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.eduwrote:
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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >