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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| July 29, 2017 09:53AM | |
Hi Rick,
I wanted to find out if the Centos 7 version is also openmp or not?
Secondly, in running 3dNwarpApply I had the following errors on the red hat system when the exact same command/files passed on my ubuntu system....any thoughts?
3dNwarpApply -interp NN -nwarp 'tmp.anat2MNI_WARP.nii tmp.anat2MNI.aff.Xat.1D anat.brain2tpl.aff6.1D INV(T2.brain2B0.aff6.1D) nl_WARP.nii' -iwarp -master B0ref_resamp.nii.gz -source ./DWI.weight+tlrc. -prefix weight22 -verb >> 3dNwarpApply_err1.txt
++ 3dNwarpApply: AFNI version=AFNI_17.1.01 (Apr 12 2017) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is 'B0ref_resamp.nii.gz'
++ opened source dataset './DWI.weight+tlrc.'
++ Processing -nwarp ++ Enter IW3D_read_nwarp_catlist( tmp.anat2MNI_WARP.nii tmp.anat2MNI.aff.Xat.1D anat.brain2tpl.aff6.1D INV(T2.brain2B0.aff6.1D) nl_WARP.nii )
+ Open dataset warp tmp.anat2MNI_WARP.nii
+ max displacments = 20.1844 14.3053 11.4142
+ Open matrix file tmp.anat2MNI.aff.Xat.1D
+ max shifts = 0.551628 2.81892 5.4792
+ Open matrix file anat.brain2tpl.aff6.1D
+ max shifts = 0.420547 2.80645 14.4052
+ Open matrix file INV(T2.brain2B0.aff6.1D)
+ max shifts = 2.08339 11.8799 32.1879
+ Open dataset warp nl_WARP.nii
+ max displacments = 5.69117 10.5456 4.94413
+ found geometry mismatch: orig=MATRIX(-1,0,0,96,0,-1,0,132,0,0,1,-93):193,231,208 new=MATRIX(1,0,0,-117.0035,0,1,0,-120.5573,0,0,1,-62.79667):230,236,173
+ --- Totalized max displacments = 28.9311 42.3562 68.4307
++ IW3D_set_geometry_nwarp_catlist: padding = 46
+ results: master_geomstring = MATRIX(1.5,0,0,-116.5035,0,1.5,0,-120.0573,0,0,1.5,-46.54667):153,153,96 actual_geomstring = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ -- warp #0 geometry = MATRIX(-1,0,0,96,0,-1,0,132,0,0,1,-93):193,231,208
+ regridding warp #0 to geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ -- warp #4 geometry = MATRIX(1,0,0,-117.0035,0,1,0,-120.5573,0,0,1,-62.79667):230,236,173
+ regridding warp #4 to geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+++++ initial structure of Nwarp_catlist: Nwarp ; Matrix[1] ; Matrix[1] ; Matrix[1] ; Nwarp ;
++ -- IW3D_reduce_nwarp_catlist -- start loop
+ looking at nwc[0]
+ .. #0 and #1 are neighbors
+ looking at nwc[1]
+ .. #1 and #2 are neighbors
+ .. IW3D_reduce_nwarp_catlist: Matrix[1]-Matrix[1] ii=1 jj=2
+ looking at nwc[2]
+ .. #2 and #3 are neighbors
+ .. IW3D_reduce_nwarp_catlist: Matrix[1]-Matrix[1] ii=2 jj=3
+ looking at nwc[3]
+ .. #3 and #4 are neighbors
+ -- loop reduction operation count = 2
++ -- IW3D_reduce_nwarp_catlist -- start loop
+ looking at nwc[0]
+ .. #0 and #3 are neighbors
+ IW3D_reduce_nwarp_catlist: warp-Matrix[1] ii=0 jj=3
+ looking at nwc[3]
+ .. #3 and #4 are neighbors
+ .. IW3D_reduce_nwarp_catlist: warp-warp ii=3 jj=4
+ ii=3: geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ jj=4: geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ -- loop reduction operation count = 2
++ -- IW3D_reduce_nwarp_catlist -- start loop
+ nwc[0] is doubly NULL
+ nwc[1] is doubly NULL
+ nwc[2] is doubly NULL
+ nwc[3] is doubly NULL
+ -- loop reduction operation count = 0
