afni.nimh.nih.gov
Home
>
AFNI Message Board
>
Topic
AFNI Message Board
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
| November 12, 2019 07:01AM | |
Registered: 5 years ago Posts: 3 |
Dear Experts,
I'm trying to convert FreeSurfer surfaces to afni.
I run this command line and I got this error.
I tried to download a new FreeSurfer license but I still got the same error:
francesca-desktop:/opt/freesurfer/subjects/PP> @SUMA_Make_Spec_FS -NIFTI -sid PP
FreeSurferEnv.csh (vers=13) requires csh/tcsh -- current shell:
FreeSurferEnv.csh: CSURF_DIR reset to current dir
-----------------------------------------------------------------------
csurf font changes:
xset fp default (reset to default)
xset +fp /opt/csurf/lib/fonts/75dpi-helvetica
xset fp rehash
-----------------------------------------------------------------------
csurf setenv changes:
CSURF_DIR=/opt/csurf
SUBJECTS_DIR=/opt/freesurfer/subjects
FUNCTIONALS_DIR=/opt/csurf/sessions
TCL_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tcl8.5
TK_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tk8.5
[dist=Ubuntu]
pre-appended to LD_LIBRARY_PATH:
+ /opt/csurf/tcltktix/lib/Linux-x86_64
+ /opt/csurf/gsl/lib/Linux-x86_64
+ /opt/csurf/lib/Linux-x86_64
+ /opt/csurf/afni/lib/Linux-x86_64
-----------------------------------------------------------------------
pre-appended to csh path:
+ /opt/csurf/afni/bin/Linux-x86_64
+ /opt/csurf/mni_autoreg/bin/Linux-x86_64
+ /opt/csurf/tcltktix/bin/Linux-x86_64
+ /opt/csurf/bin/Linux-x86_64
+ /opt/csurf/bin/noarch
-----------------------------------------------------------------------
other setenv changes (mostly bak compat):
FREESURFER_HOME=/opt/csurf (mri_surf2surf)
AFNI_PLUGINPATH=/opt/csurf/afni/lib/Linux-x86_64
DIAG=0x4040 (surfer bins 2000)
MRI_DIR=/opt/csurf (surfer bins 2000)
PERL5LIB=/opt/csurf/mni_autoreg/perl (MNI)
MNI_CONFIG_PATH=/opt/csurf/mni_autoreg/cfg (MNI)
LANG=en_US (RH9)
-----------------------------------------------------------------------
FreeSurfer0.8 from CSURF_DIR=/opt/csurf
MGH freesurfer from FSURF_DIR=/opt/freesurfer
surf directory found at './subjects/fsaverage-ADDITIONS/surf'
consider running program from './subjects/fsaverage-ADDITIONS'
program failure: exiting...
francesca-desktop:/opt/freesurfer/subjects/PP> @SUMA_Make_Spec_FS -fspath /opt/freesurfer/subjects/PP -NIFTI -sid PP
FreeSurferEnv.csh (vers=13) requires csh/tcsh -- current shell:
FreeSurferEnv.csh: CSURF_DIR reset to current dir
-----------------------------------------------------------------------
csurf font changes:
xset fp default (reset to default)
xset +fp /opt/csurf/lib/fonts/75dpi-helvetica
xset fp rehash
-----------------------------------------------------------------------
csurf setenv changes:
CSURF_DIR=/opt/csurf
SUBJECTS_DIR=/opt/freesurfer/subjects
FUNCTIONALS_DIR=/opt/csurf/sessions
TCL_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tcl8.5
TK_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tk8.5
[dist=Ubuntu]
pre-appended to LD_LIBRARY_PATH:
+ /opt/csurf/tcltktix/lib/Linux-x86_64
+ /opt/csurf/gsl/lib/Linux-x86_64
+ /opt/csurf/lib/Linux-x86_64
+ /opt/csurf/afni/lib/Linux-x86_64
-----------------------------------------------------------------------
pre-appended to csh path:
+ /opt/csurf/afni/bin/Linux-x86_64
+ /opt/csurf/mni_autoreg/bin/Linux-x86_64
+ /opt/csurf/tcltktix/bin/Linux-x86_64
+ /opt/csurf/bin/Linux-x86_64
+ /opt/csurf/bin/noarch
-----------------------------------------------------------------------
other setenv changes (mostly bak compat):
FREESURFER_HOME=/opt/csurf (mri_surf2surf)
AFNI_PLUGINPATH=/opt/csurf/afni/lib/Linux-x86_64
DIAG=0x4040 (surfer bins 2000)
MRI_DIR=/opt/csurf (surfer bins 2000)
PERL5LIB=/opt/csurf/mni_autoreg/perl (MNI)
MNI_CONFIG_PATH=/opt/csurf/mni_autoreg/cfg (MNI)
LANG=en_US (RH9)
-----------------------------------------------------------------------
FreeSurfer0.8 from CSURF_DIR=/opt/csurf
MGH freesurfer from FSURF_DIR=/opt/freesurfer
++ creating directory './SUMA' for results...
