Re: [Freesurfer] Question about cortical surface area

Hi, what's the reason that FS's default surface for measuring surface area is the white matter surface and not the pial surface? why isn't surface area measured on the intermediate surface (average of gray.and white which should be less biased by sulci and gyri, i think)? thanks, -joost > > > On

[Freesurfer] GM/WM volumes

Hello Freesurfer experts, Sorry for the repost, but I'm still hoping someone can answer our questions found below. We have generated a list of volumes, using asegstats2table (based on aseg.stats files). We want to compute total grey matter (including subcortical GM) and white matter volumes for ri

Re: [Freesurfer] Question about cortical surface area

Hi Joost, we provide both so you can have the flexibility to do what you want with them. The naming conventions are for historical reasons (we had a white matter representation before we had a pial one). cheers Bruce On Thu, 29 Apr 2010, j janssen wrote: > Hi, > > what's the reason that FS'

Re: [Freesurfer] converting dicom files into mgz, looking forward to some help, thank you!

Hi Changming, unpacksdcmdir only works with Siemens dicoms I think (that's what the "s" is for). Try giving mri_convert the name of *one* slice in the anatomical series as input. cheers Bruce On Thu, 29 Apr 2010, [gbk] ²ýÃ÷ wrote: Dear Freesurfers: i failed every time i tried to tran

[Freesurfer] How to find out which package of FSL is used by FreeSurfer

Hi, The FreeSurfer package is bundled with a subset of FSL. However, I think most of us also installed the full FSL package. The global variable FSL_DIR points to the directory of FSL. My question is if it is possible to read from recon-all log files which FSL package is used? Ed __

Re: [Freesurfer] converting dicom files into mgz, looking forward to some help, thank you!

you cannot use unpacksdcmdir to unpack GE dicom, it is only for siemens. Try using this script: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/dcmunpack you should be able to use it in the same way. doug wrote: Dear Freesurfers: i failed every time i tried to transform m

Re: [Freesurfer] How to find out which package of FSL is used by FreeSurfer

Look in scripts/recon-all.env doug Ed Gronenschild wrote: > Hi, > > The FreeSurfer package is bundled with a subset of FSL. > However, I think most of us also installed the full FSL package. > The global variable FSL_DIR points to the directory of FSL. > > My question is if it is possible to read

Re: [Freesurfer] How to find out which package of FSL is used by FreeSurfer

fsl is no longer distributed with freesurfer, with the exception of 'flirt', which is included in the freesurfer/bin dir. On Thu, 2010-04-29 at 11:49 -0400, Douglas N Greve wrote: > Look in scripts/recon-all.env > > doug > > Ed Gronenschild wrote: > > Hi, > > > > The FreeSurfer package is bundl

[Freesurfer] FMRI values at surface vertices?

Hi all, Sorry if this is a dumb question-is there any way to create a Matlab-readable (e.g. Text) file containing the fMRI values at each surface vertex of a painted surface? Please let me know if you have any idea! Thank you so much, Elise

Re: [Freesurfer] FMRI values at surface vertices?

Use mri_vol2surf to map your fmri to the surface, save it in either mgh format. Then use mri=MRIread('yourfile.mgh'). The pixel data are in the .vol field of the mri struct. doug Dickinson, Annelise (NIH/NIMH) [F] wrote: > Hi all, > > Sorry if this is a dumb question-is there any way to create a

Re: [Freesurfer] FMRI values at surface vertices?

Hi Elise, if you save the output of vol2surf in .mgz (or some other volume format like nifti) you can use either MRIread or load_mgh to read it into matlab. cheers, Bruce On Thu, 29 Apr 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote: > Hi all, > > Sorry if this is a dumb question-is there any