Re: [Freesurfer] Freesurfer 4.5 on Ubuntu 18.04 ?

External Email - Use Caution Hello Paulo, What is the location of the freesurfer license file (?), i.e., I would make sure the freesurfer license file is under $FREESURFER_HOME and then see if you get different results running the command. Even with the license file though, I’m

Re: [Freesurfer] Freesurfer analyses in MATLAB

sorry, I don't know what it is you are doing here. what are beta2 and X2? what is DV? what are you plotting against what? On 11/14/19 3:25 PM, cody samth wrote: > > External Email - Use Caution > > Hi I'm interested in running some analyses in matlab using freesurfer > commands. I'm

Re: [Freesurfer] mask for cortical thickness

Pass the mask you want to mri_glmfit with either --label or --mask (depending on your format). You can convert the aparc to labels using mri_annotation2label , then pick the label you want. In this case, you cannot use --cache as that has been computed using whole hemi. You can generate your

Re: [Freesurfer] Recon-all Error

This is something that is being triggered by use -3T. Is there a reason you are using that option? On 11/19/19 5:15 PM, Meena M. Makary wrote: > > External Email - Use Caution > > Hi, > > I have been getting this error with one of my subjects Recon-all. I am > attaching the recon-all

Re: [Freesurfer] Local Gyrification Index: freesurfer version

It has not changed (and is no longer supported) On 11/19/19 6:48 AM, Steve Petersen wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > What freesurfer version do you recommend to perform the local > gyrification index, version 6 or 6 development version? > > >

Re: [Freesurfer] Question about the input for longitudinal processing pipeline

I have not run images with contrast, but I think it should  work. Some people have tried to use the mp2rage UNI scan, but it often fails because of very bright voxels outside of the brain. If you can remove those (eg, skull stripping), then it might work. Alternatively, if you have a

Re: [Freesurfer] Fwd: surface group analysis with qdec

I responded to this a few days ago. Below is what I said The problem is that all of your class=0 subjects have a 0 duration meaning that you cannot compute a duration slope for this class. In this special case, you can run a different-offset, same-slope analysis with --fsgd dur.fsgd doss

Re: [Freesurfer] Volume (WM Parcellation) of RightCerebralCortex--Freesurfer 6.0

yes On 11/18/19 8:59 PM, An Lijun wrote: > > External Email - Use Caution > > Thanks for your reply! > You mean LeftCerebralCortex is actually lhCortex in aseg.stats, right? > > Best Regards, > An Lijun > > > Greve, Douglas N.,Ph.D. > 于2019年11月19日周二

[Freesurfer] mask for cortical thickness

External Email - Use CautionHi there, I would like to analyze clusterwise correction for multiple comparisons using masks (exsample; superior frontal cortex and middle frontal cortex).I know that "2spaces" means adjust p-values for two hemispheres as follow; mri_glmfit-sim --glmdir