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] 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] 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

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] Running mri_glmfit-sim with pre-computed Monte-Carlo

That one gives the following error: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cache 2 abs cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dod

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

you need to add --cache threshold sign (and don't use --sim-sign or --sim) On 10/20/2014 05:42 PM, Thomas DeRamus wrote: > It does not I'm afraid. The error I get says the following: > > mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir > /media/rkbatch/gyrification/fsaverage/mul

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

It does not I'm afraid. The error I get says the following: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces ERROR: must spec --sim Does the same if I remove the --sim-sign abs

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

You should not spec --sim. If you do not, does it work? doug On 10/20/2014 04:10 PM, Thomas DeRamus wrote: > I guess the better term would be to say that I'm not sure if the > cluster correction is using the monte-carlo I made from the label file > correctly. > > I see on the wiki and in the ma

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

I guess the better term would be to say that I'm not sure if the cluster correction is using the monte-carlo I made from the label file correctly. I see on the wiki and in the mailing list you can use a different directory and then spec that folder using mri_glmfit-sim with the --cache-dir flag. W

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

what do you mean it has trouble understanding? What is your command line and terminal output. Also, are you following these instructions? https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo On 10/20/2014 03:50 PM, Thomas DeRamus wrote: > Dear Freesurfer Experts, > > I have a label

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

Dear Freesurfer Experts, I have a label file of a number of ROI's I've made based on a mask. I'm trying to get an idea of what cluster are significant within a focused region of the label file. To make the correction a little less sever, I pre-computed some monte-carlo values using mri_mcsim mri