Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

2016-12-12 Thread Ismail Koubiyr
Alright, thanks a lot for your help Bruce. Best, Ismail PhD candidate Neurocentre Magendie, INSERM Bordeaux, France 2016-12-12 17:33 GMT+01:00 Bruce Fischl : > because filling in the T1 may cause artifacts > > On Mon, 12 Dec 2016, Ismail Koubiyr wrote: > > Would you please give me the reasons

Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

2016-12-12 Thread Bruce Fischl
because filling in the T1 may cause artifacts On Mon, 12 Dec 2016, Ismail Koubiyr wrote: Would you please give me the reasons why the former would be better ? Ismail PhD candidate Neurocentre Magendie, INSERM Bordeaux, France 2016-12-12 15:47 GMT+01:00 Bruce Fischl : the former I thin

Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

2016-12-12 Thread Ismail Koubiyr
Would you please give me the reasons why the former would be better ? Ismail PhD candidate Neurocentre Magendie, INSERM Bordeaux, France 2016-12-12 15:47 GMT+01:00 Bruce Fischl : > the former I think, but it's an empirical question > Bruce > On Mon, 12 Dec 2016, Ismail Koubiyr wrote: > > > Hi

Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

2016-12-12 Thread Bruce Fischl
the former I think, but it's an empirical question Bruce On Mon, 12 Dec 2016, Ismail Koubiyr wrote: > Hi Bruce, > Thanks for your answer. > What do you think would be better, run recon-all on the original data (with > lesions) then edit the aseg for the juxtacortical lesions or use a lesion > fill

Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

2016-12-12 Thread Ismail Koubiyr
Hi Bruce, Thanks for your answer. What do you think would be better, run recon-all on the original data (with lesions) then edit the aseg for the juxtacortical lesions or use a lesion filling on the T1 and then run recon-all on it. Thanks again. Cheers, Ismail PhD candidate Neurocentre Magendie

Re: [Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

2016-12-09 Thread Bruce Fischl
I Ismail yes, if you have juxtacortical lesions you should label them as such in the aseg, then I think it should work cheers Bruce On Fri, 9 Dec 2016, Ismail Koubiyr wrote: > Dear Freesurfer experts, > We are facing a problem in our study and would need your advice on it. > We want to get an

[Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

2016-12-09 Thread Ismail Koubiyr
Dear Freesurfer experts, We are facing a problem in our study and would need your advice on it. We want to get an accurate measurement for the cortical thickness from our MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be used with the FLAIR option so that we can a more acc

Re: [Freesurfer] MS lesions

2009-08-11 Thread Bruce Fischl
Hi Miguel, I think Koen Van Leemput (ccd) has some tools for this, but in general we don't characterize MS lesions much, although we do generically label damaged white matter. cheers, Bruce On Tue, 11 Aug 2009, Jose Soares wrote: Hi, what kind of information can I get with FreeSUrfer abou

Re: [Freesurfer] MS lesions

2009-08-11 Thread Pedro Paulo de Magalhães Oliveira Junior
I don't think FreeSurfer will give any direct measure of MS. In the wiki page of FreeSurfer there's a paper about MS: http://www.nmr.mgh.harvard.edu/~fischl/reprints/Brain2003v126p1734Sailercorticalthickness.pdf --- Pedro Paulo de M. Oliveira

[Freesurfer] MS lesions

2009-08-11 Thread Jose Soares
Hi, what kind of information can I get with FreeSUrfer about MS lesions? Number of lesions? Lesion volume? Thanks, Miguel. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbusca