This is well-known, and is even in the --help:

BUGS:

When the output format is paint, the output file must be specified with a partial path (eg, ./data-lh.w) or else the output will be written into the subject's anatomical directory.

On the other hand, if you have a relatively new version of surf2surf and tksurfer, you can just specify mgh as the output type:

mri_surf2surf ... --trgsurfval blah-lh.mgh ...

tksurfer ... -overlay blah-lh.mgh ...

Don Hagler wrote:

I should have mentioned that a simple workaround is to precede the trgsurfval with "./" to explicitly specify that it should be created in the current working directory.

...

From: "Don Hagler" dhaglerjr@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_surf2surf Date: Thu, 09 Feb 2006 14:35:38 -0800

Hi guys,

There seems to be a minor bug in mri_surf2surf when trg_type = w. If trgsurfval is given as a relative path name (e.g. no directory sepcified with intention to create in current working directory), the output file name can be prefixed by" lh." or "rh." and it can be put in the subjects surf directory. Being put in that directory only happens when trgsubject is not ico.

Don

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