[Freesurfer] Freesurfer Start Up

Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x

Re: [Freesurfer] Freesurfer Start Up

) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the

Re: [Freesurfer] Freesurfer Start Up

...@nmr.mgh.harvard.edu>> wrote: Hi Isaiah recon-all -i -s -sd -all should do the trick. should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inpu

Re: [Freesurfer] Freesurfer Start Up

, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files

Re: [Freesurfer] Freesurfer Start Up

mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Isaiah recon-all -i -s -sd -all should do the trick. should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried

Re: [Freesurfer] Freesurfer Start Up

to:fis...@nmr.mgh.harvard.edu>> wrote: Hi Isaiah recon-all -i -s -sd -all should do the trick. should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inpu

Re: [Freesurfer] Freesurfer Start Up

egmentations) > > cheers > Bruce > > On Thu, 31 Jul 2014, Isaiah C. Smith wrote: > >> Thank you so much, Bruce. I think that I got it. Overall, I am trying to >> create a source volume conduction model, calculate the lead field matrix, >> and then create a s

Re: [Freesurfer] Freesurfer Start Up

econ-all > > cheers > Bruce >> On Wed, 30 Jul 2014, Isaiah C. Smith wrote: >> >> The command is not found. >> Last login: Tue Jul 29 17:42:52 on ttys001 >> freesurfer-Darwin-lion-stable-pub-v5.3.0 >> Setting up environment for FreeSurfer

Re: [Freesurfer] Freesurfer Start Up

The files after recon-all > On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" > wrote: > > the format of what? >> On Thu, 31 Jul 2014, Isaiah C. Smith wrote: >> >> Thank you, >> I will go there now. But regarding the output of freesurfer, the format will

Re: [Freesurfer] Freesurfer Start Up

ls, parcellations, > etc...) >> On Thu, 31 Jul 2014, Isaiah C. Smith wrote: >> >> The files after recon-all >>> On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" >>> wrote: >>> >>> the format of what? >>>> On Thu, 31 Jul

Re: [Freesurfer] Freesurfer Start Up

Thanks Sent from my iPhone > On Jul 31, 2014, at 10:47 AM, "Bruce Fischl" > wrote: > > Hi Isaiah > > you should go through the tutorials on our website - they detail all this > information > > cheers > Bruce > > >> On Thu, 31 Jul 2014,

Re: [Freesurfer] Freesurfer Start Up

hu, 31 Jul 2014, Isaiah C. Smith wrote: Yes, how do i view the files and where can I find where every has been placed On Jul 31, 2014, at 8:26 AM, "Bruce Fischl" mailto:fis...@nmr.mgh.harvard.edu>> wrote: there are many, many files in many different formats (e.g. volumes in .mgz f

[Freesurfer] Freesurfer and MNE

I have the MRI data, but I am confused as to how to proceed with the mne_setup_mri for the brain, skull and scalp volume conduction models because the brain and T1 are the defaults. Do I need to add some other slices? And does the subject data need to be placed in /freesurfer/subjects for it to

[Freesurfer] Flaws in my segmentation

Hello, There is some flaw in my segmentation that is not allowing me to change produce a mesh in MNE. How do I fix the segmentation in freesurfer so that skull surfaces do not overlap? Isaiah (Error Shown Below) Checking that inner skull surface is inside outer skull surface...[failed] Surface

[Freesurfer] Output Time

Hello Experts, I was wondering if there is a way to short time of recon-all; I see that by using some of the parameters, one can get rid of different outputs. For mne forward models and inverses is there a recommended list of necessary and unnecessary outputs? Isaiah Smith