A question about transformation matrix

AFNI Message Board
1

Hello,

I got an error information as below:

** FATAL ERROR: -matvec file not a 3x4 matrix!
** Program compile date = May 21 2017
** ERROR: Could not oblique/shift anat to epi data

I checked the matrix using in the code, it is a 3*4 matrix. Well, at least it contains 12 numbers.
Here it is:

3dAllineate matrices (DICOM-to-DICOM, row-by-row):

   1.00309    -0.0030288   -0.00490386      -0.45253    0.00511126       1.00771    0.00498307      -1.09497    0.00639334   -0.00971128      0.991483      -2.43748

So I don’t understand what the problem is. Please could someone help with this?

Many thanks,
Sarah

2

It would be useful to see the exact command that produced the error. There are two formats for the affine matrices in AFNI. To convert between the two, use cat_matvec.

3

Hi Daniel,

The command I used to generate the matrix is:
3dAllineate -prefix anat_within_aligned -base ${subj}_avg_anat+orig -1Dmatrix_save align_to_avg -source anat+orig

And then I used that matrix in afni_proc.py:
afni_proc.py -subj_id $subj.vol
-blocks tshift align volreg scale
-copy_anat ${subj}avg_anat+orig
-dsets run*+orig.HEAD
-tcat_remove_first_trs 0
-align_opts_aea -pre_matrix $top_dir/align_to_avg.aff12.1D -cost lpa -partial_coverage -anat_has_skull ‘no’
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-scr_overwrite
-execute

The matrix doesn’t have any problem when I did surface analysis. But when I tried to use the same matrix to do the volume based analysis, it gave me that error.

Sarah

4

Hi Daniel,

I tried the method you mentioned, unfortunately, I got another error:

#Script is running (command trimmed):
cat_matvec -ONELINE ./sub04_avg_anat_al_junk_e2a_only_mat.aff12.1D /Volumes/fMRI_Data/AFNI_PROCESSED_DATA/vis_loc/sub04_20170516/xform_test.aff12.1D -I > ./sub04_avg_anat_al_junk_mat.aff12.1D
** FATAL ERROR: File ‘/Volumes/fMRI_Data/AFNI_PROCESSED_DATA/vis_loc/sub04_20170516/xform_test.aff12.1D’ has 4 values per row, which isn’t 12

I’m totally confused now.

Sarah

5

Sorry, you’re missing one key piece of information. The files that end in “.aff12.1D” should have 12 values per row. If you redirect from another file or otherwise create a text file with 3 rows of 4 values, you should not use the .aff12.1D extension. Just use the .1D extension instead. Here are some example of how to use cat_matvec with these matrices. I start by creating a 4x3 matrix manually on the command line and then swap between the two formats.

cat > test.1D
1 0 0 10
0 1 0 -10
0 0 1 20
^C
% cat_matvec test.1D
1 0 0 10
0 1 0 -10
0 0 1 20
% cat_matvec -ONELINE test.1D
1 0 0 10 0 1 0 -10 0 0 1 20
% cat_matvec -ONELINE test.1D > test.aff12.1D
% cat_matvec -ONELINE test.aff12.1D
1 0 0 10 0 1 0 -10 0 0 1 20
% cat_matvec test.aff12.1D
1 0 0 10
0 1 0 -10
0 0 1 20

% cp test.1D test2.aff12.1D
% cat_matvec test2.aff12.1D
** FATAL ERROR: File ‘test2.aff12.1D’ has 4 values per row, which isn’t 12
** Program compile date = Nov 9 2017