RE: [Freesurfer] mri_watershed -> BEM surfaces problem

matlab's reducepatch Date: Thu, 10 Apr 2008 10:39:37 -0700 From: [EMAIL PROTECTED] To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed -> BEM surfaces problem P.S. Also, I was wondering if there is a utility to reduce the number of vertices of a given surface (i.e. to make a le

Re: [Freesurfer] Interactions for continuous variables

I think the problem is that the last line is a blank line. Remove that and retry. doug Jerry Yeou-Wei Chen wrote: I am getting the following error when I run mri_glmfit with my custom design matrix: WARNING: matlab elment type is 940126218, which is not a matrix. could not allocate 82268570

Re: [Freesurfer] Interactions for continuous variables

I am getting the following error when I run mri_glmfit with my custom design matrix: WARNING: matlab elment type is 940126218, which is not a matrix. could not allocate 822685706 x 805908489 matrix Cannot allocate memory unsupported matlab format -849662976 (unknown) Cannot allocate memory Belo

Re: [Freesurfer] wmparc creation

Does the "mri" dir exist in the directory that you are running it from? joel bruss wrote: Hello- I ran recon-all and it reported that everything ran with no errors but, when I go into mri, there is no wmparc.mgz file. I tried running: mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --ri

[Freesurfer] wmparc

I'll try this again as I'm stuck and in need of help. I ran recon-all and it reported that everything ran with no errors but, when I go into mri, there is no wmparc.mgz file. I tried running: mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg

Re: [Freesurfer] Black digits and black background

Juergen and Scott, I found and fixed the source of this bug this afternoon. I've posted an updated tksurfer.bin for the Intel Mac Leopard here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/macintel Copy it to your $FREESURFER_HOME/bin directory, and type: chmod a+x $FREES

Re: [Freesurfer] Mean Centering

You can enter mean-centered (demeaned) values into the fsgd, but be aware that this is something that you usually do not want to do (though maybe ok for an interaction term?). Below is something I posted a few weeks ago on this subject. doug The important idea here is the difference between c

[Freesurfer] applying a transform to volumes + surfaces?

Hi Freesurfers- Apologies for my recent multitude of questions (and big thanks for Bruce and colleagues for all their fabulous troubleshooting!). But I was wondering about applying transforms to my freesurfer data. I know this was asked on the listserv re: transformation on other dataset, but I t

[Freesurfer] mri_watershed -> BEM surfaces problem

Hi, In order to get the three BEMs for 3D source reconstruction for subject X, I used: mri_watershed -atlas -useSRAS -surf X/bem/watershed/X X/mri/T1.mgz X/bem/watershed/ws which created the BEMs in X/bem/watershed/, but the inner_skull and the brain were significantly dis

[Freesurfer] wmparc creation

Hello- I ran recon-all and it reported that everything ran with no errors but, when I go into mri, there is no wmparc.mgz file. I tried running: mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz and all was running well until it

Re: [Freesurfer] Black digits and black background

i had the same problem on ubuntu after i upgraded to the latest drivers on my ati video card. i could only get proper white labels by switching to an older driver, which wasn't a good solution for other reasons. i switched to an nvidia card and this resolved the issue. Juergen Haenggi wrote:

[Freesurfer] Mean Centering

Hello, Are regressors mean centered for mri_glmfit? Judging by one of my previous Xg.dat files, it does not appear so. If not, I plan to manually enter my design matrix, with mean centered regressors. Do I need to enter the corresponding values in the FSGD file as mean centered? or can they remai

Re: [Freesurfer] Interactions for continuous variables

Thanks for the clarification, Doug. The Wiki page for mri_glmfit says to "Specify the design matrix in matlab4 format." - Jerry On Wed, Apr 9, 2008 at 5:19 PM, Doug Greve <[EMAIL PROTECTED]> wrote: > > >From mri_glmflit --help : > > --X design matrix file > > Explicitly specify the design matrix

[Freesurfer] Black digits and black background

Dear FS experts When loading a thickness map in FS 4.0.3 for MacOS X Leopard the thickness values of the colour scale bar are not visible because they are printed in black like the background. How can I change the colour of these mm values from black to white? Thanks in advance Best regards Juer