Hi Matt Not really. Is the white matter in those regions already 110? Bruce
> On Aug 12, 2014, at 8:21 PM, "Walton, Matt" <mt.wal...@alumni.uleth.ca> wrote: > > Hey Bruce, > > Is there anyway I can make edits to the grey matter to help with the > segmentation errors (i.e reclassify grey matter in the brainmask with voxel > edit so they are included in the pial layer). Even with the addition of > control points and wm edits I'm still not getting a proper segmentation, > especially in areas like the temporal lobes and central grey matter where > signal is lower. > > Thanks, > > Matt > > >> On Thu, Aug 7, 2014 at 1:20 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Matt >> >> the young age is probably why you are having to do extra work - incomplete >> myelination. >> >> cheers >> Bruce >> >> On Thu, 7 Aug 2014, Walton, Matt wrote: >> >>> Thanks for your help. It is most appreciated. >>> I thought I would mention that these subjects are quite young (3-4 years >>> old). I've read a few posts that free surfer is not ideal for analyzing >>> young subjects, so I am wondering if this might be causing some errors. >>> Maybe there is a way to register to a paediatric template, or something? >>> >>> As well the raw T1w images always have an intensity bias in the occipital >>> lobe. I'm not sure if this is from the coil itself (32 channel phased >>> array), or just from the young subject age. Do you think ramping up the >>> normalization procedures in freesurfer would result in an improvement? >>> >>> Thought I would just let you know this, incase it helps you. >>> >>> Matt >>> >>> >>> On Thu, Aug 7, 2014 at 10:12 AM, Tirrell, Lee <ltirr...@mgh.harvard.edu> >>> wrote: >>> Hi Matt, >>> >>> Overall, I've made the following changes that have led to some >>> improvements: >>> - Remove excess dura from the brainmask that hasn't been >>> stripped away >>> - Erasing voxels from wm in areas where white matter should be, >>> even if the voxels don't show up as what on the wm mask. (If you >>> view the wm volume with the heat color map, and lower the mid >>> parameter to zero, areas that you have deleted show up in red) >>> - Control points to push out the pial surface >>> >>> Specifically for the case I sent you, I added control points >>> near 115, 89, 82 (+/- a few slices in the sagittal view) to move >>> the pial surface out further. The wm intensity is decreasing as >>> it moves out along that strand, so adding control points in >>> these areas will increase the values to help Freesurfer >>> recognize it as part of the white matter surface. >>> >>> Also, near 141, 116, 45 (sagittal view) there is a problem with >>> the wm surface. I tried deleting wm voxels as mentioned above, >>> but I don't think I was aggressive enough on the first attempt >>> so it didn't help much. I will try this again to see if it >>> leads to further improvements. >>> >>> Best, >>> Lee >>> >>> On 08/06/2014 11:54 AM, Walton, Matt wrote: >>> Hey Bruce, >>> Thanks so much. If it would help, I could upload another >>> subject, perhaps one with worse segmentation in the occipital >>> lobe. I could also upload a raw T1 image sequence (Nifiti) >>> >>> Matt >>> >>> >>> On Wed, Aug 6, 2014 at 9:48 AM, Tirrell, Lee >>> <ltirr...@mgh.harvard.edu> wrote: >>> Hi Matt, >>> >>> I've taken a look at the subject that you uploaded. >>> I initially deleted portions of the skull from the >>> brainmask that weren't removed from coronal slices >>> 101-109 (see screenshot), which led to some >>> improvement. I also edited the wm volume by >>> deleting areas that were obviously not white matter, >>> even if it didn't effect the white matter surface. >>> However, this didn't lead to much improvement. The >>> segmentation isn't as bad in this subject as in the >>> screenshot that you sent originally, so this >>> strategy may help in worse cases. >>> >>> I am going to take another look at it now to try to >>> improve the segmentation further. >>> >>> Best, >>> Lee >>> >>> On 07/30/2014 12:21 PM, Walton, Matt wrote: >>> Hey Bruce, >>> I uploaded a subject that you requested a few days >>> ago (problems with segmentation in the occipital >>> lobe). I just wanted to make sure the file >>> transferred successfully, and if you have had a >>> change to analyze. >>> >>> Thanks, >>> >>> Matt >>> >>> >>> On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt >>> <mt.wal...@alumni.uleth.ca> wrote: >>> Hey Bruce. >>> I've sent one of my subjects in which I >>> noticed the segmentation problems in the >>> occipital lobe. Sagittal slice 115 provides a >>> good example. I've also noticed that with my >>> subjects I frequently have problems with >>> segmentation of the temporal lobes, although >>> adding control points usually fixes this quite >>> well. >>> >>> Thanks for your help >>> >>> Matt >>> >>> >>> >>> On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> Hi Matt >>> >>> there are instructions on our >>> wiki. You can either ftp or use >>> the filedrop, although ftp is >>> probably best if you are uploading >>> an entire subject >>> >>> cheers >>> Bruce >>> On Mon, 28 Jul 2014, Walton, Matt >>> wrote: >>> >>> Hey Bruce. >>> Thanks for the >>> response. How do I go >>> about uploading the >>> subject? >>> >>> On Monday, July 28, >>> 2014, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Matt >>> >>> certainly >>> something is wrong, >>> but it's hard to tell >>> why from the >>> single slice. >>> You have big >>> topological defects >>> that are being >>> fixed >>> incorrectly. Can you >>> upload the subject and >>> we will take a >>> look? >>> cheers >>> Bruce >>> On Mon, 28 Jul >>> 2014, Walton, Matt >>> wrote: >>> >>> Hello >>> Freesurfer team, >>> I've used >>> freesurfer to segment >>> (recon-all) >>> >>> approximately 30 >>> different >>> subjects >>> from a study. I've >>> noticed that a large >>> number of >>> these subjects >>> have a >>> misclassification of >>> the white and pial >>> boundaries >>> in the occipital >>> lobe (such >>> that grey matter is >>> being classified as >>> white >>> matter). I believe >>> this >>> problem is originating >>> from my scanner and >>> original >>> data. I'm acquiring >>> a T1W >>> BRAVO sequence on a GE >>> Discovery 750w 3T >>> scanner, >>> using a 32 channel >>> phased >>> array head coil. For >>> many subjects, this >>> acquistion >>> gives intensity >>> >>> inhomogeneity in the >>> occipital lobe. I've >>> begun >>> using a GE >>> based correction >>> technique >>> (PURE) on the images, >>> and it appears to >>> improve >>> the intensity in >>> the >>> occipital lobe, but >>> Freesurfer is still >>> frequently >>> misclassifying. >>> >>> I'm >>> wondering what would >>> be the best way to >>> edit the >>> data. I've >>> often tried >>> to edit >>> the wm.vol, but this >>> doesn't seem to fix >>> anything. >>> For the most >>> part, the >>> wm.vol is correct to >>> begin with, but the >>> wm cutting >>> line isn't >>> segmenting >>> with the wm.vol. I've >>> also tried to add >>> control >>> points but this >>> doesn't >>> seem to improve >>> anything either. >>> >>> I've >>> attached an image >>> which I hope will >>> further >>> explain my >>> problems. >>> >>> Thanks for >>> any help >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is >>> intended only for the person to whom it >>> is >>> addressed. 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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. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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 . 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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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