[Freesurfer] qcache flag on recon-all

Dear FS experts, I have a beginner question so sorry if it is obvious for you... Is possible (and a good idea) to include the -qcache flag at the end in the recon-all -s /../ command? or I have to wait until recon-all had finished to run qcache? Many thanks -- Gonzalo Sánchez Benavides _

Re: [Freesurfer] Subcortical calabel errors

Hi Nick, The -bigventricles option gave me the same results anyway. Our machines are 4GB, and nothing else is processing. Marlisa > Marlisa, > > The -bigventricles flag is described in the recon-all -help output (in > v4.0.2, not sure about 401). You can try including it with the - > autorecon2

[Freesurfer] (no subject)

Hello, I'm wondering if surfaces need to be smoothed (and if running "recon-all -s SUBJECT -qcache" performs the smoothing) when analyzing data. Thank you. -Ryan McGarry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh

Re: [Freesurfer] qcache flag on recon-all

You can include the -qcache flag with any of the other flags (you dont have to wait until it has finished -all). On Mon, 2008-02-25 at 12:01 +0100, Gonzalo Sanchez Benavides wrote: > > Dear FS experts, I have a beginner question so sorry if it is obvious > for you... > > Is possible (and a good

Re: [Freesurfer] (no subject)

The -qcache option performs smoothing at 5, 10, 15, 20 and 25mm FWHM (plus 0mm, ie no smoothing). On the design tab in Qdec, there are selections for smoothing levels, and it will use the smoothed files produced by -qcache. On Mon, 2008-02-25 at 12:40 -0500, James Olkin wrote: > Hello, >I'm w

[Freesurfer] multiple runs and optseq

Hi, We had a question about multiple runs and optseq. If we compute our sequence as one long 12 minute run, then we get a sequence with a VRF around 25. But of course, that's too long and we would want to split it into two. If we calculate a run half as long, then we get a VRF around 10. If we

Re: [Freesurfer] (no subject)

And just to be clearer, qcache does not actually smooth the surfaces but the thickness values on the surface. There is no need to smooth the surfaces themselves. doug Nick Schmansky wrote: The -qcache option performs smoothing at 5, 10, 15, 20 and 25mm FWHM (plus 0mm, ie no smoothing). O

Re: [Freesurfer] multiple runs and optseq

Overall, it probably won't affect it much. The final VRF for combined runs will be greater than or equal to the sum of the VRFs for the individuals. doug Sheeba Arnold wrote: Hi, We had a question about multiple runs and optseq. If we compute our sequence as one long 12 minute run, the

Re: [Freesurfer] mri_surf2surf

Oh, I see the problem. It needs to have a registration surface to go from smhead to ico. You can't do what you want to do with mri_surf2surf (not sure what you can do). doug Daniel Wakeman wrote: It still doesn't work. The error message is the same as the one I previously sent. Am I d

[Freesurfer] changing tissue priors

Hello, I'm a beginning FS user, and I've been working on segmenting some atypical brains. A colleague has worked out grey/white/csf tissue priors for these subjects and I wanted to insert these into freesurfer before segmentation and parcellation. Does anyone know how freesurfer stores

[Freesurfer] Calling mri_convert from Java code

Hello: I need to call mri_convert utility from Java code. The problem is when I am making a system call, I am getting the following error : > FreeSurfer license file /Application/freesurfer/.license not found. If you are outside the NMR-Martinos center, go to http://surfer.nmr.mgh.harvard

Re: [Freesurfer] changing tissue priors

Hi David, there are different sets of priors we use. One is the .gca atlas, used for volume segmentation. You can use mri_ca_train to rebuild these if you really want to, although ideally you would have complete segmentations (including e.g. thalamus, caudate etc...). Then there are the cortic

Re: [Freesurfer] surface co-ordinates

Sorry, look at the power point slides just above that section, the ones here: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.pdf doug Mishkin Derakhshan wrote: On Wed, Feb 20, 2008 at 10:46 PM, Doug Greve <[EMAIL PROTECTED]> wrote:

[Freesurfer] inflation and registration to a sphere

Hi, After reading the wiki and the references on the wiki, specifically [1] and [2], I'm still a little confused about how the inflation and registration to a sphere occurs. ie. what energy functions are being minimized at each step. I think it is a 3 step process, where 1. Surfaces are inflated