Hi,
Do you want me to email you in a few days about this?
Allie
On Tue, Apr 19, 2011 at 10:25 AM, Khoa Nguyen khoa@nmr.mgh.harvard.eduwrote:
Got it. I'll look at it and get back to you.
On Tue, 19 Apr 2011, Allie Rosen wrote:
Hi,
http://dl.dropbox.com/u/14127241/C42.tar.gz
Here is the link to the subject. I hope this works!!
Allie
On Tue, Apr 19, 2011 at 9:38 AM, Khoa Nguyen <khoa@nmr.mgh.harvard.edu
wrote:
Another way you can try is upload it to your google doc account and send
me the link. Someone did that before.
On Tue, 19 Apr 2011, Allie Rosen wrote:
Hi,
No, I'm not from the centre. I'm working on putting the files in Dropbox and sending you a link to them, because apparently I don't have ftp access.
Allie
On Tue, Apr 19, 2011 at 8:37 AM, Khoa Nguyen <khoa@nmr.mgh.harvard.edu
wrote:
Are you from the center? If so you can just cd into /space/outgoing and
copy your file there. If not, you can follow the instructions in the box at the top using a terminal.
On Tue, 19 Apr 2011, Allie Rosen wrote:
Hi,
I'm really sorry, but I don't understand those instructions. Do I login to the freesurfer website? Or do I login through a terminal somehow? Do I type the stuff in the boxes into the terminal?
Thanks, Allie
On Tue, Apr 19, 2011 at 8:18 AM, Khoa Nguyen < khoa@nmr.mgh.harvard.edu
wrote: > > Hi Allie,
> You can compress the subject dir and upload it following the > instructions > here > http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > > > On Tue, 19 Apr 2011, Allie Rosen wrote: > > Hi Khoa, > > > How do I upload subjects? >> >> Thanks, >> Allie >> >> >> >> On Tue, Apr 19, 2011 at 8:06 AM, Khoa Nguyen < >> khoa@nmr.mgh.harvard.edu >> >> wrote: >> >>> >>> >>> Hi Allie, >> >> >> Can you upload the subject? I'll take a look and see if I can >>> figure >>> out >>> what's wrong. >>> >>> -Khoa >>> >>> >>> On Tue, 19 Apr 2011, Allie Rosen wrote: >>> >>> Hi, >>> >>> >>> This (recon-all after wm.mgz and brainmask.mgz edits) didn't work. >>> >>>> The >>>> part >>>> that wasn't included in the pial or white matter surfaces is still >>>> not >>>> included. The intensities in the white matter regions are no >>>> different >>>> than >>>> in white matter regions that were included in the white matter. >>>> Any >>>> other >>>> suggestions? >>>> >>>> Thanks, >>>> Allie >>>> >>>> >>>> >>>> On Mon, Apr 18, 2011 at 7:53 PM, Allie Rosen < >>>> rosen.allie@gmail.com >>>> >>>>> >>>>> wrote: >>>> >>>> Hi Bruce, >>>> >>>> >>>> I am running recon-all tonight using wm voxels that I manually >>>> >>>>> added >>>>> (I >>>>> also edited brainmask.mgz to add missing grey matter). To me it >>>>> doesn't >>>>> really look like a case of the white matter not having a high >>>>> enough >>>>> intensity. It simply looks like the whole lobe was ignored, >>>>> regardless >>>>> of >>>>> intensity. But I'll check tomorrow to see if the intensity is >>>>> low. >>>>> >>>>> Thanks, >>>>> Allie >>>>> >>>>> >>>>> On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl < >>>>> fischl@nmr.mgh.harvard.edu>wrote: >>>>> >>>>> What is the intensity of the white matter in the regions you >>>>> drew >>>>> in? >>>>> A >>>>> >>>>> couple of control points might help if it is less than 110 >>>>> >>>>> >>>>>> >>>>>> >>>>>> On Apr 18, 2011, at 12:36 PM, Allie Rosen < >>>>>> rosen.allie@gmail.com> >>>>>> wrote: >>>>>> >>>>>> Hi Sita, >>>>>> >>>>>> Thanks for all the responses! I've actually had the same problem >>>>>> for >>>>>> multiple subjects. I'm using version 5.0.0. I'll try fixing the >>>>>> cerebellum >>>>>> as well. I've attached pictures of where I am adding wm voxels. >>>>>> They >>>>>> aren't >>>>>> really in the same