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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.freesurfer.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:
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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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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:
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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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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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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
Germany
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