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 <k...@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 <k...@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 <k...@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 < >>>>>>> k...@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.al...@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 < >>>>>>>>>> fis...@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.al...@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 << >>>>>>>>>>> s...@nmr.mgh.harvard.edu> >>>>>>>>>>> s...@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 >>>>>>>>>>>>> < <s...@nmr.mgh.harvard.edu>s...@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. 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