Re: [Freesurfer] surface arithmetic?

Yea, just run mris_preproc on both subjects. There are even some options there for computing paired differences (simple differences or differences relative to the mean, etc) On 8/7/18 6:10 PM, Rockers, Elijah D. wrote: External Email - Use Caution Hello, I have a subject with two M

Re: [Freesurfer] WM segmentation

External Email - Use Caution I would add that a properly eroded WM mask is not very effective for fMRI denoising at least relative to spatial and temporal ICA-based denoising. An uneroded mask behaves similarly to global signal regression, which removes both global noise and global

[Freesurfer] surface arithmetic?

External Email - Use Caution Hello, I have a subject with two MRIs and surface reconstructions, several years apart. I would like to directly compare these surfaces if possible, for instance, to subtract (new - old) to see a "difference surface" or something similar. Is there

Re: [Freesurfer] WM segmentation

1. You can dig up our old 1999 recon papers if you are really interested. Lots of segmentation techniques are not probabilistic. 2. Again, we don't output probabilities. YOu are better off eroding as Matt suggested. 3. mris_fill fills the interior of a surface - nothing to do with mri_fill.

Re: [Freesurfer] WM segmentation

External Email - Use Caution Hi Bruce, Thank you very much for your reply. The idea is to create a WM mask that I can use for the denoising step of resting state connectivity analysis. Do you mind if I ask you a few follow up questions? 1 - "our primary cortical segmentation of t

Re: [Freesurfer] Lobe parcellation without cingulate from --lobesStrict

External Email - Use Caution Dear Douglas, thank you very much. I've already done the first mri_annotation2label. Now I should go to the mri_mergelabels step, which I am trying to do with the following code: *mri_mergelabels -i PRI002/label/lh.superiorfrontal -i PRI002/label/lh.r

Re: [Freesurfer] mris_register segmentation fault while running recon-all with -cm option on a scan with .6mm isotropic voxels

Hi Francois, this is an mris_register bug from last month that should be fixed in the most recent dev distribution. best, Andrew From: on behalf of "Lalonde, Francois (NIH/NIMH) [E]" Reply-To: FS Help Date: Tuesday, August 7, 2018 at 2:33 PM To: FS Help Subject: [Freesurfer] mris_register s

Re: [Freesurfer] XL Defect Detected

Hi Alex you have to identify what is causing it first. There should be an overlay named ?h.defect_labels that you can load on the ?h.inflated.nofiex surface to find defect 31, then go into the volume and see what is causing it (skull attached, etc...) cheers Bruce On Tue, 7 Aug 2018, Rockh

Re: [Freesurfer] WM segmentation

Hi Ben our primary cortical segmentation of the wm is not probabilistic. In any case you want partial volume fractions I expect, not posterior probabilities. I would use mris_fill to create a mask of the WM from the ?h.white surfaces, if you want the most accuracy cheers Bruce On Tue, 7 Au

Re: [Freesurfer] wm.mgz values

Hi Aaron they are various wm.mgz voxel values that get set based on different filters/topological considerations. cheers Bruce On Mon, 6 Aug 2018, Aaron Tanenbaum wrote: External Email - Use Caution Hello Freesurfers. I was wondering of for the purposes of editing wm.mg

Re: [Freesurfer] -- check skull stripping No such file or directory

Hi Renew have you checked that the inputs are reasonable? If you want us to take a look put it on our ftp site cheers Bruce On Mon, 6 Aug 2018, Renew Andrade wrote: External Email - Use Caution Dear Community! I have an issue with recon-all in this subject. Below is the ter

Re: [Freesurfer] Origin of freesusrfer output

External Email - Use Caution Thanks Doug, For your kind detailed replies. This is really great help. - Original Message - From: "Douglas Greve" To: "freesurfer" Sent: Tuesday, August 7, 2018 9:01:01 PM Subject: Re: [Freesurfer] Origin of freesusrfer output On 8/7/18 1:4

Re: [Freesurfer] Origin of freesusrfer output

On 8/7/18 1:45 AM, Ritesh Mahajan wrote: > External Email - Use Caution > > Hi Doug, > > I checked the link you suggested. What i understood from this is the origin > shift(physical co-ordinate of first voxel) is happening due to the rotation > of axis to RAS co-ordinate system. To cou

[Freesurfer] XL Defect Detected

Hi all, I am running recon-all and the command is stuck on the output CORRECTING DEFECT 31 (vertices=8161, convex hull=3290, v0=29848) XL defect detected... It has been on that step overnight. Is there some way to ignore the defect or correct it without taking so long? This is using