[Freesurfer] Problems converting SPM functionals to bshort

2007-06-19 Thread Lars Kuchinke
Hi all, is it possible to convert my functional SPM images (3d) to bshort (or bfloat) format using mri_convert? Is still get stucked here, since mri_convert only allows me to convert one image instead of the full time series... Is there an option to convert a list of old SPM 3d images? I'm a

Re: [Freesurfer] Problems converting SPM functionals to bshort

2007-06-19 Thread Doug Greve
An easy way is with mri_concat, something like: mri_concat yourspm*.img --o yourspm.bhdr why bfloat/bshort? If you want nifti: mri_concat yourspm*.img --o yourspm.nii doug On Tue, 19 Jun 2007, Lars Kuchinke wrote: Hi all, is it possible to convert my functional SPM images (3d) to bshor

Re: [Freesurfer] incorrect slice orientations

2007-06-19 Thread Catherine Hartley
Was the log file helpful? Sorry to be so persistent with this, but I'm leaving tomorrow for two weeks and was hoping to be able to run autorecon2 and 3 while I'm away, but as this is already causing problems in autorecon1 (bad talaraich reg), I don't think I should go any further until I c

[Freesurfer] Q: masking statistical overlays

2007-06-19 Thread raij
Dear Fellow Surfers, Is there a FreeSurfer way to mask a stat map overlay, on the inflated cortical surface, in a way that the masked vertex points (a) are transparent in the overlay display (just the underlying dark gray/light gray curvature is showing)? (b) do not effect label-specific HDR tim

Re: [Freesurfer] Q: masking statistical overlays

2007-06-19 Thread Bruce Fischl
Hi Tommi, the w-file format is sparse and doesn't have to cover the surface, but the .mgz does. Bruce On Tue, 19 Jun 2007 [EMAIL PROTECTED] wrote: Dear Fellow Surfers, Is there a FreeSurfer way to mask a stat map overlay, on the inflated cortical surface, in a way that the masked vertex po