[Freesurfer] some questions about thickness map

Hi, I want to know the what the thickness map represents. As Bruce said in 'measuring the thickness of human cerebral cortex from magnetic resonance images', page 1, paragraph 6, 'The distance between these two surfaces then gives the thickness of the cortical gray matter at any

Re: [Freesurfer] howto cut canonical occipital patches?

Hi Sebastien, the canonical occipital patch doesn't contain STS, and probably not FFA either. The whole-hemi patch does, but requires more cuts. Bruce On Fri, 7 Jul 2006, Sebastian Moeller wrote: Hi All, I recently finished the surface transform of my first human brain with freesurfer.

Re: [Freesurfer] howto cut canonical occipital patches?

someone else may have done it, but I haven't. When you make your cuts think about if you were trying to physcially flatten the surface and whether you could do it without tears. If not, then you need to introduce addtional cuts, otherwise you'll get lots of distortion in the flattening.

Re: [Freesurfer] mri_convert: dicom to nifti 4D

Hi Adam, I've created a new version of mri_convert which should hangle multi-frame GE dicom data properly. You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert Run it as you would ordinarily, but add -dicomread2 to the cmd line. I want to

[Freesurfer] recon-all exited with errors

Hi, I came across an error in the third stage of reconstruction using freesurfer. The images,scripts etc are at space/megraid/42/ACE/PILOTDATA/DATA_PROCESS The recon log says that recon-all exited with errors and stopped at Surf Reg rh. I am a new user and was hoping that you could help me out

Re: [Freesurfer] recon-all exited with errors

hmm, not sure what's going on here as your orig is newer than your inflated, which it shouldn't be: ls -lrt rh.* -rw-rw-r-- 1 nandita nandita 3202384 Jun 29 15:53 rh.orig.nofix -rw-rw-r-- 1 nandita nandita 3202704 Jun 29 15:53 rh.smoothwm.nofix -rw-rw-r-- 1 nandita nandita 3203048 Jun 29

[Freesurfer] dependency issue for tk related binaries

In testing: $ /usr/local/freesurfer/bin/tkmedit /usr/local/freesurfer/bin/tkmedit: error while loading shared libraries: libtix8.1.8.3.so: cannot open shared object file: No such file or directory $ sudo rpm -Uvh glut-3.7-12.i386.rpm itcl-3.2-88.i386.rpm tix-8.1.4-88.i386.rpm

Re: [Freesurfer] dependency issue for tk related binaries

Patrice, The freesurfer installation includes tcl/tk/tix/blt and gsl, in the $FREESURFER_HOME/libs directory, and the setup script, $FREESURFER_HOME/SetUpFreeSurfer.csh, will setup the paths to these. What is the output when you type: source $FREESURFER_HOME/SetUpFreeSurfer.csh and what