@auto_tlrc, Cannot open dataset

AFNI Message Board
1

Hello,

I am getting the following error when running the @auto_tlrc script:

3dNotes -h “align_epi_anat.py -anat MPRAGE.nii -epi
/Users/manglani.2/Data/BAMMS/BAM005/Rest/GTG/4D.nii -epi_base 0 -epi2anat
-prep_off -partial_axial -anat_has_skull no -epi_strip 3dAutomask
-master_tlrc 2.0 -tlrc_apar MPRAGE_TLR.nii -suffix _tlrcMNI.nii”
./4D_tlrcMNI.nii+orig

Error: Cannot open dataset
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_4D*
#Script is running:
\rm -f ./__tt_MPRAGE*

All file permissions have been set to -rwx. Any troubleshooting steps would be greatly appreciated!

Thanks!
Heena

2

Hi Heena,

I do not think @auto_tlrc calls align_epi_anat.py. Or maybe
AEA.py is the actual program? It would be helpful to see
much more output, though I suspect the problem has to do
with using NIFTI datasets and compression.

What is the output from:

afni -get_processed_env | grep -e ZIP -e COMP

  • rick
3

Hi Heena,

Given that “afni -get_processed_env | grep -e ZIP -e COMP” does
indeed show "AFNI_AUTOGZIP=YES ", you should either turn that
variable off or run align_epi_anat.py with AFNI datasets.

As it stands, you are probably getting .nii.gz compressed datasets,
but the program does not see them.

  • rick
4

Hi Rick,

I am actually getting .nii files of the epi data aligned to the MPRAGE image (in TLR space). Would you still recommend that I set AFNI_AUTOGZIP to off? If so, how would I do that (apologies for my lack of familiarity with afni).

Just an FYI, despite getting that error, I was able to run the rest of my preprocessing script and everything seems to be in the correct (standard) space. However, I would still like to know why it was having trouble opening the files and the potential effect it may be having on my data that I haven’t caught yet.

Thanks!
Heena

5

Hi Heena,

This is a bit too confusing without some real information.
Do you have the text file containing the complete screen
output from the analysis? If so, would you send that to
me via email, along with the actual processing script?

Thanks,

  • rick
6

Hi Heena,

What is the output from:

ls -l MRRAGE*

Can you run that 3dNotes command directly and see
what happens? If you get the “Cannot open dataset”
error, look at the input files and see what exists
and what does not.

  • rick
7

Sorry, you did indeed send enough information (I forgot
about the directory listings). It is the final dataset that does
not exist: 4DMNI.nii+orig.

That “-suffix MNI.nii” option does not make align_epi_anat.py
write NIFTI format. I am not sure whether there is any option
for that. You could use 3dcopy to convert after AEA.py though.

  • rick