[ 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 <greve@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.davidgriffiths@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

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