Hello,

I am trying to register my stats volume (output from 3dDeconvolve) into Talairach space.

The first command transforms the subject's structural to the template. It is

@auto_tlrc -no_ss -base template_file+tlrc -input ABB_brain+orig

This works fine. The next step is where the error appears. The command is

align_epi_anat.py -anat ABB_brain+orig -epi MsmmcOutBrick_run_010ts+orig -epi_base 0 -child_epi stat+orig.HEAD -epi2anat -anat_has_skull no -epi_strip None -volreg off -deoblique off -tshift off -tlrc_apar ABB_brain+orig

I am placing the entire notices that appear on the command window.

#++ align_epi_anat version: 1.19
#++ turning off volume registration
#++ Talairach transformed anatomical: /tcd-disk4/Barcelona/controls/ABB/ABB_brain+orig
#++ -child_epi option given
#Script is running:
3dAttribute DELTA /tcd-disk4/Barcelona/controls/ABB/MsmmcOutBrick_run_010ts+orig
#++ Spacing for EPI to tlrc alignment is 1.875000 mm
#Script is running:
3dAttribute DELTA /tcd-disk4/Barcelona/controls/ABB/ABB_brain+orig
#++ Spacing for anat to EPI deobliquing is 1.000000 mm
#++ Removing all the temporary files
#Script is running:
rm -f __tt_MsmmcOutBrick_run_010ts*
#Script is running:
rm -f __tt_ABB_brain*
#Script is running (command trimmed):
3dcopy ABB_brain+orig __tt_ABB_brain
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (May 21 2009) [64-bit]
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix __tt_MsmmcOutBrick_run_010ts_ts MsmmcOutBrick_run_010ts+orig'[0]'
++ 3dbucket: AFNI version=AFNI_2008_07_18_1710 (May 21 2009) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./MsmmcOutBrick_run_010ts+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./MsmmcOutBrick_run_010ts+orig.BRIK is 7.618600 degrees from plumb.
#++ resampling epi to match anatomical data
#Script is running (command trimmed):
3dresample -master __tt_ABB_brain+orig -prefix __tt_MsmmcOutBrick_run_010ts_ts_rs -inset __tt_MsmmcOutBrick_run_010ts_ts+orig'' -rmode Cu
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_MsmmcOutBrick_run_010ts_ts+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_MsmmcOutBrick_run_010ts_ts+orig.BRIK is 7.618600 degrees from plumb.
#++ removing skull or area outside brain
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 __tt_MsmmcOutBrick_run_010ts_ts_rs+orig
#++ Applying threshold of 1059.165771 on /tcd-disk4/Barcelona/controls/ABB/__tt_MsmmcOutBrick_run_010ts_ts_rs+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix __tt_MsmmcOutBrick_run_010ts_ts_rs_wt -a __tt_MsmmcOutBrick_run_010ts_ts_rs+orig -expr 'min(1,(a/1059.165771))'
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (May 21 2009) [64-bit]
++ Authored by: A cast of thousands

++ Output dataset ./__tt_MsmmcOutBrick_run_010ts_ts_rs_wt+orig.BRIK
#++ Aligning anatomical data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix __tt_ABB_brain_al_wtal -weight __tt_MsmmcOutBrick_run_010ts_ts_rs_wt+orig -source __tt_ABB_brain+orig -prefix __tt_ABB_brain_al -base __tt_MsmmcOutBrick_run_010ts_ts_rs+orig -nocmass -1Dmatrix_save ABB_brain_al_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (May 21 2009) [64-bit]
++ Authored by: Emperor Zhark
++ Loading datasets
++ 1381690 voxels in -source_automask+4
++ Zero-pad: xbot=0 xtop=4
++ zero-pad: ybot=4 ytop=0
++ zero-pad: zbot=0 ztop=4
++ 4142208 voxels [40.6%] in weight mask
++ Output dataset ./__tt_ABB_brain_al_wtal+orig.BRIK
++ Number of points for matching = 4142208
++ Local correlation: blok type = 'RHDD(6.54321)'
++ shift param auto-range: -78.0..78.0 -83.1..83.1 -51.4..51.4
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
+ 12 free parameters
++ Normalized convergence radius = 0.001000
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ Memory usage now = 101609840 (102 million): about to start alignment loop
++ ========== sub-brick #0 ========== [total CPU=3.9 s]
++ *** Fine pass begins ***
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - copying weight image
+ - using 4142208 points from base image
+ * Exit alignment setup routine
+ 3968808 total points stored in 7271 'RHDD(6.54321)' bloks
+ - Initial cost = 0.002492
+ - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
+ - Finalish cost = -0.001562 ; 522 funcs
+ - Final cost = -0.001562 ; 54 funcs
+ Final fine fit Parameters = 0.3779 0.6892 -5.7449 0.2276 -0.7527 0.3695 0.9849 0.9904 1.0270 0.0002 -0.0168 -0.0049
+ - Fine CPU time = 162.1 s
++ Computing output image
++ image warp: parameters = 0.3779 0.6892 -5.7449 0.2276 -0.7527 0.3695 0.9849 0.9904 1.0270 0.0002 -0.0168 -0.0049
++ Memory usage now = 408094956 (408 million): end of sub-brick alignment
++ Memory usage now = 157289972 (157 million): end of sub-brick loop (after cleanup)
++ Output dataset ./__tt_ABB_brain_al+orig.BRIK
++ Memory usage now = 118707033 (119 million): after writing output dataset
++ Wrote -1Dmatrix_save ABB_brain_al_mat.aff12.1D
++ total CPU time = 167.3 sec Elapsed = 174.9
++ Memory usage now = 16001313 (16 million): end of program (after final cleanup)
++ ###########################################################
#++ Aligning /tcd-disk4/Barcelona/controls/ABB/MsmmcOutBrick_run_010ts+orig to anat
#++ Inverting anat to epi matrix
#Script is running:
cat_matvec -ONELINE ABB_brain_al_mat.aff12.1D -I > MsmmcOutBrick_run_010ts_al_mat.aff12.1D
#++ Applying transformation of epi to anat
#Script is running (command trimmed):
3dAllineate -base ABB_brain+orig -1Dmatrix_apply MsmmcOutBrick_run_010ts_al_mat.aff12.1D -prefix MsmmcOutBrick_run_010ts_al -input MsmmcOutBrick_run_010ts+orig -master SOURCE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (May 21 2009) [64-bit]
++ Authored by: Emperor Zhark
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./MsmmcOutBrick_run_010ts+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./MsmmcOutBrick_run_010ts+orig.BRIK is 7.618600 degrees from plumb.
++ Loading datasets
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU=0.0 s]
Can't connect? tcp_connect[connect]: Connection refused
++ Output dataset ./MsmmcOutBrick_run_010ts_al+orig.BRIK
++ total CPU time = 0.3 sec Elapsed = 0.6
++ ###########################################################
#++ Concatenating talairach/post, volume registration, epi to anat transformations
#Script is running:
3dAttribute WARP_TYPE /tcd-disk4/Barcelona/controls/ABB/ABB_brain+orig
Error: Empty output.
Traceback (most recent call last):
File "/usr/local/afni/bin/align_epi_anat.py", line 2466, in ?
ps.epi_alnd = \
File "/usr/local/afni/bin/align_epi_anat.py", line 1614, in align_epi2anat
tlrc_type = int(com.val(0,0))
TypeError: int() argument must be a string or a number



Any suggestions as to what may be the cause of the problem?

Best,

Arun