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FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading shared
libraries: libpng12.so.0: cannot open shared object file: No such file or
directory" - do I need to add /usr/local/freesurfer/lib/* to path or
something along those lines?
SURFACE INFO ========================================
type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 102020
num faces : 204036
num strips : 0
surface area: 65520.5
AvgVtxArea 0.642232
AvgVtxDist 0.940503
StdVtxDist 0.417776
ctr : (-31.9056, -18.8197, 16.3545)
vertex locs : surfaceRAS
Volume Geometry (vg)
volume geometry:
extent : (176, 224, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : (-0.9990, -0.0436, 0.0000)
y_(ras) : (-0.0436, 0.9990, 0.0000)
z_(ras) : ( 0.0000, 0.0000, 1.0000)
c_(ras) : (-0.5431, 8.9290, -17.0723)
file : /media/ian/bronson/subject/T1_nifti.nii.gz
Volume Geometry vox2ras
-0.99905 -0.04362 0.00000 92.25847;
-0.04362 0.99905 0.00000 -99.12585;
0.00000 0.00000 1.00000 -145.07230;
0.00000 0.00000 0.00000 1.00000;
Volume Geometry vox2ras-tkr
-1.00000 0.00000 0.00000 88.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 112.00000;
0.00000 0.00000 0.00000 1.00000;
cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT
BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v
1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine:
xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic
CompilerName: GCC CompilerVersion: 30400
cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp:
2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id:
mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User:
fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion:
3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400
cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT
BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28
2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox
Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC
CompilerVersion: 30400
cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion:
$Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13
2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp
$ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux
PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion:
30400
cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT
BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57
2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox
Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC
CompilerVersion: 30400
cmd[5]: mris_register -curv ../surf/lh.sphere
/usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif
../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp:
2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id:
mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser
Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion:
3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400
mris_info
creationtime 2020/05/06-14:18:48-GMT
sysname Linux
hostname ryzen-cumnor
machine x86_64
surfacefile /home/ian/cdm_registered_test/registered_lh.white
hemicode 1
talairach_flag 0
rescale 0.000000
nvertices 102020
nfaces 204036
total_area 65520.492188
group_avg_vtxarea_loaded 0
avgvtxarea 0.642232
avgvtxdist 0.940503
stdvtxdist 0.417776
vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote:
can you run mris_info on the output surfcae? And maybe send a
freeview snapshot of it (in 3d rendering mode)
On Wed, 6 May 2020, Ian wrote:
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Thanks Tim and Doug.
I have the files generating and loading properly
now, but I'm not convinced it's giving the output
I'm looking for.
I am trying to convert the "fsaverage" subject's
surface coordinates to my own subject's surface
space.
FSaverage's lh.white file is 5898808 bytes:
5898808 Apr 11 2013
/usr/local/freesurfer/subjects/fsaverage/surf/lh.white
After converting with this command:
mri_surf2surf --hemi lh --srcsubject fsaverage
--sval-xyz white --trgsubject fs_target --tval-xyz
{input_dir}/T1_nifti.nii.gz --trgsurfval
{output_dir}/registered_lh.white
My newly registered lh.white file is half the size:
3316997 May 6 10:41
/home/ian/cdm_registered_test/registered_lh.white
(and appears to have half the vertices accordingly.)
So this must be incorrect, or at least not my
intended purpose.
To try and be clear, I'm looking to get the position
of every vertex in fsaverage's surfaces "on" the
surface of my subject's surfaces. So if there's a
vertex at the peak of a particular sulcii on
fsaverage, I'm looking to find where the peak of
that sulcii is on my subject.
Thanks,
Ian
On 06/05/2020 09:08, Tim Schäfer wrote:
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Just a note: there should be no need to
convert to gifti, nibabel can read
the FreeSurer binary surface format
directly with
`nibabel.freesurfer.io.read_geometry()`.
The docs are here:
https://nipy.org/nibabel/reference/nibabel.freesurfer.html#nibabel.freesur
fer.io.read_geometry
Best,
Tim
On May 5, 2020 at 7:59 PM
"Douglas N. Greve"
<dgr...@mgh.harvard.edu>
wrote:
You should load the
surfaces in FV. If it load
in FV ok but nibable is
crashing, you should
contact them.
On 5/5/2020 1:05 PM, Ian
Hardingham wrote:
External
Email - Use
Caution
Thank you both.
