59AM

Re: surfclust questions

ptaylor December 12, 2018 08:11AM