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  

|
January 02, 2019 04:56PM
Hi,

I am trying to save images from the 3dLME results with 3dClustsim clusterized.

My Afni command is

afni -com 'SET_XHAIRS A.OFF' \
-com 'OPEN_WINDOW A.axialimage mont=3x5:4' \
-com 'OPEN_WINDOW A.sagittalimage mont=3x5:4' \
-com 'SWITCH_UNDERLAY A.avg152T1_2p5.nii' \
-com 'SWITCH_OVERLAY A.output.myLME+tlrc' \
-com 'SET_FUNC_RANGE A.0' \
-com 'SET_SUBBRICKS A 0 8 8'\
-com 'SET_DICOM_XYZ A 0 -0.75 15.5'\
-com 'SET_THRESHNEW A 0.005 *p'
-com 'SAVE_JPEG A.axialimage Axial.jpg blowup=3'\
-com 'SAVE_JPEG A.sagittalimage Sagittal.jpg blowup=3'

I already calculated 3dClustsim and apply them to 'output.myLME+tlrc' by 3drefit. But with the command above, I can't get the images clusterized.
So I just ran

afni -com 'SET_XHAIRS A.OFF' \
-com 'OPEN_WINDOW A.axialimage mont=3x5:4' \
-com 'OPEN_WINDOW A.sagittalimage mont=3x5:4' \
-com 'SWITCH_UNDERLAY A.avg152T1_2p5.nii' \
-com 'SWITCH_OVERLAY A.output.myLME+tlrc' \
-com 'SET_FUNC_RANGE A.0' \
-com 'SET_SUBBRICKS A 0 8 8'\
-com 'SET_DICOM_XYZ A 0 -0.75 15.5'\
-com 'SET_THRESHNEW A 0.005 *p'

and manually click 'Clusteize' on the Afni window and change NN level and # of voxel, and click 'set'. Then I need to put the name of images manually to
save them. I need to do these tedious jobs whenever I open Afni window to save them.

Is there any way to change NN level and # of voxel in the 'Clusterize' via command line, for example, I roughly guess that it might be '-com 'Clusterize_NN' 3'?

Thanks.

Jung
Subject Author Posted

Saving images with command line

chaj January 02, 2019 04:56PM

Re: Saving images with command line

ptaylor January 02, 2019 05:11PM

Re: Saving images with command line

chaj January 03, 2019 01:26PM

Re: Saving images with command line

ptaylor January 03, 2019 01:49PM