places as in the online tutorials. Could you >>>>>> take >>>>>> a >>>>>> quick >>>>>> look to see if they're in the right place? >>>>>> >>>>>> Thanks, >>>>>> Allie >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori << >>>>>> sita@nmr.mgh.harvard.edu> >>>>>> sita@nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> >>>>>> Hi Allie, >>>>>> >>>>>> >>>>>> pial surface which looks like this can only be corrected by >>>>>>> correcting >>>>>>> the wm.mgz. Also I would suggest to try and fix the cerebellum >>>>>>> and >>>>>>> see >>>>>>> if it >>>>>>> corrects the surfaces as well. Since part of the cerebellum is >>>>>>> stripped >>>>>>> off, >>>>>>> it's probably affecting the segmentation as well but I could be >>>>>>> wrong. >>>>>>> what >>>>>>> version of freesurfer are you using. >>>>>>> >>>>>>> >>>>>>> Sita. >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>> >>>>>>> Hi Sita, >>>>>>> >>>>>>> >>>>>>> Can I still add voxels to wm.mgz even though the points would >>>>>>> be >>>>>>> >>>>>>> outside >>>>>>>> even the pial boundary? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Allie >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori >>>>>>>> < sita@nmr.mgh.harvard.edusita@nmr.mgh.harvard.edu>wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Hi Allie, >>>>>>>> >>>>>>>> >>>>>>>> This probably needs white matter edits but it's hard to tell >>>>>>>> >>>>>>>>> from >>>>>>>>> one >>>>>>>>> slice. Please refer to our white matter edits wiki and >>>>>>>>> toplogical >>>>>>>>> defects >>>>>>>>> wiki and see if it helps in fixing the errors in your >>>>>>>>> datasets. >>>>>>>>> Also >>>>>>>>> it >>>>>>>>> looks like part of the Cerebellum is stripped off. You might >>>>>>>>> want >>>>>>>>> to >>>>>>>>> correct >>>>>>>>> that as well. >>>>>>>>> >>>>>>>>> < >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>>>>>>>> >>>>>>>>> < >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect >>>>>>>>> >>>>>>>>> >>>>>>>>> Sita. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, 18 Apr 2011, Allie Rosen wrote: >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> >>>>>>>>> Once processed, several of my subjects have had errors >>>>>>>>> around >>>>>>>>> the >>>>>>>>> >>>>>>>>> occipital >>>>>>>>> >>>>>>>>>> lobe. Attached is an example. I've already tried editing >>>>>>>>>> brainmask.mgz >>>>>>>>>> and >>>>>>>>>> running recon-all, but as you can see, this didn't change >>>>>>>>>> the >>>>>>>>>> pial >>>>>>>>>> or >>>>>>>>>> wm >>>>>>>>>> borders. What can I do to fix this? >>>>>>>>>> >>>>>>>>>> Thank you, >>>>>>>>>> Allie Rosen, MSc Candidate >>>>>>>>>> Graduate Student, Department of Neurosurgery >>>>>>>>>> Toronto Western Hospital 14-327 >>>>>>>>>> 399 Bathurst St. >>>>>>>>>> University of Toronto >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the >>>>>>>>>> person >>>>>>>>>> to >>>>>>>>>> >>>>>>>>>> whom >>>>>>>>>> >>>>>>>>>> it >>>>>>>>> is >>>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>>> error >>>>>>>>> and >>>>>>>>> the >>>>>>>>> e-mail >>>>>>>>> contains patient information, please contact the Partners >>>>>>>>> Compliance >>>>>>>>> HelpLine at >>>>>>>>> http://www.partners.org/complianceline >>>>>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>>>>> sent >>>>>>>>> to >>>>>>>>> you >>>>>>>>> in >>>>>>>>> error >>>>>>>>> but does not contain patient information, please contact the >>>>>>>>> sender >>>>>>>>> and >>>>>>>>> properly >>>>>>>>> dispose of the e-mail. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> <2.png> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> <3.png> >>>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>