[ 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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