Re: [Freesurfer] version

If your OS is also 64bit, then you can use the x86_64 dist of freesurfer. You can confirm this by typing: uname -m and you should see: x86_64 4GB is plenty of RAM and 320GB is plenty of disk-space. Nick > Hi, > I want to use freesurfer to quantify cortical thickness, and I want > t

[Freesurfer] version

Hi, I want to use freesurfer to quantify cortical thickness, and I want to use the software under Linux fedora core 4. My computer's equipment is Quad-Core processor Intel Q6600, DDR2 memory 4GB, Sata2 disks 320G, GeFORCE8600. Which version do you recommend? i386? or x86_84? Thanks __

Re: [Freesurfer] mri_convert problem while unpacking functionals

I can unpack these without a problem locally. Nick is preparing a new minor stable release in which these fixes will be present. doug ps. If you just can't wait, you can get new versions of the following (linux) binaries mri_convert mri_parse_sdcmdir mri_probedicom here:ftp://surfer.nmr.mg

Re: [Freesurfer] mri_convert problem while unpacking functionals

Is this data on line here at the NMR center? Can you point me to it? Dan Dillon wrote: Dear FreeSurfers, Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line: unpacksdcmdir -src 07120620/ -targ . -generic -

[Freesurfer] mri_convert problem while unpacking functionals

Dear FreeSurfers, Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line: unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out We then modify the .out file from 1localizer ok 512 51

Re: [Freesurfer] conversion

You should be able to use mri_convert for this. mri_convert --in_type mgz --out_type analyze INPUT.mgz OUTPUT.img http://surfer.nmr.mgh.harvard.edu/fswiki/mri_5fconvert Thanks. Mithra. On Dec 10, 2007 2:54 PM, Anca-Larisa Sandu <[EMAIL PROTECTED]> wrote: > I have a question about conversion

Re: [Freesurfer] tkmedit-sess error

Can you try running it with: -volid orig.mgz let me know if that works doug anisha narula wrote: Hello, I am doing a retinotopy study, and when I view the slices using the sliceview-sess command I obtain activation in the regions desired. However, when I view results on the flattened patc

Re: [Freesurfer] conversion

mri_convert file.mgz file.img should do it cheers, Bruce On Mon, 10 Dec 2007, Anca-Larisa Sandu wrote: I have a question about conversions. Is it possible to convert a file with the extension ".mgz" from Freesurfer to a file with the extension ".img", which can be read for example in SPM? If i

Re: [Freesurfer] conversion

Try something like mri_convert orig.mgz orig.img Anca-Larisa Sandu wrote: I have a question about conversions. Is it possible to convert a file with the extension ".mgz" from Freesurfer to a file with the extension ".img", which can be read for example in SPM? If it is possible how should I do

[Freesurfer] conversion

I have a question about conversions. Is it possible to convert a file with the extension ".mgz" from Freesurfer to a file with the extension ".img", which can be read for example in SPM? If it is possible how should I do this conversion? Thank you in advance! Anca Sandu __

Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

Fantastic. Thanks for the speedy responses. Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota Nick Schmansky wrote: Jim, There is a way to insert special flags into the recon-all command stream for a particular binary. See the section 'E

Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

Jim, There is a way to insert special flags into the recon-all command stream for a particular binary. See the section 'EXPERT OPTIONS FILE' in recon-all --help. So you would create a file called expert.opts containing: mris_make_surfaces -fix_mtl and then add the string '-expert expert.opts'

Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

yes, although the white matter volume that comes from mris_wm_volume is affected by the aseg (since non-wm voxels that are interior to the ?h.white surface are removed from the volume calculation) cheers, Bruce On Mon, 10 Dec 2007, Chris Watson wrote: Hi, So if the volumes are estimated fro

Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

Hi, So if the volumes are estimated from the surfaces and not aseg.mgz, does this mean it is unnecessary to edit aseg.mgz? Or is it still necessary, but only for the subcortical structures? Is it best to make pial surface/wm.mgz edits and control points for grey and white matter, and aseg.mgz

Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

Hi Jim, yes, I think that should be fine Bruce On Mon, 10 Dec 2007, James N. Porter wrote: Hello Bruce- From the wiki, I gather that I would rerun recon-all from -finalsurfs onward, as that is the step that calls make_final_surfaces. In order to insert the fix_mtl flag I'll have to run that

Re: [Freesurfer] Surfaces, asegs, aparcs, Subcortical Structures

Hello Bruce- From the wiki, I gather that I would rerun recon-all from -finalsurfs onward, as that is the step that calls make_final_surfaces. In order to insert the fix_mtl flag I'll have to run that section via a separate command line outside of recon-all. Are there any other subsequent step

Re: [Freesurfer] ROI labels for geometry vertices

Hi Bruce, Thanks a lot! This one does work as described and provides me with information I need. -- Sergey Hi Sergey, here's read_annotation.m. It should also return the embedded colormap that's in the .annot file, including structure names. Not sure why it's not in your distribution. c

[Freesurfer] tkmedit-sess error

Hello, I am doing a retinotopy study, and when I view the slices using the sliceview-sess command I obtain activation in the regions desired. However, when I view results on the flattened patches, activation is messed up. I tried running the tkmedit-sess command. tkmedit-sess -analysis rtopy -cont