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 >>>> >>>> >>>> >>>> >>>> >>>> >>> >>