[Freesurfer] Using qdec to compare groups of twins?

Hello, Could you please advise as to whether or not the following analysis is suitable? I would like to compare groups of monozygotic twins (MZ concordant vs. MZ control ; MZ discordant affected twin vs. unaffected twin) using qdec. This is not as straightforward as group comparisons usually a

Re: [Freesurfer] question on tksurfer tcl

try adding: set labelstyle 1 On Tue, 2 Dec 2008, j janssen wrote: Hi, using version 4.0.5 my goal: to display in tksurfer an inflated brain with curvature and an *outlined* label, using a tcl-script. there are probably numerous ways, i did: tksurfer "subject" rh inflated -gray -tcl tksurf.

[Freesurfer] Error with motion-correction session(ms-sess)

Hi, Mr or Ms My name is Kenta in Japan. I'm undergraduate student. Please help me! I've tried some things to solve the error with mc-sess. But I could not solve this error. The mc-sess processing didn't completely run and following message showed up. I'm using matlab R2007a, macOS10.5.5, and fr

[Freesurfer] How to compare left vs right hemi (flip RL)

Hi, Is there any way to compare left vs right hemisphere (surface morpho. and functional data). I mean, is there any function to flip one hemisphere in order to compare it with the other one? Thanks, Frederic Andersson ___ Freesurfer mailing list

Re: [Freesurfer] recon-all rerun

recon-all will copy the brainmask.auto.mgz to the brainmask.mgz so they should be the same. Allison On Tue, 2 Dec 2008, Barkay, Gavriel wrote: Hi, I ran recon-all -all crashed for reasons unrelated to FreeSurfer. I re-ran the analysis without -clean. Is the new skull stripped volume stored in

Re: [Freesurfer] Rerunning previously edited subjects on 4.10, no fill.

Hi Inge, what does the aseg look like? Are the ventricles and caudate properly labeled in both versions? Bruce On Tue, 2 Dec 2008, Inge K. Amlien wrote: Hi list! I am experiencing a problem when reprocessing 70-something previously edited (FS 4.05) subjects on FS version 4.10. It seems f

[Freesurfer] question on tksurfer tcl

Hi, using version 4.0.5 my goal: to display in tksurfer an inflated brain with curvature and an *outlined* label, using a tcl-script. there are probably numerous ways, i did: tksurfer "subject" rh inflated -gray -tcl tksurf.tcl where tksurf.tcl contains: make_lateral_view rotate_brain_x -90

Re: [Freesurfer] question on tksurfer tcl

try just running tksurfer with the -label-outline option. j janssen wrote: Hi, using version 4.0.5 my goal: to display in tksurfer an inflated brain with curvature and an *outlined* label, using a tcl-script. there are probably numerous ways, i did: tksurfer "subject" rh inflated -gray -

Re: [Freesurfer] How to compare left vs right hemi (flip RL)

We don't have a good way to do this yet. I've have been working on one but have dropped the ball. Some people will analyzed both the correctly-oriented data and left-right reversed for each subject, but this is not the best way to do it. doug FrŽedeŽric Andersson wrote: Hi, Is there any wa

Re: [Freesurfer] Using qdec to compare groups of twins?

Do you just want to do a paired analysis? Do you want to include other covariates? Burmicz, Ryzarda wrote: Hello, Could you please advise as to whether or not the following analysis is suitable? I would like to compare groups of monozygotic twins (MZ concordant vs. MZ control ; MZ discor

Re: [Freesurfer] Error with motion-correction session(ms-sess)

Looks like matlab is having trouble running from the shell. I have no idea what causes this, you may have to ask your system administrator for help. doug wrote: Hi, Mr or Ms My name is Kenta in Japan. I'm undergraduate student. Please help me! I've tried some things to solve the error

Re: [Freesurfer] Possible to constrain FDR to a label in the volume?

Yea, there's not a mask to label. There is a mask to brain, but I'm not sure if you can substitute your own mask for it. I just tried to run it, and could not get FDR to work at all in tkmedit. Is it working for you at all? doug Dan Dillon wrote: Dear FreeSurfers, I've created a basal g

RE: [Freesurfer] Possible to constrain FDR to a label in the volume?

Hi Doug. Yup, the FDR button is working for me in tkmedit. I see the mask to brain, but as you can probably guess I'm interested in masking to the basal ganglia. DD From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tuesday, December 02, 2008 12:04 PM To: Dan Dillon Cc: freesurfer@nmr.mgh.ha

[Freesurfer] comparing hemispheres

Hi Frederic, To amplify, are you are talking about vertex by vertex analyses in the context of between group comparisons? As Doug says, the optimal tools are not there yet. As you know, you can always drop the threshold on the other side and see if activations/thickness blobs emerge in the same

[Freesurfer] CSF calculation

Dear all, Is there anyway to calculate CSF volume using freesurfer? I only know freesurfer supports GM and WM calculation based on aseg.mgz and aseg.stats . Thanks, Anthony New Email addresses available on Yahoo! Get the Email name you've always wanted on the new @ymail and @rocketmai

Re: [Freesurfer] CSF calculation

Hi Anthony, we compute ventricular CSF but not sulcal CSF (which you can't really see in a T1-weighted image). cheers, Bruce On Tue, 2 Dec 2008, Anthony wrote: Dear all, Is there anyway to calculate CSF volume using freesurfer? I only know freesurfer supports GM and WM calculation based on