external dataset setting

AFNI Message Board
1

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?

2

Hello,

I have not yet tried that with sub-brick selection, but it points to one field you may be missing (are there error messages?).

If the external dataset is only one volume, then you should make sure that AFNI_REALTIME_Base_Image is not still set to 3. So consider adding:

export AFNI_REALTIME_Base_Image=0

Does it work with that?

Thanks,

  • rick