Hi Kevin, Apologies for the delay. The output is below.Is it not assiging enough vertices to the label after it has been saved in tkmedit?
tksurfer 1000027 lh smoothwm surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/flanders/work/alex/freesurfer/subjects surfer: /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info INFO: Src volume /tmp/mritotal_17663/orig_8_dxyz.mnc INFO: Target volume /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. DimSizes: 3, 86, 110, 68, 1 DataType: 1 MINC Linear Transform 2.0000 0.0000 0.0000 -86.0950 0.0000 2.0000 0.0000 -126.5100 0.0000 0.0000 2.0000 -58.2500 0.0000 0.0000 0.0000 1.0000 Done reading minc surfer: vertices=148018, faces=296032 surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Using /usr/local/freesurfer/lib/Linux/libtclfsgdf.so Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % 1199 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label...
-----Original Message----- From: Kevin Teich [mailto:kteich@nmr.mgh.harvard.edu] Sent: Fri 8/12/2005 7:56 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Editing labels The internal representation of the label format is treated differently between tkmedit and tksurfer. Labels are lists of RAS coords. When you load one into tkmedit, it converts each RAS coord to a voxel index for its internal data structure. When you save it out, it converts the voxel index to an RAS coord, but this can be different than the original RAS coord because it is always the corner of the voxel, where as the original point can be anywhere inside the voxel. However, when tksurfer loads the label, even though the RAS coords in the label don't match exactly with the RAS coords of the surface vertices, it should find the closest vertex coord for each RAS coord, and add that to the label.
Can you send the output that tksurfer makes to the shell when you load a label that becomes fragmented like this?
On Thu, 11 Aug 2005, Fornito, Alexander wrote:
Hi Kevin, It shouldn't. I created the labels by the doing the following: 1 - manully raced an ROI using another program (Analyze) in volume space and saved the ROI as a greyscale mask in analyze format 2 - used mri_convert to convert both the original T1 and ROI to COR format. 3 - Generated the surface of the T1 and loaded the ROI as an overlay in tksurfer 4 - Filled the overlay using custom fill and saved it as a label.
I'm not sure how I would check the image dimensions of the label, but I assume step 2 would have put it into 1mm3, which would then convert to 1mm2 when projected onto the surface (?).
-----Original Message----- From: Kevin Teich [mailto:kteich@nmr.mgh.harvard.edu] Sent: Thu 8/11/2005 5:18 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Editing labels
I've been trying to edit some labels in tkmedit and have noticed that if I save a label in tkmedit and then project it back onto the surface in tksurfer, it appears fragmented (ie., speckled). This happens even if I save a label that was created in tksurfer in tkmedit without even editing it (ie., create label in tksurfer, load it in tkmedit, save it in tkmedit (without editing), and then load it back in tksurfer). I don't understand why this should happen, particulalry in the latter case, as the label should remain unchanged. Can anyone explain why this might happen? Thanks, Alex
Does your data have a voxel resolution different than 1mm squared?