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 <[email protected]>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 <[email protected] >> >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 <[email protected] >>>> >>>>> 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 < >>>>>> [email protected] >>>>>> >>>>>> 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 <[email protected] >>>>>>>> > >>>>>>>> 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 < >>>>>>>>> [email protected]>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 <[email protected]> >>>>>>>>>> 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 << >>>>>>>>>> [email protected]> >>>>>>>>>> [email protected]> 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 >>>>>>>>>>>> < <[email protected]>[email protected]>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 >>>>>>>>>> [email protected] >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>> >>>> >>
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