-- found 6 LH surfaces
-- found 6 RH surfaces
mri_convert -ot nii /opt/freesurfer/subjects/PP/mri/orig.mgz /opt/freesurfer/subjects/PP/./SUMA/orig.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /opt/freesurfer/subjects/PP/mri/orig.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/orig.nii...
++ created AFNI file './SUMA/PP_SurfVol.nii'
Made roi label table for AFNI - fs_table.niml.lt
mri_convert -ot nii mri/T1.mgz /opt/freesurfer/subjects/PP/./SUMA/T1.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/T1.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/T1.nii...
mri_convert -ot nii mri/aparc+aseg.mgz /opt/freesurfer/subjects/PP/./SUMA/aparc+aseg.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/aparc+aseg.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/aparc+aseg.nii...
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file aparc+aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aparc+aseg.nii
+ loading and re-writing dataset aparc+aseg.nii (./aparc+aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
3dmerge: edit and combine 3D datasets, by RW Cox
++ default -1dindex = 0
++ default -1tindex = 1
++ editing input dataset in memory (64.0 MB)
.
-- Wrote edited dataset: ./aparc+aseg_rank.nii
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_rank.nii
+ loading and re-writing dataset aparc+aseg_rank.nii (./aparc+aseg_rank.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aparc+aseg_rank.
mri_convert -ot nii mri/aparc.a2009s+aseg.mgz /opt/freesurfer/subjects/PP/./SUMA/aparc.a2009s+aseg.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/aparc.a2009s+aseg.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/aparc.a2009s+aseg.nii...
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file aparc.a2009s+aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aparc.a2009s+aseg.nii
+ loading and re-writing dataset aparc.a2009s+aseg.nii (./aparc.a2009s+aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg.
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
3dmerge: edit and combine 3D datasets, by RW Cox
++ default -1dindex = 0
++ default -1tindex = 1
++ editing input dataset in memory (64.0 MB)
.
-- Wrote edited dataset: ./aparc.a2009s+aseg_rank.nii
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_rank.nii
+ loading and re-writing dataset aparc.a2009s+aseg_rank.nii (./aparc.a2009s+aseg_rank.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg_rank.
mri_convert -ot nii mri/aseg.auto.mgz /opt/freesurfer/subjects/PP/./SUMA/aseg.auto.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/aseg.auto.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/aseg.auto.nii...
mri_convert -ot nii mri/aseg.mgz /opt/freesurfer/subjects/PP/./SUMA/aseg.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/aseg.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/aseg.nii...
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aseg.nii
+ loading and re-writing dataset aseg.nii (./aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aseg.
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
3dmerge: edit and combine 3D datasets, by RW Cox
++ default -1dindex = 0
++ default -1tindex = 1
++ editing input dataset in memory (64.0 MB)
.
-- Wrote edited dataset: ./aseg_rank.nii
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aseg_rank.nii
+ loading and re-writing dataset aseg_rank.nii (./aseg_rank.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aseg_rank.
mri_convert -ot nii mri/brain.finalsurfs.mgz /opt/freesurfer/subjects/PP/./SUMA/brain.finalsurfs.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/brain.finalsurfs.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/brain.finalsurfs.nii...
mri_convert -ot nii mri/brain.mgz /opt/freesurfer/subjects/PP/./SUMA/brain.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/brain.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/brain.nii...
mri_convert -ot nii mri/brainmask.auto.mgz /opt/freesurfer/subjects/PP/./SUMA/brainmask.auto.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/brainmask.auto.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/brainmask.auto.nii...
mri_convert -ot nii mri/brainmask.mgz /opt/freesurfer/subjects/PP/./SUMA/brainmask.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/brainmask.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/brainmask.nii...
mri_convert -ot nii mri/norm.mgz /opt/freesurfer/subjects/PP/./SUMA/norm.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/norm.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/norm.nii...
