Following up on this post: https://afni.nimh.nih.gov/afni/community/board/read.php?1,82612,82706#msg-82706
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?