[Freesurfer] volume registration; volume connections;

2017-09-04 Thread Daniel van de Velden
Dear Freesurfer-Team, I am trying to study volume based neuronal activities via a Spatio Temporal Clustering Test. Therefore I need to morph my subjects to an average subject. I couldn't find a non-linear morphing command to perform this. Is there any function and can I extract to resulting

Re: [Freesurfer] Pial surface volume

2017-09-04 Thread Bruce Fischl
sure, mris_volume will give you the interior volume of any closed surface using the divergence formula. Note that this is *not* the volume of the ribbon but rather the volume of the entire interior cheers Bruce On Mon, 4 Sep 2017, Fereshte wrote: Hello FreeSurfer developersIs it possible to

Re: [Freesurfer] volume registration; volume connections;

2017-09-04 Thread Bruce Fischl
Hi Daniel yes, CVS can extend the nonlinear surface warp into the volume cheers Bruce On Mon, 4 Sep 2017, Daniel van de Velden wrote: Dear Freesurfer-Team, I am trying to study volume based neuronal activities via a Spatio Temporal Clustering Test. Therefore I need to morph my subjects to

Re: [Freesurfer] volume registration; volume connections;

2017-09-04 Thread Daniel van de Velden
Dear Bruce, thanks for your reply. Since the documentation of the output of this function is poor, could you tell me what resulting files I can expect by performing CVS? Also my other question: Since the connectivity between vertices can be read from ?h.sphere.reg, is this also possible to get t

Re: [Freesurfer] Cerebellum Segmentation

2017-09-04 Thread Bruce Fischl
hmmm, not much gray/white contrast in the cerebellum. Can you send me the aseg.presurf.mgz also? On Mon, 4 Sep 2017, José Gómez-Feria Ferreiro wrote: Hello Bruce, Thank you for your email. I understand the issue about distinguishing between grey and white matter. However, I can get a nice seg

Re: [Freesurfer] Cerebellum Segmentation

2017-09-04 Thread Bruce Fischl
that looks to me like it accurately segmented all the un-partial-volumed white matter in the cerebellum. Are you hoping it would segment the smaller folia as wm? I guess it could, but those voxels all look like they have gm in them too On Mon, 4 Sep 2017, José Gómez-Feria Ferreiro wrote: H

Re: [Freesurfer] Pial surface volume

2017-09-04 Thread Fereshte
Using the Pial surface; Does it mean mris_volume will give the inner cortical boundary of the surface and not the outer boundary? Sincerely, Fereshte Ramezani On Mon, Sep 4, 2017 at 9:53 PM Fereshte wrote: > > On Mon, Sep 4, 2017 at 6:46 PM Bruce Fischl > wrote: > >> sure, mris_volume will give

Re: [Freesurfer] Pial surface volume

2017-09-04 Thread Bruce Fischl
it will give the interior volume of whatever surface you give it as a command line argument. On Mon, 4 Sep 2017, Fereshte wrote: Using the Pial surface; Does it mean mris_volume will give the inner cortical boundary of the surface and not the outer boundary?  Sincerely, Fereshte Ramezani On

Re: [Freesurfer] Pial surface volume

2017-09-04 Thread Fereshte
What's the algorithm used to expand inner cortical boundary ( to achieve the outer cortical boundary in pial surface) in FreeSurfer? On Mon, Sep 4, 2017 at 9:58 PM Bruce Fischl wrote: > it will give the interior volume of whatever surface you give it as a > command line argument. > > On Mon, 4 Se

Re: [Freesurfer] Pial surface volume

2017-09-04 Thread Bruce Fischl
Hi Fereshte the algorithm is documented in the recon1 1999 NeuroImage and 2000 PNAS papers cheers Bruce On Mon, 4 Sep 2017, Fereshte wrote: What's the algorithm used to expand inner cortical boundary ( to achieve the outer cortical boundary in pial surface) in FreeSurfer? On Mon, Sep 4, 201

[Freesurfer] longitudinal freesurfer- different scanners

2017-09-04 Thread Michelle VanTieghem
Hello, Would it be ok to use the longitudinal pipeline for scans that were acquired on different scanners (e.g time 1 and time 2 on the same scanner, time 3 on different scanner)? Would the longitudinal pipeline help to account for different scanners, since it creates the average base image for al

Re: [Freesurfer] Using Total Cortical White Matter Volume as a "whole brain" covariate

2017-09-04 Thread Douglas Greve
It is not clear what correction is best to use for surface area (we usually do not correct thickness). We recommend at least using eTIV to account for simple differences in head size which are known to directly affect area but obviously will not account for atrophy. I would think that total ce

Re: [Freesurfer] Version 6.0 - ?h.white.preaparc vs. ?h.white for determining the need to edit brainmask.mgz, wm.mgz, add control points, etc.

2017-09-04 Thread Douglas Greve
The final white surface probably won't change much from the preaparc, so it could be used to find fairly large errors. On 2/15/17 3:31 PM, Mira Michelle Raman wrote: Hi, My main question to the 6.0 experts is: Is the lh.white.preaparc close enough to the lh.white to determine whether ed

Re: [Freesurfer] Functional Connectivity Motion Regression

2017-09-04 Thread Douglas Greve
use mcprextreg (this is described in the wiki, isn't it?) On 8/23/17 10:21 PM, Leathem, Logan Daniel wrote: Hi Freesurfer list, My group is switching to the fsfast functional connectivity pipeline. We would like to continue regressing out the six-parameter rigid body head motion as a nuisanc

Re: [Freesurfer] Pial surface volume

2017-09-04 Thread Fereshte
Hi Bruce, Thank you for your replies. Cheers On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl wrote: > Hi Fereshte > > the algorithm is documented in the recon1 1999 NeuroImage and 2000 PNAS > papers > > cheers > Bruce > On Mon, 4 Sep 2017, Fereshte wrote: > > > What's the algorithm used to expand inn