Dear freesurfer users,
I am having a problem visualizing results using tksurfer using the following command: tksurfer fsaverage lh inflated -annot lh.MIR137_area.glmdir/MIR137_test/mc-z.abs.sig.ocn.annot -fthresh 2 -curv -gray &
Please also see the terminal output stating that the vertices do not have an annotation. I do not have much experience with freesurfer - is there a way to resolve this?
Thank you for your help!
Sinead
[kellys37@tcin-n01 Freesurfer_data]$ setting fthresh to 2.0000 subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /projects/pi-donoghug/HPC_11_00168/Freesurfer_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /projects/pi-donoghug/HPC_11_00168/Freesurfer_data checking for nofix files in 'inflated' Reading image info (/projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage) Reading /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz surfer: Reading header info from /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: curvature read: min=-0.673989 max=0.540227 reading colortable from annotation file... colortable with 12 entries read (originally none) Found embedded color table in annotation. 149719 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /home/support/tcin/apps/freesurfer/5.2.0/tktools/tksurfer.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_common.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_wrappers.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... %
what is the actual problem? Most of the vertices will not have an annotation because you are looking at an annotation of clusters from a statistical analysis. doug
On 7/31/13 9:46 AM, Sinead Kelly wrote:
Dear freesurfer users,
I am having a problem visualizing results using tksurfer using the following command: tksurfer fsaverage lh inflated -annot lh.MIR137_area.glmdir/MIR137_test/mc-z.abs.sig.ocn.annot -fthresh 2 -curv -gray &
Please also see the terminal output stating that the vertices do not have an annotation. I do not have much experience with freesurfer - is there a way to resolve this?
Thank you for your help!
Sinead
[kellys37@tcin-n01 Freesurfer_data]$ setting fthresh to 2.0000 subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /projects/pi-donoghug/HPC_11_00168/Freesurfer_data/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /projects/pi-donoghug/HPC_11_00168/Freesurfer_data checking for nofix files in 'inflated' Reading image info (/projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage) Reading /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz surfer: Reading header info from /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: curvature read: min=-0.673989 max=0.540227 reading colortable from annotation file... colortable with 12 entries read (originally none) Found embedded color table in annotation. 149719 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /home/support/tcin/apps/freesurfer/5.2.0/tktools/tksurfer.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_common.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_wrappers.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... %
-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8
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Douglas Greve -
Sinead Kelly