[Freesurfer] Problem with mri_glmfit

Dear FreeSurfer experts, I have a problem with mri_glmfit. I am using the following script: mri_glmfit \ --y lh.AspergerStudy.thickness.10.mgh \ --fsgd FSGD/AspergerStudy.fsgd dods \ --C Contrasts/AS-HC.mtx \ --C Contrasts/HC-AS.mtx \ --surf fsaverage lh

Re: [Freesurfer] LME univariate data

Dear Kersten, I have a question about LME model. After I acquired p value, could I know which group is bigger? Thanks, Lanbo On Fri, Mar 16, 2018 at 12:13 AM, lanbo Wang wrote: > Dear Kersten, > > Thanks a lot, it's really help. I have another question, after I got > results that two group hav

[Freesurfer] tkmedit: no tools window

Hi, When I launch tkmedit, I only get the "Display" window with no "Tools" window so I don't have any menus (I wanted to overlay a label file -- not sure how I do that from the command line either). I don't see any errors in the terminal from where I launch tkmedit -

[Freesurfer] convert labels to volume in MNI?

Hi, Newbie questionI want to take FreeSurfer labels (from an atlas in fsaverage space) and convert it into a volumetric NIFTI mask. I ran the following command, but I must be missing something because the output is not in the right space (far too posterior): $FREESURFER_HOME/bin/mri_label

Re: [Freesurfer] tkmedit: no tools window

Hi Gina tkmedit has been deprecated for many years. Can you try using freeview instead? cheers Bruce On Tue, 27 Mar 2018, gj wrote: > Hi, > > When I launch tkmedit, I only get the "Display" window with no "Tools" > window so I don't have any menus (I wanted to overlay a label file -- > not sur

Re: [Freesurfer] Problem with mri_glmfit

My guess is that you have a rogue white space after the backslash in "dods \". Try putting the entire command on one line without backslashs On 3/27/18 6:29 AM, Naiara Aguirre Vidal wrote: Dear FreeSurfer experts, I have a problem with mri_glmfit. I am using the following script: mri_glmfit \

Re: [Freesurfer] convert labels to volume in MNI?

how are you verifying that it is not in the right place? You should view it on the 2mm MNI152 using freeview. Also, your label should be a label in fsaverage space. On 3/27/18 9:52 AM, gj wrote: > Hi, > > Newbie questionI want to take FreeSurfer labels (from an atlas in > fsaverage space) a

[Freesurfer] Custom color map in Freeview

Hi all, I’m wondering whether there’s a way to create a custom color map in Freeview that would operate as a alternative to the preset Greyscale, Heatmap, NIH, PET, Jet and GE Color options. Ideally, I could assign each number value a given color, e.g. every “0” value in an .nii file is black,

Re: [Freesurfer] Custom color map in Freeview

It looks like a customized look up table will work for your case. You can simply select "Lookup table" as the colormap and load your own lookup table. To create your own look up table, you can refer to the content of FreeSurferColorLUT.txt file in your freesurfer installation directory. Best,

[Freesurfer] Brain volumetry: vessels

Good morning! I want to ask what type of brain vessels include structure "vessel" (left and right) in result stats file from brain volumetry measurement by freesurfer: artery, vein or booth? Thank You very much! patrik krumpolec ___ Freesurfer mailing l