Hi There,
When running align_epi_anat, got error message as follows.
I do not know what happen. Please help me.
Thanks a lot for your help. - Jian
#++ align_epi_anat version: 1.17
#++ turning off volume registration
#Script is running (command trimmed):
3dAttribute DELTA S20vol.4+orig
#++ Spacing for EPI to tlrc alignment is 2.000000 mm
#Script is running (command trimmed):
3dAttribute DELTA S2vol+orig
#++ Spacing for anat to EPI deobliquing is 1.000000 mm
#++ Removing all the temporary files
#Script is running:
rm -f __tt_S20vol.4*
#Script is running:
rm -f __tt_S2vol*
#Script is running (command trimmed):
3dcopy S2vol+orig __tt_S2vol
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
#++ Removing skull from anatomical data
#Script is running (command trimmed):
3dSkullStrip -input __tt_S2vol+orig -prefix __tt_S2vol_ns
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 84, avoid_vent -1
The intensity in the output dataset is a modified version
of the intensity in the input volume.
To obtain a masked version of the input with identical values inside
the brain, you can either use 3dSkullStrip's -orig_vol option
or run the following command:
3dcalc -a __tt_S2vol+orig -b __tt_S2vol_ns+orig -expr 'a*step(b)' \
-prefix __tt_S2vol_ns_orig_vol
to generate a new masked version of the input.
#Script is running (command trimmed):
3dinfo __tt_S2vol_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset align-anat/__tt_S2vol_ns+orig is not oblique
#Script is running (command trimmed):
3dinfo S20vol.4+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset align-anat/S20vol.4+orig is not oblique
#++ Creating representative epi sub-brick
#Script is running (command trimmed):
3dbucket -prefix __tt_S20vol.4_ts S20vol.4+orig'[0]'
++ 3dbucket: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
#++ resampling epi to match anatomical data
#Script is running (command trimmed):
3dresample -master __tt_S2vol_ns+orig -prefix __tt_S20vol.4_ts_rs -inset __tt_S20vol.4_ts+orig'' -rmode Cu
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dAutomask -prefix junk __tt_S20vol.4_ts_rs+orig && 3dcalc -a __tt_S20vol.4_ts_rs+orig -b junk+orig -prefix __tt_S20vol.4_ts_rs_ns -expr 'step(b)*a'
++ 3dAutomask: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset __tt_S20vol.4_ts_rs+orig
++ Forming automask
+ Fixed clip level = 499.687500
+ Used gradual clip level = 415.007385 .. 550.117493
+ Number voxels above clip level = 1415494
+ Clustering voxels ...
+ Largest cluster has 1393347 voxels
+ Clustering voxels ...
+ Largest cluster has 1388322 voxels
+ Filled 1805 voxels in small holes; now have 1390127 voxels
+ Filled 40779 voxels in large holes; now have 1430906 voxels
+ Clustering voxels ...
+ Largest cluster has 1430832 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 14297808 voxels
+ Mask now has 1430832 voxels
++ 1430832 voxels in the mask [out of 15728640: 9.10%]
++ first 60 x-planes are zero [from R]
++ last 55 x-planes are zero [from L]
++ first 41 y-planes are zero [from A]
++ last 20 y-planes are zero [from P]
++ first 83 z-planes are zero [from I]
++ last 41 z-planes are zero [from S]
++ Output dataset ./junk+orig.BRIK
++ CPU time = 7.420000 sec
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__tt_S20vol.4_ts_rs_ns+orig.BRIK
#Script is running (command trimmed):
rm junk+orig.HEAD
#Script is running (command trimmed):
rm junk+orig.BRIK
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 __tt_S20vol.4_ts_rs_ns+orig
#++ Applying threshold of 1220.000000 on /mnt/autofs/netRAID04/Comparability/IOWA/2024/day1/S20sdt/align-anat/__tt_S20vol.4_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix __tt_S20vol.4_ts_rs_ns_wt -a __tt_S20vol.4_ts_rs_ns+orig -expr 'min(1,(a/1220.000000))'
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__tt_S20vol.4_ts_rs_ns_wt+orig.BRIK
#++ Aligning anatomical data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix __tt_S2vol_ns.alignafni.S20vol.4.shr_wtal -weight __tt_S20vol.4_ts_rs_ns_wt+orig -source __tt_S2vol_ns+orig -prefix S2vol.alignafni.S20vol.4.shr -base __tt_S20vol.4_ts_rs_ns+orig -nocmass -1Dmatrix_save S2vol.alignafni.S20vol.4.shr_mat.aff12.1D -master SOURCE -warp aff -onepass
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ Authored by: Emperor Zhark
++ Loading datasets
++ Zero-pad: not needed
++ 1430822 voxels [9.1%] in weight mask
++ Output dataset ./__tt_S2vol_ns.alignafni.S20vol.4.shr_wtal+orig.BRIK
++ Number of points for matching = 672486
++ Local correlation: blok type = 'RHDD(6.54321)'
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ ========== sub-brick #0 ========== [total CPU=1.5 s]
++ *** Fine pass begins ***
+ - Final cost = -0.373495 ; 78 funcs
++ Output dataset ./S2vol.alignafni.S20vol.4.shr+orig.BRIK
++ Wrote -1Dmatrix_save S2vol.alignafni.S20vol.4.shr_mat.aff12.1D
++ total CPU time = 95.3 sec Elapsed = 96.8
++ ###########################################################
#Script is running:
rm -f AddEdge/*
#Script is running:
mkdir AddEdge
#Script is running (command trimmed):
3dcopy -overwrite __tt_S20vol.4_ts_rs_ns+orig AddEdge/S20vol.4_ns
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite __tt_S2vol_ns+orig AddEdge/S2vol_ns
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite S2vol.alignafni.S20vol.4.shr+orig AddEdge/S2vol.alignafni.S20vol.4.shr
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
#Script is running (command trimmed):
cd AddEdge; @AddEdge S20vol.4_ns+orig S2vol_ns+orig S2vol.alignafni.S20vol.4.shr+orig; cd ..
++ 3dMean: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ 3dAutobox: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
+++ Executing 3dcalc()
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type short brick(s)
++ Sub-brick 0 scale factor = 11.158523
++ Computing output statistics
++ Output dataset /tmp/3dcalc#0001+orig.BRIK
++ Auto bbox: x=58..200 y=41..219 z=71..218
++ output dataset: ./tmp_box+orig.BRIK
++ 3dedge3: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./_ae.S20vol.4_ns_e+orig.BRIK
++ 3dedge3: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./S2vol_ns_e+orig.BRIK
3dBrickstat: Command not found. -----------here first error message, Jian
perc: Subscript out of range.
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset _ae.epi_sc+orig
** Program compile date = Mar 13 2009
invalid input dataset <_ae.S20vol.4_ns_S2vol_ns_e+orig>
++ 3dedge3: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Mar 13 2009) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./S2vol.alignafni.S20vol.4.shr_rs_e+orig.BRIK
3dBrickstat: Command not found.