mri_convert -ot nii mri/nu.mgz /opt/freesurfer/subjects/PP/./SUMA/nu.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/nu.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/nu.nii...
mri_convert -ot nii mri/lh.ribbon.mgz /opt/freesurfer/subjects/PP/./SUMA/lh.ribbon.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/lh.ribbon.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/lh.ribbon.nii...
mri_convert -ot nii mri/rh.ribbon.mgz /opt/freesurfer/subjects/PP/./SUMA/rh.ribbon.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/rh.ribbon.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/rh.ribbon.nii...
mri_convert -ot nii mri/wm.asegedit.mgz /opt/freesurfer/subjects/PP/./SUMA/wm.asegedit.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/wm.asegedit.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/wm.asegedit.nii...
mri_convert -ot nii mri/wm.mgz /opt/freesurfer/subjects/PP/./SUMA/wm.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/wm.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/wm.nii...
mri_convert -ot nii mri/wm.seg.mgz /opt/freesurfer/subjects/PP/./SUMA/wm.seg.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/wm.seg.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/wm.seg.nii...
-- running 'mris_convert lh.smoothwm lh.smoothwm.asc'
--------------------------------------------------------------------------
GNU libc version: 2.27
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
download a new one from the following page:
[surfer.nmr.mgh.harvard.edu]
--------------------------------------------------------------------------
Reading lh.smoothwm.asc ...
Performing affine transform...
Writing surface...
-- running 'mris_convert lh.pial lh.pial.asc'
--------------------------------------------------------------------------
GNU libc version: 2.27
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
download a new one from the following page:
[surfer.nmr.mgh.harvard.edu]
--------------------------------------------------------------------------
-- Error ConvertSurface (SUMA_ConvertSurface.c:589):
if_name lh.pial.asc not found.
failure: could not create surface lh.pial.gii
--> is your FreeSurfer license installed?
program failure: exiting...
Thanks for the help!
Best
Francesca
I'm trying to convert FreeSurfer surfaces to afni.
I run this command line and I got this error.
I tried to download a new FreeSurfer license but I still got the same error:
francesca-desktop:/opt/freesurfer/subjects/PP> @SUMA_Make_Spec_FS -NIFTI -sid PP
FreeSurferEnv.csh (vers=13) requires csh/tcsh -- current shell:
FreeSurferEnv.csh: CSURF_DIR reset to current dir
-----------------------------------------------------------------------
csurf font changes:
xset fp default (reset to default)
xset +fp /opt/csurf/lib/fonts/75dpi-helvetica
xset fp rehash
-----------------------------------------------------------------------
csurf setenv changes:
CSURF_DIR=/opt/csurf
SUBJECTS_DIR=/opt/freesurfer/subjects
FUNCTIONALS_DIR=/opt/csurf/sessions
TCL_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tcl8.5
TK_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tk8.5
[dist=Ubuntu]
pre-appended to LD_LIBRARY_PATH:
+ /opt/csurf/tcltktix/lib/Linux-x86_64
+ /opt/csurf/gsl/lib/Linux-x86_64
+ /opt/csurf/lib/Linux-x86_64
+ /opt/csurf/afni/lib/Linux-x86_64
-----------------------------------------------------------------------
pre-appended to csh path:
+ /opt/csurf/afni/bin/Linux-x86_64
+ /opt/csurf/mni_autoreg/bin/Linux-x86_64
+ /opt/csurf/tcltktix/bin/Linux-x86_64
+ /opt/csurf/bin/Linux-x86_64
+ /opt/csurf/bin/noarch
-----------------------------------------------------------------------
other setenv changes (mostly bak compat):
FREESURFER_HOME=/opt/csurf (mri_surf2surf)
AFNI_PLUGINPATH=/opt/csurf/afni/lib/Linux-x86_64
DIAG=0x4040 (surfer bins 2000)
MRI_DIR=/opt/csurf (surfer bins 2000)
PERL5LIB=/opt/csurf/mni_autoreg/perl (MNI)
MNI_CONFIG_PATH=/opt/csurf/mni_autoreg/cfg (MNI)
LANG=en_US (RH9)
-----------------------------------------------------------------------
FreeSurfer0.8 from CSURF_DIR=/opt/csurf
MGH freesurfer from FSURF_DIR=/opt/freesurfer
surf directory found at './subjects/fsaverage-ADDITIONS/surf'
consider running program from './subjects/fsaverage-ADDITIONS'
program failure: exiting...
