[Freesurfer] Monte carlo simulation and permutation test

Dear Mr or Ms, How can I do Monte carlo simulation for multiple comparison correction? I also want to know about permutation test. could you tell me how to use them? yczhang - 雅虎邮箱，您的终生邮箱！___ Freesurfer ma

[Freesurfer] Monte carlo simulation for multiple comparison on a surface

Dear Mr or Ms, How can I do Monte carlo simulation for multiple comparison correction on a surface. which command should I launch? I also want to know about permutation test. could you tell me how to use them? yczhang - 雅虎邮箱，您的终生邮箱！

RE: [Freesurfer] Monte carlo simulation for multiple comparison on asurface

Hello You should start with the mriglm fit command Check out the wiki for more information, and sample commands (see 4.0) https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis cheers Cibu _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] mgh.harvard.edu] On Behalf Of Z

Re: [Freesurfer] segmentation region export

They are in aseg.mgz, you can extract them into a nifti file with mri_binarize --i aseg.mgz --match 251 --o CC_Posterior.nii 251 is the code for CC Posterior (found in $FREESURFER_HOME/FreeSurferColorLUT.txt) doug vin wrote: hi, I am trying to export segmented regions as NIFTI, and it wo

[Freesurfer] Image deidentification

Hi freesurfers, I have been unable to find a program/method to view the header file on some nifty files made from mri_convert with MPRAGE scans. I want to make sure the files we are creating do not have patient information in the headers. Is there an easy way to check this? Thanks. Best, Co

[Freesurfer] thickness measurement

Dear Group, in the lh.aparc.stats i can find this variables: SurfArea GrayVol ThickAvg MeanCurv GausCurv what is the difference between them? for the thickness is use the thick avg, right? thank you Asaf ___ Freesurfer mailing list Freesurfer@nmr.mg

Re: [Freesurfer] Image deidentification

nifti generally does not have the capability to save patient info. I might if the software that created it has a nifti extension (FreeSurfer does not, yet). There is a comment field in the nifti header, so it is possible it could be there, but unlikely (it would not be with a FreeSurfer program

[Freesurfer] segmentation region export

hi, I am trying to export segmented regions as NIFTI, and it works for the regions like Thalamus whole. But when freesurfer finished autorecon, than it showed lot of sub regions for example : Thalamic sub regions and also CC_Posterior, CC_Mid_Posterior, CC_central (CC= Corpus Callosum) and...Mid

Re: [Freesurfer] thickness measurement

SurfArea is the surface area of the parcellation in mm^2. GrayVol is the volume of gray matter in the parc (basically thickness time area) in mm^3 ThickAvg is the average thickness (use this for your thickness study) MeanCurv is the average mean curvature. GausCurv is the average gaussian cu

[Freesurfer] mri_ca_normalize

Hi, I am getting an error with the command: mri_ca_normalize -mask /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz -seg /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/cma_seg_noAA.mgz /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/nu.mgz -noatlas -noxform /Users/N

Re: [Freesurfer] mri_ca_normalize

Hi Nurunisa, for mri_ca_normalize all the options have to come before the mandatory parameters. cheers, Bruce On Tue, 4 Nov 2008, Nurunisa Neyzi wrote: Hi, I am getting an error with the command: mri_ca_normalize -mask /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz -seg /

Re: [Freesurfer] mri_ca_normalize

Nurunisa, For mri_ca_normalize, the flags must be the first args, like this: mri_ca_normalize -noatlas -noxform -mask ... otherwise the flags will be ignored if they are at the end of the command (which is bad, but thats the way this works for this bin). Nick On Tue, 2008-11-04 at 15:58 -0500