Re: [Freesurfer] problem with spmregister on mac

Hi Maryam, You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical. -Yuhong On Thu, Feb

Re: [Freesurfer] Variables meaning -White matter hypointensities vs. non-WM-hypointensities?

Hi San Jung, it's just a question of where they occur. The wm-hypos are dark white matter on a T1-weighted sequence, and the non-wm-hypos are the same in gray matter (e.g. the putamen) cheers Bruce On Thu, 3 Feb 2011, San Jung wrote: > Hi. > > I'm visiting researcher for Behavior neurology. >

Re: [Freesurfer] reconstruction question

Hi Evan how big is that defect? The topology correction complexity goes as the square of the convex hull of the largest defect, so fast for small ones but a long time for big ones. Usually big ones only occur if there is something seriously wrong though (e.g. skull attached to the white matter

[Freesurfer] reconstruction question

Hello, My name is Evan Luther and I have been working with Dr. David Ress at the University of Texas at Austin to create a high resolution (.7 mm) volume using FreeSurfer. In the last step of our data pipeline I enter the command: recon-all -segmentation -fill -tessellate -smooth1 -inflate1 -qsph

[Freesurfer] fsl tutorial data

anyone have it saved anywhere? ___ 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 you believe

[Freesurfer] Variables meaning -White matter hypointensities vs. non-WM-hypointensities?

Hi. I'm visiting researcher for Behavior neurology. I'm trying to compare pathology and MRI image data in ischemic vascular disease patients. In our group, there are a lot of image researchers and they already made MRI free surfer DATA. My PI advised me to use free surfer data for my study.

Re: [Freesurfer] Regression: Activation as a function of condition

The 1vFix for the altered paradigm looks like the something vs fix for the original, so that is good. To my eye, the 2vFix for the altered looks reasonable, but you're right that it's hard to tell. A better comparison is to compare 2vFix for the altered against something like 7v3 or 5v1. There

Re: [Freesurfer] Surface area interpretation confusion

Hi Jürgen, that can happen if the different parts of it are differentially scaled in the spherical warp. For example if an individual has a secondary fold that is uncommon in the atlas population. cheers Bruce On Thu, 3 Feb 2011, Jürgen Hänggi wrote: Dear FS experts Sorry, for reposting t