I've made edits
and these are
the current
commands:
mri_surf2surf
--hemi lh
--srcsubject
fsaverage
--sval-xyz white
--trgsubject
fs_target
--tval-xyz
{input_dir}/T1_nifti.nii.gz
--trgsurfval
{output_dir}/registered_lh.white
mri_surf2surf
--hemi rh
--srcsubject
fsaverage
--sval-xyz white
--trgsubject
fs_target
--tval-xyz
{input_dir}/T1_nifti.nii.gz
--trgsurfval
{output_dir}/registered_rh.white
mri_surf2surf
--hemi lh
--srcsubject
fsaverage
--sval-xyz pial
--trgsubject
fs_target
--tval-xyz
{input_dir}/T1_nifti.nii.gz
--trgsurfval
{output_dir}/registered_lh.pial
mri_surf2surf
--hemi rh
--srcsubject
fsaverage
--sval-xyz pial
--trgsubject
fs_target
--tval-xyz
{input_dir}/T1_nifti.nii.gz
--trgsurfval
{output_dir}/registered_rh.pial
These execute
successfully and
the file size
looks about
right, but
after using
mris_convert to
convert to Gifti
format nibabel
crashes on
trying to load
them - is there
anything
obviously wrong
in my commands?
I'll also take
a look at
mris_apply_reg.
On 05/05/2020
18:01, Douglas
N. Greve wrote:
Don't
specify
a
--trg_type.
But
add
--tval-xyz
mris_apply_reg
will
do
the
same
thing,
but
the
interface
might
be a
little
easier
On
5/5/2020
12:49
PM,
Bruce
Fischl
wrote:
no
definitely
not
"w"
format,
which
we
don't
use
for
anything
anymore.
YOu
should
use
tval-xyz
also
I
think
On
Tue,
5
May
2020,
Ian
Hardingham
wrote:
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Email
-
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Caution
It
would
appear
not,
as
I'm
getting
an
error
on
my
pial
output
files
but
not
my
white
ones.
Here
are
my
commands:
mri_surf2surf
--hemi
lh
--srcsubject
fsaverage
--sval-xyz
white
--trgsubject
fs_target
--trgsurfval
./registered_lh.white
--trg_type
w
mri_surf2surf
--hemi
rh
--srcsubject
fsaverage
--sval-xyz
white
--trgsubject
fs_target
--trgsurfval
./registered_rh.white
--trg_type
w
mri_surf2surf
--hemi
lh
--srcsubject
fsaverage
--sval-xyz
pial
--trgsubject
fs_target
--trgsurfval
./registered_lh.pial
--trg_type
w
mri_surf2surf
--hemi
rh
--srcsubject
fsaverage
--sval-xyz
pial
--trgsubject
fs_target
--trgsurfval
./registered_rh.pial
--trg_type
w
The
white
calls
output
seems
to
be
fine,
but
the
pial
ones
aren't.
I
somewhat
naively
trued
trg_type
pial
but
that
wasn't
correct.
On
05/05/2020
17:33,
Ian
Hardingham
wrote:
Thanks
Bruce,
extremely
helpful.
Can
I
just
check
that
the
"w"
format
is
what
is
used
by
both
the
lh/rh.pial
and
the
lh/rh.white
files?
I
only
ask
because
my
surf2surf
command
outputs
the
exact
output
filename
if
the
end
is
".white",
but
if
it's
".pial"
it
outputs
".pial.w",
which
I
find
a
little
curious.
Ian
On
05/05/2020
16:34,
Bruce
Fischl
wrote:
yes,
check
out
options
like:
--sval-xyz
if
you
need
further
help
though
I'll
have
to
defer
to
Doug
:)
Bruce
On
Tue,
5
May
2020,
Ian
Hardingham
wrote:
External
Email
-
Use
Caution
Bruce,
I've
read
the
docs
on
mri_surf2surf
-
I
wish
to
get
surface
files
out
(again,
lh.pial,
rh.pial,
lh.white,
and
rh.white)
rather
than
values
for
something
such
as
thickness
-
is
there
an
option
for
mri_surf2surf
to
allow
this?
On
05/05/2020
14:43,
Bruce
Fischl
wrote:
Hi
Ian
you
can
use
mri_surf2surf
to
map
surfaces
between
subjects,
but
our
atlas
isn't
really
a
surface.
You
can
use
the
surfaces
in
the
fsaverage
dir,
but
they
are
meant
for
visualization
and
are
much
smoother
than
individuals
cheers
Bruce
On
Tue,
5
May
2020,
Ian
wrote:
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Email
-
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Caution
Hi
Freesurfers.
I
have
a
subject
S
with
recon-all
having
been
run
on
it.
I
have
the
subject-specific
surface
files
/surf/lh.pial,
rh.pial,
lh.white,
and
rh.white.
I
would
like
an
Atlas's
lh.pial,
rh.pial,
lh.white,
and
rh.white
in
subject
space.
Any
helpers
on
how
to
achieve
this?
Thanks,
Ian
--
Ian
Hardingham
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_______________________________________________
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_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu
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_______________________________________________
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mailing
list
Freesurfer@nmr.mgh.harvard.edu
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_______________________________________________
Freesurfer
mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent
Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe
University Frankfurt am Main,
Germany
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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