Re: [Freesurfer] Cortical Misegmentation

2015-03-06 Thread Pedro Rosa - Gmail
Hi, Bruce. I am currently putting the file (Well-C0-T1w-023-20050425_124.zip) - it will take a while. I was able to make it a lot better using the Topological Defect correction in tkmedit. Is it suitable for this task? I have not tried adding control points. This is an older data with a quite

Re: [Freesurfer] Cortical Misegmentation

2015-03-06 Thread Bruce Fischl
Hi Pedro the instructions are at: http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange have you tried control points in the temporal wm? And what receive coil did you use? You might be better off with something like 1.1mm isotropic if you can change the acquisition cheers Bruce On Fri,

Re: [Freesurfer] Cortical Misegmentation

2015-03-05 Thread Lee Tirrell
You can find information on using our ftp site here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Thanks, Lee On Mar 5, 2015, 22:16, at 22:16, Pedro Rosa wrote: >Sure. How can I do it? > >Sent from my iPhone > >> On Mar 6, 2015, at 00:01, Bruce Fischl >wrote: >> >> Can you put i

Re: [Freesurfer] Cortical Misegmentation

2015-03-05 Thread Pedro Rosa
Sure. How can I do it? Sent from my iPhone > On Mar 6, 2015, at 00:01, Bruce Fischl wrote: > > Can you put it on our ftp site instead? > > > >> On Mar 5, 2015, at 9:37 PM, Pedro Rosa wrote: >> >> Hi, >> It will upload in an hour, I guess: >> https://www.dropbox.com/sh/n9talmyxiafdt56/AADF

Re: [Freesurfer] Cortical Misegmentation

2015-03-05 Thread Bruce Fischl
Can you put it on our ftp site instead? > On Mar 5, 2015, at 9:37 PM, Pedro Rosa wrote: > > Hi, > It will upload in an hour, I guess: > https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0 > Thanks a lot, > Pedro. > >> On Mar 5, 2015, at 23:32, Bruce Fischl wrote: >> >

Re: [Freesurfer] Cortical Misegmentation

2015-03-05 Thread Pedro Rosa
Hi, It will upload in an hour, I guess: https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0 Thanks a lot, Pedro. > On Mar 5, 2015, at 23:32, Bruce Fischl wrote: > > Hmmm, if you upload it we will take a look > Bruce > > > >> On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmai

Re: [Freesurfer] Cortical Misegmentation

2015-03-05 Thread Bruce Fischl
Hmmm, if you upload it we will take a look Bruce > On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail > wrote: > > That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo time > 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm. > > Pedro Rosa > >> On Thur

Re: [Freesurfer] Cortical Misegmentation

2015-03-05 Thread Pedro Rosa - Gmail
That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo time 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm. Pedro Rosa On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote: > What are your acquisition parameters, voxel size etc...? > > >

Re: [Freesurfer] Cortical Misegmentation

2015-03-05 Thread Bruce Fischl
What are your acquisition parameters, voxel size etc...? > On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail > wrote: > > Hi, Bruce. > Yes, it it the T1.mgz. Is it a large topological error? Can I correct it > editing wm.mgz? > Thanks, > Pedro. >> On Thursday, March 5, 2015 at 10:52 PM, Bruce F

Re: [Freesurfer] Cortical Misegmentation

2015-03-05 Thread Pedro Rosa - Gmail
Hi, Bruce. Yes, it it the T1.mgz. Is it a large topological error? Can I correct it editing wm.mgz? Thanks, Pedro. On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote: > What is the background image? Is it the t1 that your reconned? Can you give > us the details about it? > > > > On M

Re: [Freesurfer] Cortical Misegmentation

2015-03-05 Thread Bruce Fischl
What is the background image? Is it the t1 that your reconned? Can you give us the details about it? > On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail > wrote: > > Dear FreeSurfer, > I have found several subjects to have temporal lobe misegmentations (usually > neocortical, as attached, but

[Freesurfer] Cortical Misegmentation

2015-03-05 Thread Pedro Rosa - Gmail
Dear FreeSurfer, I have found several subjects to have temporal lobe misegmentations (usually neocortical, as attached, but sometimes mesial tempporal), and less frequently in the insula. I could find in the manual editing page from the Wiki a way to fix this. How should I do it? Thanks a lot,