Re: [Freesurfer] T1 white matter segmentation

Hi Mohamad it doesn't need to be an mprage, but it does need to be reasonably high resolution (no voxel dimension greater than about 1.5mm) and T1-weighted cheers Bruce On Tue, 21 Oct 2014, Alshikho, Mohamad J. wrote: > In this case if I don't have T1 MPRAGE can I use any other available T1 li

Re: [Freesurfer] Longitudinal prediction

Hi Alex, the parameter is a single number that happens to be measured at time 1 right, eg baseline age? Lets call that parameter 'A' for the discussion below. Also you have exactly 2 time points in all subjects? There is two alternatives: 1. Simple approach (2-stage-model): You compute the

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

How do I change the path so that it's reading from the label I made (Socialbrain) in lieu of the cortex? On Mon, Oct 20, 2014 at 5:42 PM, Thomas DeRamus wrote: > That one gives the following error: > > mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir > /media/rkbatch/gyrificati

Re: [Freesurfer] skewed CT viewed in tkregister2

Hi, no problem. I used the command "mri_convert" but I just checked the slice thickness on it, and it's has a thickness of 2. So that's probably the problem then? Sorry for all the issues, I thought this CT would work. Thanks, m From: freesurfer-boun...@

Re: [Freesurfer] Do not have 'recon edit' button! Please help!

Perhaps it is just clicking on the 'voxel edit button' and ticking 'recon editing' from that box? Will this be the same as the original 'Recon edit' button? On 20/10/2014 14:24, "Bruce Fischl" wrote: >Hi Areti > >what version of freeview are you using? >Bruce >On Mon, 20 Oct 2014, Smaragdi

Re: [Freesurfer] unpacksdcmdir

Run it with -help to get more info On 10/21/14 12:25 AM, Alshikho, Mohamad J. wrote: > Hi Doug, > I ran the following command line dcmunpack -scr in my > script and it gives me a list of the run/series. How can I save this list as > a log file. I tried to add the flag -targ and the flag -log b

[Freesurfer] Research Assistant Job: Northwestern Univ. Alzheimer's Disease Center (Chicago, IL)

Research Study Assistant job available at Northwestern University’s Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL. The research assistant will be responsible for analysis of neuroimaging datasets, in order to contribute to neuroscientific studies of normal aging and pathologi

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

I think you need to pass it --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor --label rh.SocialBrainMask doug On 10/21/2014 10:31 AM, Thomas DeRamus wrote: > How do I change the path so that it's reading from the label I made > (Socialbrain) in lieu of the cortex? > > On Mon, Oct

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

sorry it is --cache-label On 10/21/2014 12:40 PM, Thomas DeRamus wrote: > And if you remove it it just goes back to the "must specify sim" error. > > On Tue, Oct 21, 2014 at 11:39 AM, Thomas DeRamus > wrote: > > It says the label flag is unrecognized. > > mri_g

Re: [Freesurfer] mri_volcluster problems

It is more straightforward if you use -log10(p). If you want to do an unsigned test, then run it twice, once with pos and once with neg, then multiply the resulting cluster-wise p-values by 2. doug On 10/21/2014 02:11 AM, Joo Tan wrote: > > Hi > > > I have a few questions regarding the use of “

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

there are 3 args you have to give it: --cache-dir, --cache-label, and --cache (and the --glmdir as well) On 10/21/2014 12:52 PM, Thomas DeRamus wrote: > Those seem to be giving the "must specify sim" error as well I'm afraid. > > mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-label

Re: [Freesurfer] Longitudinal prediction

Dear Martin, thank you very much for your answer ! and thanks for all the details !- yes, we have exactly 2 time points in all subjects and the parameter is a single number. In qdec - it seems that qdec table has to include the parameter 'A' both at time 1 and at time 2 in order for "long_qdec_ta

Re: [Freesurfer] Longitudinal prediction

Hi Alex, you have to duplicate the parameter (it is basically fixed across time). If you put 0 for tp2, it will average the two values, which is not what you want. Otherwise I think it is the correct approach. Best, Martin On 10/21/2014 04:31 PM, Alex Hanganu wrote: Dear Martin, thank you