+++++ final structure of Nwarp_catlist: (NULL) ; (NULL) ; Nwarp ;
++ Warping: [nvar=1]ab{nwarp_catlist[0] [NULL entry?] [NULL entry?] [warp]} + -- invert max|AA|=64.153511
+ - init nstep=8 qq=1/2^8=0.003906
+ - init step 1
+ - init step 2
+ - init step 3
+ - init step 4
+ - init step 5
+ - init step 6
+ - init step 7
+ - init step 8
+ - start iterations: normAA=36.756603 inewtfac=0.248055
+ - iterate 1 nrat=0.027847
+ - iterate 2 nrat=0.019870
+ - switch to inewtfac=0.306100
+ - iterate 3 nrat=0.019028
+ - iterate 4 nrat=0.013255
+ - switch to inewtfac=0.377727
+ - iterate 5 nrat=0.010855
+ - iterate 6 nrat=0.007080
+ - switch to inewtfac=0.466116
+ - iterate 7 nrat=0.005142
+ - iterate 8 nrat=0.002772
+ - switch to inewtfac=0.575187
+ - iterate 9 nrat=0.001922
+ - iterate 10 nrat=0.000805
+ - switching from linear interp
+ - iterate 11 nrat=0.000343
+ - iterate 12 nrat=0.000151
+ - switch to inewtfac=0.678901
+ - iterate 13 nrat=0.000076
+ -- iteration converged
'** ERROR: EDIT_full_copy: invalid dataset input ptr=0x6e92a00
** ERROR: Can't copy nwarp dataset #0 ?!?
** FATAL ERROR: Warping failed for some reason
((
** Program compile date = Apr 12 2017
Output of ldd on redhat ..........just as a note for linux-vdso.so.1 this is also blank on the ubuntu machine that worked.
linux-vdso.so.1 => (0x00007ffc98ff8000)
libXt.so.6 => /usr/lib64/libXt.so.6 (0x00002b2e2c23d000)
libXft.so.2 => /usr/lib64/libXft.so.2 (0x00002b2e2c4a4000)
libXp.so.6 => /usr/lib64/libXp.so.6 (0x00002b2e2c6ba000)
libXpm.so.4 => /usr/lib64/libXpm.so.4 (0x00002b2e2c8c3000)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x00002b2e2cad5000)
libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x00002b2e2cce7000)
libSM.so.6 => /usr/lib64/libSM.so.6 (0x00002b2e2cf02000)
libICE.so.6 => /usr/lib64/libICE.so.6 (0x00002b2e2d10a000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x00002b2e2d326000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00002b2e2d664000)
libz.so.1 => /usr/lib64/libz.so.1 (0x00002b2e2d88b000)
libm.so.6 => /usr/lib64/libm.so.6 (0x00002b2e2daa1000)
libdl.so.2 => /usr/lib64/libdl.so.2 (0x00002b2e2dda3000)
libc.so.6 => /usr/lib64/libc.so.6 (0x00002b2e2dfa7000)
libgomp.so.1 => /hpc/software/gcc/4.8.3/lib64/libgomp.so.1 (0x00002b2e2e368000)
libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00002b2e2e576000)
libfontconfig.so.1 => /usr/lib64/libfontconfig.so.1 (0x00002b2e2e792000)
libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00002b2e2e9cf000)
libXrender.so.1 => /usr/lib64/libXrender.so.1 (0x00002b2e2ec75000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x00002b2e2ee7f000)
libuuid.so.1 => /usr/lib64/libuuid.so.1 (0x00002b2e2f083000)
libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00002b2e2f288000)
/lib64/ld-linux-x86-64.so.2 (0x00002b2e2c01b000)
librt.so.1 => /usr/lib64/librt.so.1 (0x00002b2e2f4aa000)
libexpat.so.1 => /usr/lib64/libexpat.so.1 (0x00002b2e2f6b2000)
Edited 2 time(s). Last edit at 07/29/2017 10:23AM by AjaySK.
I wanted to find out if the Centos 7 version is also openmp or not?
Secondly, in running 3dNwarpApply I had the following errors on the red hat system when the exact same command/files passed on my ubuntu system....any thoughts?
