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 >> >> >> >> >> >
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 >>> >>> >>> >>> >>> >> >
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 >>>> >>>> >>>> >>>> >>>> >>>> >>> >>
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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >
Hi,
Do you want me to email you in a few days about this?
Allie
On Tue, Apr 19, 2011 at 10:25 AM, Khoa Nguyen khoa@nmr.mgh.harvard.eduwrote:
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.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 <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 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>
freesurfer@nmr.mgh.harvard.edu
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Allie Rosen -
Khoa Nguyen