Hi experts,
I’m doing retinotopy by using @RetinoProc and my epi images were obtained obliquely (axial to calcarine sulcus) so I made T1 image oblique as epi. When I ran the script with this dataset, error message about 3dwarpdrive was poped up. I think this is because of the oblique images, but I couldn’t understand why this was happend. Belows are my script and error message. I’ll appreciate if you give me any of advice. Thank you.
############## script
#!/bin/bash
cd ~/Desktop/Retinotopy/data_sbj
cd sbj2
mkdir retinoResult
@RetinoProc
-sid sbj2
-surf_vol FreeSurfer/SUMA/sbj2_SurfVol+orig.HEAD
-spec_left FreeSurfer/SUMA/sbj2_lh.spec
-spec_right FreeSurfer/SUMA/sbj2_rh.spec
-anat_vol T1_MPRAGE_SAG_1_0ISO_0009/sbj2_MP_algntoEP+orig.HEAD
-TR 2
-period_ecc 64
-period_pol 64
-nrings 1
-nwedges 1
-fwhm_ecc 8
-fwhm_pol 8
-pre_ecc 0
-pre_pol 0
-ccw ROTATION_132_0003/sbj2_ROT3+orig
ROTATION_132_0004/sbj2_ROT4+orig
ROTATION_132_0005/sbj2_ROT5+orig
ROTATION_132_0006/sbj2_ROT6+orig
-exp EXPAND_132_0007/sbj2_EXP7+orig
EXPAND_132_0008/sbj2_EXP8+orig
-out_dir retinoResult
################ Error
*********** Warning *************
Dataset centers are 112.673802 mm
apart. If registration fails, try
adding option -align_centers
Hit Enter to proceed or ctrl+c to quit.
resampling AVol@Epi+orig to match /Users/minsunpark/Desktop/Retinotopy/data_sbj/sbj2/FreeSurfer/SUMA/sbj2_SurfVol+orig
Warning: AVol@Epi_resamp_+orig exists in /Users/minsunpark/Desktop/Retinotopy/data_sbj/sbj2/retinoResult
Enter O/S/Q to Overwrite/Skip/Quit:
o
3dresample -master /Users/minsunpark/Desktop/Retinotopy/data_sbj/sbj2/FreeSurfer/SUMA/sbj2_SurfVol+orig -prefix AVol@Epi_resamp_ -rmode Cu -inset AVol@Epi+orig
Registering /Users/minsunpark/Desktop/Retinotopy/data_sbj/sbj2/FreeSurfer/SUMA/sbj2_SurfVol+orig to AVol@Epi_resamp_+orig
3dZeropad -I 8 -S 8 -A 8 -P 8 -L 8 -R 8
-mm -prefix ./___tmp__zpAVol@Epi_resamp_sbj2_SurfVol_pad /Users/minsunpark/Desktop/Retinotopy/data_sbj/sbj2/FreeSurfer/SUMA/sbj2_SurfVol+orig
++ 3dZeropad: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
++ output dataset: ./___tmp__zpAVol@Epi_resamp_sbj2_SurfVol_pad+orig.BRIK
++ 3dZeropad: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
++ output dataset: ./___tmp__zpAVol@Epi_resamp_sbj2_SurfVol_refpad+orig.BRIK
++ 3dWarpDrive: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
++ Authored by: RW Cox
++ Loading datasets
++ Checking inputs
++ Creating empty output dataset
ijk_to_xyz: [ 1 0 0 ]
[ 0 0 -1 ]
[ 0 -1 0 ]
ijk_to_xyz: -136 136 136
xyz_to_ijk: [ 1 0 0 ]
[ 0 -0 -1 ]
[ 0 -1 -0 ]
xyz_to_ijk: 136 136 136
++ Coarse initialize xw[0.0%]*…
++ dx=0.0 dy=0.0 dz=0.0 roll=-9.0 pitch=-18.0 yaw=-9.0
++ Beginning alignment setup
++ mri_warp3D_align_setup ENTRY
- processing weight: [edge(18,18,18)] [blur(4.0)] [clip(0.0)]