3dNwarpApply -interp NN -nwarp 'tmp.anat2MNI_WARP.nii tmp.anat2MNI.aff.Xat.1D anat.brain2tpl.aff6.1D INV(T2.brain2B0.aff6.1D) nl_WARP.nii' -iwarp -master B0ref_resamp.nii.gz -source ./DWI.weight+tlrc. -prefix weight22 -verb >> 3dNwarpApply_err1.txt
++ 3dNwarpApply: AFNI version=AFNI_17.1.01 (Apr 12 2017) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is 'B0ref_resamp.nii.gz'
++ opened source dataset './DWI.weight+tlrc.'
++ Processing -nwarp ++ Enter IW3D_read_nwarp_catlist( tmp.anat2MNI_WARP.nii tmp.anat2MNI.aff.Xat.1D anat.brain2tpl.aff6.1D INV(T2.brain2B0.aff6.1D) nl_WARP.nii )
+ Open dataset warp tmp.anat2MNI_WARP.nii
+ max displacments = 20.1844 14.3053 11.4142
+ Open matrix file tmp.anat2MNI.aff.Xat.1D
+ max shifts = 0.551628 2.81892 5.4792
+ Open matrix file anat.brain2tpl.aff6.1D
+ max shifts = 0.420547 2.80645 14.4052
+ Open matrix file INV(T2.brain2B0.aff6.1D)
+ max shifts = 2.08339 11.8799 32.1879
+ Open dataset warp nl_WARP.nii
+ max displacments = 5.69117 10.5456 4.94413
+ found geometry mismatch: orig=MATRIX(-1,0,0,96,0,-1,0,132,0,0,1,-93):193,231,208 new=MATRIX(1,0,0,-117.0035,0,1,0,-120.5573,0,0,1,-62.79667):230,236,173
+ --- Totalized max displacments = 28.9311 42.3562 68.4307
++ IW3D_set_geometry_nwarp_catlist: padding = 46
+ results: master_geomstring = MATRIX(1.5,0,0,-116.5035,0,1.5,0,-120.0573,0,0,1.5,-46.54667):153,153,96 actual_geomstring = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ -- warp #0 geometry = MATRIX(-1,0,0,96,0,-1,0,132,0,0,1,-93):193,231,208
+ regridding warp #0 to geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ -- warp #4 geometry = MATRIX(1,0,0,-117.0035,0,1,0,-120.5573,0,0,1,-62.79667):230,236,173
+ regridding warp #4 to geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+++++ initial structure of Nwarp_catlist: Nwarp ; Matrix[1] ; Matrix[1] ; Matrix[1] ; Nwarp ;
++ -- IW3D_reduce_nwarp_catlist -- start loop
+ looking at nwc[0]
+ .. #0 and #1 are neighbors
+ looking at nwc[1]
+ .. #1 and #2 are neighbors
+ .. IW3D_reduce_nwarp_catlist: Matrix[1]-Matrix[1] ii=1 jj=2
+ looking at nwc[2]
+ .. #2 and #3 are neighbors
+ .. IW3D_reduce_nwarp_catlist: Matrix[1]-Matrix[1] ii=2 jj=3
+ looking at nwc[3]
+ .. #3 and #4 are neighbors
+ -- loop reduction operation count = 2
++ -- IW3D_reduce_nwarp_catlist -- start loop
+ looking at nwc[0]
+ .. #0 and #3 are neighbors
+ IW3D_reduce_nwarp_catlist: warp-Matrix[1] ii=0 jj=3
+ looking at nwc[3]
+ .. #3 and #4 are neighbors
+ .. IW3D_reduce_nwarp_catlist: warp-warp ii=3 jj=4
+ ii=3: geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ jj=4: geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ -- loop reduction operation count = 2
++ -- IW3D_reduce_nwarp_catlist -- start loop
+ nwc[0] is doubly NULL
+ nwc[1] is doubly NULL
+ nwc[2] is doubly NULL
+ nwc[3] is doubly NULL
+ -- loop reduction operation count = 0
+++++ final structure of Nwarp_catlist: (NULL) ; (NULL) ; Nwarp ;
++ Warping: [nvar=1]ab{nwarp_catlist[0] [NULL entry?] [NULL entry?] [warp]} + -- invert max|AA|=64.153511
+ - init nstep=8 qq=1/2^8=0.003906
