[Freesurfer] intrasubject segmentation variance

Dear freesurfers, i was running Freesurfer on the same subject on two independent Computers. The first Computer PC1has 2 physical Intel processors with 2 logical each - (dual core) - 1.6GHz with 4Gb Ram and the second PC2 has 2 physical Intel processors with 4 logical - (quad core) - 3 GHz with

RE: [Freesurfer] intrasubject segmentation variance

Thomas, There are some comments on your question. Freesurfer is not multithreaded so it won't benefit from multicore unless you start one analysis on each core. Your running times are high. My Opteron usually takes 23 hs to perform the recon-all in 3.0.5 version of FreeSurfer. One issue

[Freesurfer] WMparc step command line

could someone send me the command line for the last step in recon3 stream. The new version differs from the wiki table and I need to run just that last WMParc step. Thanks Amy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.m

Re: [Freesurfer] WMparc step command line

recon-all -wmparc -s subject Amy DeLuca wrote: could someone send me the command line for the last step in recon3 stream. The new version differs from the wiki table and I need to run just that last WMParc step. Thanks Amy ___ Freesurfer mailing lis

[Freesurfer] About tissue probability maps from aseg.mgz

Dear surfers, I want to ask whether it is possible to have a tissue probability map of the brain according to aseg.mgz. If I am not wrong aseg.mgz is the MAP estimate of a Markov Random Field based segmentation hence we shall get the probability maps for each label or tissue. Is it possible?

Re: [Freesurfer] About tissue probability maps from aseg.mgz

Hi Burak, I think if you give mri_ca_label the cmdline option -write_probs it will write out the label p values at each iteration of the ICM alorithm. Note that these are not real probabilities, but monotonically related to them. It's also pretty old code that I wrote for debugging and haven'

Re: [Freesurfer] intrasubject segmentation variance

Hi Pedro, thanks for your reply. I think, the MPRAGE data is ok with 1mm³ isotropic voxelsize aquired on a Trio system. The orientation is probably a problem because i just feed the images the way they come from the scanner direct into freesurfer. Even that freesurfer is not multithreaded, the h

Re: [Freesurfer] intrasubject segmentation variance

Thomas, There is some variability in freesurfer results due to the use of a random number generator in some algorithms. This can be eliminated by adding the -norandomness flag to recon-all, which is what is done for our testing to ensure that recon-all produces the same results from build-to-buil

[Freesurfer] Create thickness map

Hello, Is it possible to create a thickness map and use functional image's value to replace thickness value? Thanks, Ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Create thickness map

sorry, can you explain what you are trying to do? If it's just a functional overlay you can certainly do this with mri_vol2surf. cheers, Bruce On Mon, 22 Oct 2007, lan lin wrote: Hello, Is it possible to create a thickness map and use functional image's value to replace thickness value? T