[Freesurfer] mri_convert and nifti

I have just discovered a small bug in the NIFTI reader in FreeSurfer. The bug caused the sform/qfrom matrix to be slightly off for oblique volumes that are non-isotropic (the more oblique and the more non-isotropic, the worse). Part of the error involves the matrix being slightly non-orthogon

Re: [Freesurfer] statistical power analysis

I guess the easiest way is to save the output cluster number (--ocn option to mri_surfcluster), then create a segmentation lookup table (like FreeSurferColorLUT.txt), one row for each of your clusters. Then run mri_segstats, passing the ocn as the --seg, your new color table as --ctab, the mr

[Freesurfer] statistical power analysis

Hello all, I have just completed a group analysis of cortical thickness, including running the full Monte Carlo simulation to obtain cluster-wise multiple comparison corrections. Now I would like to know, for the clusters I'm interested in, how best to go about doing a statistical power analysis

Re: [Freesurfer] talairach registration

Cameron, If a bad talairach alignment prevents the creation of the surfaces (the files in the subjects surf directory), then just exclude the '--surf orig' flag from the tkregister2 cmd line. Use the 'Compare' button to switch between the template (the blurry image) and your subject. It is a lot

Re: [Freesurfer] talairach registration

Does the lh.orig surface exist for that subject? Cameron Ellis wrote: Hi, Hopefully this is something simple. When I try to check the talairach transform for my subjects I type: tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig and then I get this error: subject = SM1C2_autorecona

[Freesurfer] talairach registration

Hi, Hopefully this is something simple. When I try to check the talairach transform for my subjects I type: tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig and then I get this error: subject = SM1C2_autoreconall Reading lh surface orig MRISread(/space/troy/3/users/retrievalnewest/SM

Re: [Freesurfer] ca normalize

Don, I've received the input data that you sent me which is failing the mri_ca_normalize step for you. It appears that this data fails the skull-strip step, as the brainmask.mgz is very wrong (large sections of brain are missing). In general, it is always a good idea to check the brainmask.mgz f

Re: [Freesurfer] ca normalize

actually you should check the talairach, which I think is why the skull stripping is failing (in fact the intensity normalization failed because of the talairach problem, which caused everything afterwards to fail) On Mon, 8 Jan 2007, Nick Schmansky wrote: Don, I've received the input data t

Re: [Freesurfer] Flag: -subjectid unrecognized

Hi Chunchun, please look at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting and gives all the information it asks for, and then we can help you out. thanks doug Chunchun Ni wrote: hi, I converted one analyze file to MGZ format, then try use the recon-all -autorecon-all -subjid bert (replac

[Freesurfer] Flag: -subjectid unrecognized

hi, I converted one analyze file to MGZ format, then try use the recon-all -autorecon-all -subjid bert (replace subjectid by myid ), but the command run nothing but Flag: -subjectid unrecognized. Anybody has some idea how to fix it? Thanks for any help! Chunchun _