3dBlurToFWHM Can't open dataset

AFNI Message Board
1

Dear afni users,

I am having a problem to run the 3dBlurToFWHM. The error is:
3dBlurToFWHM -FWHM 6 -automask -prefix rm.pb04.$subj.r$run.blur -input pb03.$subj.r$run.volreg+tlrc
++ 3dBlurToFWHM: AFNI version=AFNI_16.0.00 (Jan 1 2016) [64-bit]
** FATAL ERROR: Can’t open dataset ‘pb03…r.volreg+tlrc’
** Program compile date = Jan 1 2016

I tried the Is command, it seems everything is ok.
ls -l pb03.bil.r01.volreg+tlrc*
-rwxrwx—+ 1 username 214794240 Feb 3 17:10 pb03.bil.r01.volreg+tlrc.BRIK
-rwxrwx—+ 1 username 13782 Feb 3 17:10 pb03.bil.r01.volreg+tlrc.HEAD

and this is the output for 3dinfo;
----- HISTORY -----
=== History of inputs to 3dcalc ===
=== Input a: 3dDespike -NEW -nomask -prefix pb01.bil.r01.despike pb00.bil.r01.tcat+orig
3dTshift -tzero 0 -quintic -prefix pb02.bil.r01.tshift pb01.bil.r01.despike+orig
[3dNwarpApply -master FT_anat_ns+tlrc -dxyz 2.5 -source pb02.bil.r01.tshift+orig -nwarp ‘anat.un.aff.qw_WARP.nii mat.r01.warp.aff12.1D’ -prefix rm.epi.nomask.r01
Input b:
[3dDespike -NEW -nomask -prefix pb01.bil.r01.despike pb00.bil.r01.tcat+orig
3dTshift -tzero 0 -quintic -prefix pb02.bil.r01.tshift pb01.bil.r01.despike+orig
3dcalc -a pb02.bil.r01.tshift+orig -expr 1 -prefix rm.epi.all1
3dNwarpApply -master FT_anat_ns+tlrc -dxyz 2.5 -source rm.epi.all1+orig -nwarp ‘anat.un.aff.qw_WARP.nii mat.r01.warp.aff12.1D’ -ainterp NN -quiet -prefix rm.epi.1.r01
3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc
3dcopy rm.epi.min.r01+tlrc mask_epi_extents

3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr ‘a*b’ -prefix pb03.bil.r01.volreg

I do not know what is the problem…any help will be highly appreciated
Thank you!

2

Note that the error message references the input
dataset name, ‘pb03…r.volreg+tlrc’, meaning the
$subj and $run variables are empty. That is a
script problem. Just to see, try setting subj to
bil and run to 01. I will guess you are using the
bash shell, meaning the syntax would be:

set subj=bil
set run=01
3dBlurToFWHM -FWHM 6 -automask -prefix rm.pb04.$subj.r$run.blur -input pb03.$subj.r$run.volreg+tlrc
  • rick
3

Thanks so much!

Its working now!

Myriam