@SUMA_Make_Spec_FS error

AFNI Message Board
1

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:
http://surfer.nmr.mgh.harvard.edu/registration.html

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:
http://surfer.nmr.mgh.harvard.edu/registration.html

– 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

2

Hi Francesca,

It look like mris_convert is suggesting you need to updates your FreeSurfer license file. You may have to contact them for how to do that most easily.

  • rick