-----Original Message----- From: Kirk, Gregory Sent: Monday, January 23, 2006 4:25 PM To: 'Kevin Teich' Subject: RE: [Freesurfer] overlay thickness maps

Yes Kevin, im still a dum dum sometimes, as your comment I Looked it in shell window, and saw all was not well.

In response to Load-Overlay-> load lh.thickness from the subject surf/ Directory get errors

% surfer: needs at least 2 marked vertices % surfer: needs at least 2 marked vertices % surfer: needs at least 2 marked vertices % mri_read(): couldn't determine type of file /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/THORNTONH/sur f/lh.thickness surfer: couldn't load /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/THORNTONH/sur f/lh.thickness sclv_read_from_volume: error in MRIreadInfo.

The overlays that are loaded in the buckner are .mgz files and it does not seem happy with these

Doug Greve is the winner in our best suggestion category with

Another method is to use mri_surf2surf to to convert the curv file into an mgh file (run it with --help to see how to use it). Then just load the mgh file as an overlay (with "compute identity").

Which when applied with- and the output is-

[gkirk@Nuit surf]$ mri_surf2surf --hemi lh --srcsubject MASONO --srcsurfval thickness --src_type curv --trgsubject MASONO --trgsurfval lh.thickness.mgz --trg_type mgz srcsubject = MASONO srcval = thickness srctype = curv trgsubject = MASONO trgval = lh.thickness.mgz trgtype = mgz surfreg = sphere.reg hemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/MASONO/surf/l h.sphere.reg Loading source data Reading curvature file /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/MASONO/surf/l h.thickness INFO: trgsubject = srcsubject Saving target data Reshaping 2 (nvertices = 107662)

Gives .mgz files that surfer is happy to use as an overlay, and produces what looks like good Thickness maps.

Thanks all

Greg.

-----Original Message----- From: Kevin Teich [mailto:kteich@nmr.mgh.harvard.edu] Sent: Friday, December 23, 2005 5:33 PM To: Kirk, Gregory Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] overlay thickness maps

There are a couple things that could be wrong. Make sure that calculating an identity registration is the proper thing to be doing here. Doug can probably tell you more about this. Next, is the file actually loading? Make sure that the output to the shell doesn't have any errors, and that there's a new line in the label/value area with the overlay's name on it. Make sure that there are actually values in that line as you move the mouse aroudn over the surface. If there are, do View->Configure->Overlay and see if you can set the threshold so that it encompasses the values, as the default threshold might be incorrect.

On Fri, Dec 23, 2005 at 03:42:31PM -0500, Kirk, Gregory wrote:

I would like to overlay lh.thickness, rh.thickness on inflated for single subject, not the glm results, how to do that is well documented

from the tutorial/tutorial group study

tried tksurfer subject lh inflated - got the gray surface

next file->load overlay -> $SUBJECTS_DIR/subject/surf choose lh.thickness

• calculate identity map

it redraws the surface but there is no colormap of the thickness