I’ve been trying to us 3dAllineate and the following error occurs:
** ERROR: mri_read_ascii: couldn’t open file Q08.DLPFC.T1.Pre+orig_al_keep_mat.aff12.1D
This isn’t the first time I’ve seen an error associated with mri_read_ascii. I’ve also seen it when I’ve used SLOMOCO when it was trying to read a text file containing SLOMOCO_SLICE_TIMING
does anyone know what this means and is there a solution?
What is your AFNI version (“afni -ver” output), and can you please copy+paste the command that you are using?
Also, it would probably be useful to know what command you used to generate:
Here is the output for afni -ver:
Precompiled binary linux_ubuntu_16_64: Mar 20 2019 (Version AFNI_19.0.26 ‘Tiberius’)
In order to generate the .1d file, the following command was used:
align_epi_anat.py -anat2epi -anat Q08.DLPFC.T1.Pre+orig -suffix _al_keep -epi Q08.DLPFC.RestingState1.Pre+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off
Cool, thanks. And what is the 3dAllineate command that is failing for you?
3dAllineate -source Q08.DLPFC.T1.Pre+orig -master Q08.DLPFC.T1.Pre_al_keep+orig -final wsinc5 -1Dmatrix_apply Q08.DLPFC.T1.Pre+orig_al_keep_mat.aff12.1D -prefix anat_w_skull_warped
I don’t think that the file after the “-1Dmatrix_apply” argument is correct. I ran your initial align_epi_anat.py command on my computer with BRIK/HEAD files, and the matrix didn’t have the “+orig” part in that file name. Can you tell me what the output of this is?
I am assuming that it will be:
If that’s the case, then does this 3dAllineate command work for you?
3dAllineate -source Q08.DLPFC.T1.Pre+orig -master Q08.DLPFC.T1.Pre_al_keep+orig -final wsinc5 -1Dmatrix_apply Q08.DLPFC.T1.Pre_al_keep_mat.aff12.1D -prefix anat_w_skull_warped
I’m so sorry. You’re right, it was a mistake in the argument following '1Dmatrix_apply"
Thanks for your help. I’ll be more careful next time.
No worries-- glad that sorted it.