Re: [Freesurfer] Permission denied error with mri_surfcluster command

All the values are between 0 and 1, so I suspect this is a map of p-values, not a map of -log10(p). Is that right? If so, convert it to -log10(p) and rerun. You can do this in matlab with p = MRIread('rh_time.mgh'); sig = p; sig.vol = -log10(abs(p.vol)); MRIwrite(sig,'sig.mgh'); On 03/03/2016

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Can you send me rh_time_spval.mgh? On 03/01/2016 04:42 PM, Jennifer Legault wrote: > Hi Doug, > > Thank you for responding. I actually realized what was the matter (I > had specified the path for fsaverage which led to the error; this is > no longer an issue so long as I use "--subject

Re: [Freesurfer] Permission denied error with mri_surfcluster command

can you send your command line and terminal output? On 02/25/2016 01:52 PM, Jennifer Legault wrote: > Hi Douglas, > > Thank you for all your help. When I say "volume" I do mean the FS > thickness*area measure. I ran the mri_glmfit with --osgm and for the > FWHM received the value of .925737.

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Hi Douglas, Thank you for all your help. When I say "volume" I do mean the FS thickness*area measure. I ran the mri_glmfit with --osgm and for the FWHM received the value of .925737. Assuming that this rounds up to 1, I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Thank you for your response. Do I need to run the glm_fit-sim command to make the csd file? I feel this would be inappropriate for my data since I already ran the LME model. Second, is there an argument to make an output file that can be visualized via freeview? In other words, how can I view

Re: [Freesurfer] Permission denied error with mri_surfcluster command

On 02/11/2016 11:19 AM, Jennifer Legault wrote: > Thank you for your response. Do I need to run the glm_fit-sim command > to make the csd file? I feel this would be inappropriate for my data > since I already ran the LME model. No, look in $FREESURFER_HOME/average/mult-comp-cor/fsaverage.

Re: [Freesurfer] Permission denied error with mri_surfcluster command

That's very useful, thank you. In terms of FWHM, I am examining gray matter volume, not cortical thickness, and was previously instructed by Martin Reuter not to smooth these data. Do you think it would make sense then to just use the fwhm01? And in terms of the voxel-wise threshold, is there a

Re: [Freesurfer] Permission denied error with mri_surfcluster command

by "volume" do you mean a VBM-type analysis or do you mean the volume that comes out of FS (thickness*area)? If you are going to use a clusterwise correction, then you have to have a FWHM measurement. You can try analyzing it in mri_glmfit with --osgm just to get the FWHM out of it. You

Re: [Freesurfer] Permission denied error with mri_surfcluster command

I meant for the output files, so the --o in particular On 02/10/2016 01:47 PM, Jennifer Legault wrote: > Douglas, > > Thank you for your quick response. When I add --sd [path_location], I > get the following error: > Loading source values > mri_read(): couldn't determine type of file

[Freesurfer] Permission denied error with mri_surfcluster command

Dear experts, I am trying to use the cluster thresholding command for my freesurfer LME outputs as referred to here . Any feedback or comments would be greatly appreciated. I am aware that there have been permission denied

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Douglas, Thank you for your quick response. When I add --sd [path_location], I get the following error: Loading source values mri_read(): couldn't determine type of file [path_location]/rh_time_spval ERROR: could not read rh_time_spval as type Should I use another argument? Best, Jen On

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Thank you very much for your help! I still received a "cannot read file type" error when I only added the path to the output --o part, however when I also added the path to the input file, it worked! I do have one more question: Which argument can I add so that in my output file I see the

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Try specifying the full path to the output On 02/10/2016 12:59 PM, Jennifer Legault wrote: > Dear experts, > > I am trying to use the cluster thresholding command for my freesurfer > LME outputs as referred to here > . > Any

Re: [Freesurfer] Permission denied error with mri_surfcluster command

There is a (very long) command line on that page. Mainly you need a csd file. To get that you need the FWHM of your analysis, the voxel-wise threshold, and the sign of the contrast (or abs). Then the relevant output will be the --sum. You can run it with --help to get more info. On 2/10/16