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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mindfrombrain
January 17, 2022 01:38AM
Following up on this post: [afni.nimh.nih.gov]

I have tried multiple ways of following the instructions but every time I double check the GUI, the external dataset is not actually set to anything, nor the mask, and when I run things, the values are not the same as when I manually set the mask and external dataset.

First, this is what I put into Terminal when I run things while manually setting external dataset and mask:

source ~/.profile
export AFNI_TRUSTHOST=localhost
export AFNI_REALTIME_Registration=3D:_realtime
export AFNI_REALTIME_Graph=Realtime
export AFNI_REALTIME_MP_HOST_PORT=localhost:53214
export AFNI_REALTIME_SEND_VER=YES
export AFNI_REALTIME_SHOW_TIMES=YES
export AFNI_REALTIME_Mask_Vals=ROI_means
export AFNI_REALTIME_SHOW_TIMES
afni -rt

When I try to set my mask (roi_mask2+orig) and external dataset (epi_grid+orig), which are in the same folder I'm running all this from, these are the commands I use:

source ~/.profile
export AFNI_TRUSTHOST=localhost
export AFNI_REALTIME_Registration=3D:_realtime
export AFNI_REALTIME_External_Dataset=epi_grid+orig'[0]'
export AFNI_REALTIME_Reg_Base_Mode=External_Dataset
export AFNI_REALTIME_Graph=Realtime
export AFNI_REALTIME_MP_HOST_PORT=localhost:53214
export AFNI_REALTIME_SEND_VER=YES
export AFNI_REALTIME_SHOW_TIMES=YES
export AFNI_REALTIME_Mask_Dset=roi_mask2+orig
export AFNI_REALTIME_Mask_Vals=ROI_means
export AFNI_REALTIME_SHOW_TIMES
afni -rt


Variations I've tried that also did not work:
Changing the final line, "afni -rt" to
afni -rt -AFNI_REALTIME_External_Dataset=epi_grid+orig'[0]'
or
afni -rt -DAFNI_REALTIME_External_Dataset=epi_grid+orig'[0]'
or
replacing all instances of epi_grid+orig'[0]' with epi_grid+orig
(It shouldn't matter, the file only has 1 brick)
or replacing with the full path of the file
or changing export AFNI_REALTIME_External_Dataset=epi_grid+orig'[0]' to AFNI_REALTIME_External_Dataset=epi_grid+orig'[0]'


I'm not sure, am I just missing something really obvious in trying to read the instructions? Has the format for invoking this command changed?
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Subject Author Posted

external dataset setting

mindfrombrain January 17, 2022 01:38AM

Re: external dataset setting

rick reynolds January 19, 2022 11:53AM