Hi John
Doug can say for sure, but I think you want to give it the switch
--sval-xyz so it knows to expect a surface not a scalar field over the
surface.
cheers
Bruce
On Wed, 7 Dec 2011, John Griffiths wrote:
[ Douglas and Dan - sending this again as I didn't sent it to the list
address before. Sorry. ]
Thanks guys.
When I run mri_info on the .mgz file I was using before it seems crash
(nothing happens, and have to press ctrl+c to get the console back). So I
suppose that partially explains mri_surf2surf not working. Not sure what's
going wrong there - the command I used was
mris_convert /work/imaging5/Freesurfer/CBU070282/surf/lh.pial
/home/jdg45/lh.pial_converted.mgz
For the original question - I was using a converted .mgz file because when I
just give it the path to the 'lh.pial' file in the same directory it says it
cant determine the file type -
mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval
/work/imaging5/Freesurfer/CBU070282/surf/lh.pial --tval
/home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282
Standard output:
ERROR: could not determine type of
/work/imaging5/Freesurfer/CBU070282/surf/lh.pial
Standard error:
Is there a .xxx suffix for those files I should be using?
Incidentally, the reason I'm doing this is that I want to downsample a
surface file; someone suggested to me to use mri_surf2surf with the
'trgicoorder' flag. Is this a good way to downsample a surface?
Thanks,
john
On 6 December 2011 19:02, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
surf2surf actually takes surface overlays (not surfaces
themselves) as input, and they can be in any format that FS
reads. The wiki is probably not up-to-date as those options are
ok.
doug
Daniel Wakeman wrote:
Hi John,
It seems weird that you are using .mgz files (this
suffix is for
volume files) with mri_surf2surf (whose inputs
should be surfaces).
Also, it seems that several of the options you are
trying I don't
believe exist at least according to the wiki (e.g.
-cortex -fwhm). Are
you sure you are using the right command?
D
On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths
<j.davidgriffi...@gmail.com> wrote:
Dear list,
I am having the following memory
allocation problem when running
mri_surf2surf. Can't find any mention of
this error on the list or the
internet - sorry if I've missed
anything.
mri_surf2surf --cortex --fwhm 5.0000
--hemi lh --sval
/home/jdg45/lh.pial_converted.mgz --tval
/home/jdg45/CBU070282_smoother_surf.mgz
--s CBU070282
Standard output:
srcsubject = CBU070282
srcval =
/home/jdg45/lh.pial_converted.mgz
srctype =
trgsubject = CBU070282
trgval =
/home/jdg45/CBU070282_smoother_surf.mgz
trgtype =
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi = lh
trghemi = lh
frame = 0
fwhm-in = 0
fwhm-out = 5
label-src = (null)
label-trg = lh.cortex.label
OKToRevFaceOrder = 1
Reading source surface reg
/work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg
Loading source data
Standard error:
MRIalloc: could not allocate 2032167524
slices
Cannot allocate memory
Return code: 254
Any suggestions?
Thanks,
john
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is
intended only for the person to whom it
is
addressed. If you believe this e-mail
was sent to you in error and the
e-mail
contains patient information, please
contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline .
If the e-mail was sent to you in
error
but does not contain patient
information, please contact the sender
and
properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