francesca-desktop:/opt/freesurfer/subjects/PP> @SUMA_Make_Spec_FS -fspath /opt/freesurfer/subjects/PP -NIFTI -sid PP
FreeSurferEnv.csh (vers=13) requires csh/tcsh -- current shell:
FreeSurferEnv.csh: CSURF_DIR reset to current dir
-----------------------------------------------------------------------
csurf font changes:
xset fp default (reset to default)
xset +fp /opt/csurf/lib/fonts/75dpi-helvetica
xset fp rehash
-----------------------------------------------------------------------
csurf setenv changes:
CSURF_DIR=/opt/csurf
SUBJECTS_DIR=/opt/freesurfer/subjects
FUNCTIONALS_DIR=/opt/csurf/sessions
TCL_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tcl8.5
TK_LIBRARY=/opt/csurf/tcltktix/lib/noarch/tk8.5
[dist=Ubuntu]
pre-appended to LD_LIBRARY_PATH:
+ /opt/csurf/tcltktix/lib/Linux-x86_64
+ /opt/csurf/gsl/lib/Linux-x86_64
+ /opt/csurf/lib/Linux-x86_64
+ /opt/csurf/afni/lib/Linux-x86_64
-----------------------------------------------------------------------
pre-appended to csh path:
+ /opt/csurf/afni/bin/Linux-x86_64
+ /opt/csurf/mni_autoreg/bin/Linux-x86_64
+ /opt/csurf/tcltktix/bin/Linux-x86_64
+ /opt/csurf/bin/Linux-x86_64
+ /opt/csurf/bin/noarch
-----------------------------------------------------------------------
other setenv changes (mostly bak compat):
FREESURFER_HOME=/opt/csurf (mri_surf2surf)
AFNI_PLUGINPATH=/opt/csurf/afni/lib/Linux-x86_64
DIAG=0x4040 (surfer bins 2000)
MRI_DIR=/opt/csurf (surfer bins 2000)
PERL5LIB=/opt/csurf/mni_autoreg/perl (MNI)
MNI_CONFIG_PATH=/opt/csurf/mni_autoreg/cfg (MNI)
LANG=en_US (RH9)
-----------------------------------------------------------------------
FreeSurfer0.8 from CSURF_DIR=/opt/csurf
MGH freesurfer from FSURF_DIR=/opt/freesurfer
++ creating directory './SUMA' for results...
-- found 6 LH surfaces
-- found 6 RH surfaces
mri_convert -ot nii /opt/freesurfer/subjects/PP/mri/orig.mgz /opt/freesurfer/subjects/PP/./SUMA/orig.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /opt/freesurfer/subjects/PP/mri/orig.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/orig.nii...
++ created AFNI file './SUMA/PP_SurfVol.nii'
Made roi label table for AFNI - fs_table.niml.lt
mri_convert -ot nii mri/T1.mgz /opt/freesurfer/subjects/PP/./SUMA/T1.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/T1.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/T1.nii...
mri_convert -ot nii mri/aparc+aseg.mgz /opt/freesurfer/subjects/PP/./SUMA/aparc+aseg.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/aparc+aseg.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/aparc+aseg.nii...
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file aparc+aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aparc+aseg.nii
+ loading and re-writing dataset aparc+aseg.nii (./aparc+aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
3dmerge: edit and combine 3D datasets, by RW Cox
++ default -1dindex = 0
++ default -1tindex = 1
++ editing input dataset in memory (64.0 MB)
.
-- Wrote edited dataset: ./aparc+aseg_rank.nii
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc+aseg_rank.nii
+ loading and re-writing dataset aparc+aseg_rank.nii (./aparc+aseg_rank.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aparc+aseg_rank.
mri_convert -ot nii mri/aparc.a2009s+aseg.mgz /opt/freesurfer/subjects/PP/./SUMA/aparc.a2009s+aseg.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/aparc.a2009s+aseg.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/aparc.a2009s+aseg.nii...
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file aparc.a2009s+aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aparc.a2009s+aseg.nii
+ loading and re-writing dataset aparc.a2009s+aseg.nii (./aparc.a2009s+aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg.
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
3dmerge: edit and combine 3D datasets, by RW Cox
++ default -1dindex = 0
++ default -1tindex = 1
++ editing input dataset in memory (64.0 MB)
.
