[Freesurfer] Very strange error in surface reconstruction after a2-cp

Dear FS experts, I have a very strange error after running autorecon2-cp. I never saw this kind of error with previous versions of FS. I run recon-all -all on my subject, and obtained very good surface reconstructions, with the exception of few excluded wm voxels (see attachment called

[Freesurfer] Filipping issue

Dear List, we are starting the analysis of cortical thickness for a group of patients who have only one side affected. The majority of patients have the left hemisphere affected, but some patients have the right hemisphere affected. In order to do a group analysis, we would like to flip the

[Freesurfer] R: R: Filipping issue

the subjects I don't want to flip (i.e., those with the left hemisphere affected), to pool them together in the statistic with the flipped subjects? Thank you again Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology

[Freesurfer] R: R: R: Filipping issue

Dear Doug, I registered with surfreg the hemispheres I would like to analyze. How should I proceed now for the final statistical vertex-wise analysis? Should I smooth the surfaces and perform between-group comparison with qdec? Thank you in advance Paola Paola Valsasina, MSc Research Fellow

[Freesurfer] R: R: R: R: Filipping issue

folder? Thank you in advance Kind regards Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University Vita-Salute San Raffaele Via Olgettina 60, 20132 Milan

[Freesurfer] R: R: R: R: R: Filipping issue

; in this folder there is a file called lh.sphere.reg or a file called lh.ni.sym.b40.i30.sphere.reg. Which one is the correct file? Thank you again Best regards, Paola Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division

[Freesurfer] Can -autorecon2-cp and -autorecon2-wm be run at the same time

Dear FreeSurfer experts, I am quite new to FreeSurfer and I am trying to analyze some patients. We run -autorecon2 step and we got some errors both in the intensitiy normalization and in the wm segmentation, so what we need to do now is both to add control points to the brainmask.mgz image and to

[Freesurfer] adding control points

Dear FS experts, we have run autorecon2 on a set of subjects and now we are in the process of manual editing adding control points. We read the tutorial about the manual editing; however, sometimes we have some doubts about adding or not adding control points in some regions. We had a look at

[Freesurfer] R: ICV differs systematically in repeated measurements

sequence parameters – different performance in assessing ICV)? Regards, Paola Valsasina _ Da: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Diederick Stoffers Inviato: lunedì 20 dicembre 2010 12.49 A: Freesurfer List Oggetto: [Freesurfer

[Freesurfer] R: bad output of autorecon2 - is there any way to adjust it?

, Paola Paola Valsasina Research Fellow to Prof. M. Filippi Neuroimaging Research Unit Institute of Experimental Neurology Hospital San Raffaele via Olgettina 60 20132 Milan - ITALY -Messaggio originale- Da: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Inviato: martedì 28 dicembre