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