Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

The 5.2 image has been smoothed, by a small degree, relative to 5.1. Either prior to FS processing or by FS, it would seem. On Mon, Apr 15, 2013 at 3:29 AM, Christopher Bell < christopherbell2...@gmail.com> wrote: > Looking at the image posted previously.

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

Looking at the image posted previously. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn I think it is pretty clear the 5.1 picture has better gray/white contrast. It is a very subtle difference, but you can see it if you look at some pieces of wm that were "missed" by 5.2 in this

Re: [Freesurfer] nu_correct: Command not found error

I have encountered this error in the past, and I think it was because I was not sourcing SetUpFreeSurfer.sh correctly. That is the the script that sets up the MNI_DIR I think. echo $MNI_DIR or whatever it is called and it should show you if it is being setup properly. It may be pointing to the sy

Re: [Freesurfer] parcellations to fmri space

2012 at 9:03 AM, Douglas N Greve wrote: > > Hi Chris, I don't think there is such a tool. One thing you can do is to > use the aparc+aseg.mgz as the source instead of the lh and rh surfaces > separately. This might solve all of your problems. > doug > > > On 07/0

Re: [Freesurfer] nu_correct problem

I believe this post slipped through the cracks. Anyone have any thoughts on this nu_correct error. Some subjects ran fine, so it seems to be an intermittent problem and not an installation problem. Also, is this possibly related to the avi_talairach/intensity normalization issues being discussed i

[Freesurfer] parcellations to fmri space

Hello Freesurfers, I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large v

[Freesurfer] wmparc

How much is the dilation (perpendicular to the cortical surface) for the creation of the white matter ROIs? Is there a citation for this? Chris Bell ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

[Freesurfer] bbregister

I have run a bunch of cases through bbregister and overall it worked great! 315 out of about 325 cases the alignments were very good, but on 10 subjects it did very poorly. I can not so far find anything unusual about this data. Per earlier posts, I have tried the different initilization options wi

[Freesurfer] freesurfer license file

How do I obtain a freesurfer license file? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If

Re: [Freesurfer] DODS and DOSS

demean (center) the age variable has a critical > impact on the manner in which you interpret the group contrast. > > cheers, > -MH > > On Thu, 2011-03-03 at 20:41 -0600, Christopher Bell wrote: > > FreeSurfers, > > > > I have been analyzing my qdec data in version

[Freesurfer] DODS and DOSS

FreeSurfers, I have been analyzing my qdec data in version 5.0 and have some interesting although somewhat confusing results. Basically I have run a very simple analysis with DODS and DOSS. My discrete factor is group and my covariate is age, about as simple as can be. When I look at the results