- using 0 [0.000%] voxels
** mri_warp3D_align error: weight image too zero-ish!
++ Beginning alignment loop
Fatal Signal 11 (SIGSEGV) received
3dWarpDrive main
Bottom of Debug Stack
** Command line was:
3dWarpDrive -coarserot -twopass -verb -affine_general -cubic -final quintic -1Dmatrix_save SVol@Epi.A2E.1D -base ./___tmp__zpAVol@Epi_resamp_sbj2_SurfVol_refpad+orig -prefix ./___tmp__zpAVol@Epi_resamp_sbj2_SurfVol_pad_wd ./___tmp__zpAVol@Epi_resamp_sbj2_SurfVol_pad+orig
** AFNI version = AFNI_17.2.00 Compile date = Jul 5 2017
** [[Precompiled binary macosx_10.7_Intel_64: Jul 5 2017]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /Users/minsunpark/.afni.crashlog
++ 3dZeropad: AFNI version=AFNI_17.2.00 (Jul 5 2017) [64-bit]
** 3dZeropad: Can’t open dataset ___tmp__zpAVol@Epi_resamp_sbj2_SurfVol_pad_wd+orig
*** Can’t open dataset ___tmp__zpAVol@Epi_resamp_sbj2_SurfVol_pad_wd+orig
Error: 3dwarpdrive failed.
Failed.
** ERROR: THD_read_dvecmat: can’t open dataset SVol@Epi+orig.HEAD
** FATAL ERROR: Can’t read matrix from ‘SVol@Epi+orig.HEAD::WARPDRIVE_MATVEC_INV_000000’
** Program compile date = Jul 5 2017
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./ccw.01.vr+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:./ccw.01.vr+orig.BRIK is 29.194527 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./ccw.02.vr+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:./ccw.02.vr+orig.BRIK is 29.194527 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./ccw.03.vr+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:./ccw.03.vr+orig.BRIK is 29.194527 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./ccw.04.vr+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:./ccw.04.vr+orig.BRIK is 29.194527 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./exp.01.vr+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:./exp.01.vr+orig.BRIK is 29.194527 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./exp.02.vr+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:./exp.02.vr+orig.BRIK is 29.194527 degrees from plumb.
Reusing existing detrended version ccw.01.b01+orig.HEAD
Reusing existing detrended version ccw.02.b01+orig.HEAD
Reusing existing detrended version ccw.03.b01+orig.HEAD
Reusing existing detrended version ccw.04.b01+orig.HEAD
Reusing existing detrended version exp.01.b01+orig.HEAD
Reusing existing detrended version exp.02.b01+orig.HEAD
Mapping ccw.01.b01+orig.HEAD to surface to create {ccw.01}.lh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping ccw.02.b01+orig.HEAD to surface to create {ccw.02}.lh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping ccw.03.b01+orig.HEAD to surface to create {ccw.03}.lh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping ccw.04.b01+orig.HEAD to surface to create {ccw.04}.lh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping exp.01.b01+orig.HEAD to surface to create {exp.01}.lh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping exp.02.b01+orig.HEAD to surface to create {exp.02}.lh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
No runs for ccw
No runs for clw
No runs for exp
No runs for con
No user data for pol ccw
No user data for pol clw
No user data for ecc exp
No user data for ecc con
Need at least one polar angle direction for visual field maps
Skipping VFR
Need at least one polar angle direction for visual field maps
Skipping VFR
Mapping ccw.01.b01+orig.HEAD to surface to create {ccw.01}.rh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping ccw.02.b01+orig.HEAD to surface to create {ccw.02}.rh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping ccw.03.b01+orig.HEAD to surface to create {ccw.03}.rh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping ccw.04.b01+orig.HEAD to surface to create {ccw.04}.rh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping exp.01.b01+orig.HEAD to surface to create {exp.01}.rh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
Mapping exp.02.b01+orig.HEAD to surface to create {exp.02}.rh.niml.dset
** ERROR: failed to open -sv dataset, SVol@Epi+orig
No runs for ccw
No runs for clw
No runs for exp
No runs for con
No user data for pol ccw
No user data for pol clw
No user data for ecc exp
No user data for ecc con
Need at least one polar angle direction for visual field maps
Skipping VFR
Need at least one polar angle direction for visual field maps
Skipping VFR
Close all existing AFNI and SUMA sessions
Launch SUMA and view some results with:
cd retinoResult
tcsh @ShowResult
No Demo side (NADA)