+ - init step 1
+ - init step 2
+ - init step 3
+ - init step 4
+ - init step 5
+ - init step 6
+ - init step 7
+ - init step 8
+ - start iterations: normAA=36.756603 inewtfac=0.248055
+ - iterate 1 nrat=0.027847
+ - iterate 2 nrat=0.019870
+ - switch to inewtfac=0.306100
+ - iterate 3 nrat=0.019028
+ - iterate 4 nrat=0.013255
+ - switch to inewtfac=0.377727
+ - iterate 5 nrat=0.010855
+ - iterate 6 nrat=0.007080
+ - switch to inewtfac=0.466116
+ - iterate 7 nrat=0.005142
+ - iterate 8 nrat=0.002772
+ - switch to inewtfac=0.575187
+ - iterate 9 nrat=0.001922
+ - iterate 10 nrat=0.000805
+ - switching from linear interp
+ - iterate 11 nrat=0.000343
+ - iterate 12 nrat=0.000151
+ - switch to inewtfac=0.678901
+ - iterate 13 nrat=0.000076
+ -- iteration converged
'** ERROR: EDIT_full_copy: invalid dataset input ptr=0x6e92a00
** ERROR: Can't copy nwarp dataset #0 ?!?
** FATAL ERROR: Warping failed for some reason
((
** Program compile date = Apr 12 2017
Output of ldd on redhat ..........just as a note for linux-vdso.so.1 this is also blank on the ubuntu machine that worked.
linux-vdso.so.1 => (0x00007ffc98ff8000)
libXt.so.6 => /usr/lib64/libXt.so.6 (0x00002b2e2c23d000)
libXft.so.2 => /usr/lib64/libXft.so.2 (0x00002b2e2c4a4000)
libXp.so.6 => /usr/lib64/libXp.so.6 (0x00002b2e2c6ba000)
libXpm.so.4 => /usr/lib64/libXpm.so.4 (0x00002b2e2c8c3000)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x00002b2e2cad5000)
libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x00002b2e2cce7000)
libSM.so.6 => /usr/lib64/libSM.so.6 (0x00002b2e2cf02000)
libICE.so.6 => /usr/lib64/libICE.so.6 (0x00002b2e2d10a000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x00002b2e2d326000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00002b2e2d664000)
libz.so.1 => /usr/lib64/libz.so.1 (0x00002b2e2d88b000)
libm.so.6 => /usr/lib64/libm.so.6 (0x00002b2e2daa1000)
libdl.so.2 => /usr/lib64/libdl.so.2 (0x00002b2e2dda3000)
libc.so.6 => /usr/lib64/libc.so.6 (0x00002b2e2dfa7000)
libgomp.so.1 => /hpc/software/gcc/4.8.3/lib64/libgomp.so.1 (0x00002b2e2e368000)
libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00002b2e2e576000)
libfontconfig.so.1 => /usr/lib64/libfontconfig.so.1 (0x00002b2e2e792000)
libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00002b2e2e9cf000)
libXrender.so.1 => /usr/lib64/libXrender.so.1 (0x00002b2e2ec75000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x00002b2e2ee7f000)
libuuid.so.1 => /usr/lib64/libuuid.so.1 (0x00002b2e2f083000)
libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00002b2e2f288000)
/lib64/ld-linux-x86-64.so.2 (0x00002b2e2c01b000)
librt.so.1 => /usr/lib64/librt.so.1 (0x00002b2e2f4aa000)
libexpat.so.1 => /usr/lib64/libexpat.so.1 (0x00002b2e2f6b2000)
Edited 2 time(s). Last edit at 07/29/2017 10:23AM by AjaySK.
| Subject | Author | Posted |
|---|---|---|
|
AjaySK | June 28, 2017 11:06PM |
|
Bob Cox | July 03, 2017 09:26AM |
|
AjaySK | July 28, 2017 09:53AM |
|
rick reynolds | July 28, 2017 09:58AM |
|
AjaySK | July 29, 2017 09:53AM |
|
rick reynolds | July 31, 2017 09:48AM |