-- Wrote edited dataset: ./aparc.a2009s+aseg_rank.nii
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aparc.a2009s+aseg_rank.nii
+ loading and re-writing dataset aparc.a2009s+aseg_rank.nii (./aparc.a2009s+aseg_rank.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg_rank.
mri_convert -ot nii mri/aseg.auto.mgz /opt/freesurfer/subjects/PP/./SUMA/aseg.auto.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/aseg.auto.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/aseg.auto.nii...
mri_convert -ot nii mri/aseg.mgz /opt/freesurfer/subjects/PP/./SUMA/aseg.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/aseg.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/aseg.nii...
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aseg.nii
+ loading and re-writing dataset aseg.nii (./aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aseg.
Program 3dmerge
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
3dmerge: edit and combine 3D datasets, by RW Cox
++ default -1dindex = 0
++ default -1tindex = 1
++ editing input dataset in memory (64.0 MB)
.
-- Wrote edited dataset: ./aseg_rank.nii
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Aug 28 2014) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset aseg_rank.nii
+ loading and re-writing dataset aseg_rank.nii (./aseg_rank.nii in NIFTI storage)
++ 3drefit processed 1 datasets
Notice: SessionAtlases.niml already exists, appending to it aseg_rank.
mri_convert -ot nii mri/brain.finalsurfs.mgz /opt/freesurfer/subjects/PP/./SUMA/brain.finalsurfs.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/brain.finalsurfs.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/brain.finalsurfs.nii...
mri_convert -ot nii mri/brain.mgz /opt/freesurfer/subjects/PP/./SUMA/brain.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/brain.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/brain.nii...
mri_convert -ot nii mri/brainmask.auto.mgz /opt/freesurfer/subjects/PP/./SUMA/brainmask.auto.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/brainmask.auto.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/brainmask.auto.nii...
mri_convert -ot nii mri/brainmask.mgz /opt/freesurfer/subjects/PP/./SUMA/brainmask.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/brainmask.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/brainmask.nii...
mri_convert -ot nii mri/norm.mgz /opt/freesurfer/subjects/PP/./SUMA/norm.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/norm.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/norm.nii...
mri_convert -ot nii mri/nu.mgz /opt/freesurfer/subjects/PP/./SUMA/nu.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/nu.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/nu.nii...
mri_convert -ot nii mri/lh.ribbon.mgz /opt/freesurfer/subjects/PP/./SUMA/lh.ribbon.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/lh.ribbon.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/lh.ribbon.nii...
mri_convert -ot nii mri/rh.ribbon.mgz /opt/freesurfer/subjects/PP/./SUMA/rh.ribbon.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/rh.ribbon.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/rh.ribbon.nii...
mri_convert -ot nii mri/wm.asegedit.mgz /opt/freesurfer/subjects/PP/./SUMA/wm.asegedit.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/wm.asegedit.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/wm.asegedit.nii...
mri_convert -ot nii mri/wm.mgz /opt/freesurfer/subjects/PP/./SUMA/wm.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/wm.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/wm.nii...
mri_convert -ot nii mri/wm.seg.mgz /opt/freesurfer/subjects/PP/./SUMA/wm.seg.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/wm.seg.mgz...
TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 3.72529e-09)
j_ras = (0, -1.16415e-10, -1)
k_ras = (0, 1, -1.22236e-09)
writing to /opt/freesurfer/subjects/PP/./SUMA/wm.seg.nii...
-- running 'mris_convert lh.smoothwm lh.smoothwm.asc'
--------------------------------------------------------------------------
GNU libc version: 2.27
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
download a new one from the following page:
[surfer.nmr.mgh.harvard.edu]
--------------------------------------------------------------------------
Reading lh.smoothwm.asc ...
Performing affine transform...
Writing surface...
-- running 'mris_convert lh.pial lh.pial.asc'
--------------------------------------------------------------------------
GNU libc version: 2.27
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
download a new one from the following page:
[surfer.nmr.mgh.harvard.edu]
--------------------------------------------------------------------------
-- Error ConvertSurface (SUMA_ConvertSurface.c:589):
if_name lh.pial.asc not found.
failure: could not create surface lh.pial.gii
--> is your FreeSurfer license installed?
program failure: exiting...
Thanks for the help!
Best
Francesca
| Subject | Author | Posted |
|---|---|---|
|
Frastra | November 12, 2019 07:01AM |
|
rick reynolds | November 14, 2019 08:28PM |
