Re: [Freesurfer] nonlabeled vertices in bert

2011-10-10 Thread Bruce Fischl
Hi Ben if the unlababeled vertices are in non-cortical regions, e.g. on the midline, then this is normal. We also only enforce connectivity by removing small regions. If there are multiple large parts to a parcel, we don't relabel it as this can occur using some anatomical definitions. We ca

Re: [Freesurfer] WM hypointensities and corpus callosum mislabeling

2011-10-10 Thread Bruce Fischl
Hi Warren can you send us some images to show us what you mean? Or upload an example dataset for us to look at? cheers Bruce On Mon, 10 Oct 2011, Warren Winter wrote: Hello, In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, a

Re: [Freesurfer] Cerebellum pail surface

2011-10-10 Thread Bruce Fischl
Hi Ansam, sorry, that's not so easy to do. The foliations in the cerebellum are so fine that you would need extremely high resolution in the coronal plane to be able to resolve them. Probably below .35mm. cheers Bruce On Mon, 10 Oct 2011, Ansam El Shaikh wrote: > Hi, > I'm trying to get red a

[Freesurfer] selfreqavg

2011-10-10 Thread Michelle Umali
Hi Jon, Thanks! I have a question about when selfreqavg. When do I use selfreqavg? Is it called when I run fieldsign-sess or do I have to run it in addition to the below? I've been doing the following: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -

Re: [Freesurfer] retinotopy description

2011-10-10 Thread Jonathan Polimeni
hi michelle, the Sereno et al. 1995 Science paper has details about the phase encoded retinotopic data analysis, especially in the endnotes of the article. also for more details you can look at the MATLAB code embedded in the command 'selfreqavg', which is used for the basic retinotopy analysis a

[Freesurfer] WM hypointensities and corpus callosum mislabeling

2011-10-10 Thread Warren Winter
Hello, In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, as well as mislabelings of the corpus callosum as cerebral white matter (at and/or around slice 128, sagittal). Has anyone else encountered these problems, and are there f

[Freesurfer] Cerebellum pail surface

2011-10-10 Thread Ansam El Shaikh
Hi, I'm trying to get red and green lines for cerebellum.. How can I do?. There are green and red lines for the cortex. Should I re-convert the data? Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] nonlabeled vertices in bert

2011-10-10 Thread Bruce Fischl
Can you and us a picture? Cheers Bruce On Oct 10, 2011, at 7:08 AM, Ben Hamida Cammoun Leila Faiza wrote: > Hello, > > 1) I reiterate my question, because i cannot continue processing. Some > vertices are not labeled in the rh.aparc.annot in bert as > 35643,36746,37788. > > 2)

[Freesurfer] Rejoindre mon réseau sur LinkedIn

2011-10-10 Thread Huiguang He via LinkedIn
LinkedIn Huiguang He souhaite se connecter à vous sur LinkedIn : -- Freesurfer, Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Huiguang He http://www.linkedin.com/e

[Freesurfer] nonlabeled vertices in bert

2011-10-10 Thread Ben Hamida Cammoun Leila Faiza
Hello, 1) I reiterate my question, because i cannot continue processing. Some vertices are not labeled in the rh.aparc.annot in bert as 35643,36746,37788. 2) The parcels of my subject are not connex. Below is the detail on my first email. Thank you very much for answering me De