Re: [Freesurfer] Cortical segmentation error
External Email - Use Caution Sorry for the very late reply and not explaining the problem well in the first place. I would still appreciate your assistance if possible. Like some other threads that are on the archive, I was experiencing the problem where the pial surface wasn't getting all of the gray matter. None of the threads have seem to been resolved so I hope I could get some help. Would it be alright if I sent the subject directory for you to take a look? Thank you. On Fri, Dec 13, 2019 at 4:56 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Can you be clearer as to what the problem is? If it is that the cortical > segmentation (red voxels) don't seem to follow the white/pial surfaces, > then there is nothing to worry about because the aseg is not expected to > have a good cortical segmentation (see aparc+aseg.mgz instead). > > On 12/13/2019 12:12 PM, Monica Bondy wrote: > > External Email - Use Caution > Hello FreeSurfer experts, > > I am trying to figure out how to fix the segmentation so that the cortex > is properly included. > I have had this problem with several subjects, especially in the temporal > lobe regions. > > I have tried tkmregister but it unfortunately didn't change anything. I am > in the middle of using control points to try to fix this problem but it > hasn't been ideal as it is requiring a lot of control points. Do you have > any ideas on how to fix this? > > I have attached an image of what the problem looks like below. Please let > me know if you need anything else. > > Thank you! > > 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514 > 2. Platform: macOS Mojave (version 10.14.6) > 3. uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat > Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64 > > [image: Screen Shot 2019-12-13 at 9.56.46 AM.png] > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Pial surface not including parts of cortex
External Email - Use Caution Dear Freesurfer experts, I was wondering if I could get some help with a problem that I keep experiencing. For some of the patients, their gray matter is not properly included in the pial surface. I have tried tkmregister and using control points but neither have been successful. I have read on a separate thread that editing the wm.mgz may be helpful but could I have some guidance on this please? Also, I know it can be difficult to tell the problem based on the description so please let me know if I can send something over to help. I'm still very much learning how to work freesurfer so I really appreciate your help. (Note: I am using version 5.3) Thank you, Monica ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Pial surface not including parts of cortex
External Email - Use Caution Thank you so much! I just sent the gzipped subject directory *subjectdir.gz. * My main concern is that a lot of the lateral gray matter isn't included. Here are some Talairach coordinates that illustrate the areas I'm concerned about: (-67 -27 -9) (-65 -33 22). Let me know if it didn't send properly or if I can do anything else. Thanks again, Monica On Fri, Jan 31, 2020 at 10:34 AM Bruce Fischl wrote: > Hi Monica > > sure, if you tar and gzip the entire subject dir and ftp it to us, then > send us a description that includes the voxel coords of where you think > things should be more accurate we will take a look > > cheers > Bruce > On Fri, 31 Jan 2020, > Monica Bondy wrote: > > > > > External Email - Use Caution > > > > Dear Freesurfer experts, > > I was wondering if I could get some help with a problem that I keep > > experiencing. For some of the patients, their gray matter is not properly > > included in the pial surface. I have tried tkmregister and using control > > points but neither have been successful. > > I have read on a separate thread that editing the wm.mgz may be helpful > but > > could I have some guidance on this please? Also, I know it can be > difficult > > to tell the problem based on the description so please let me know if I > can > > send something over to help. I'm still very much learning how to work > > freesurfer so I really appreciate your help. > > (Note: I am using version 5.3) > > > > Thank you, > > Monica > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical segmentation error
External Email - Use Caution Thanks for getting back to me. I've recently asked for help in another thread and sent in the subject directory because the control points didn't work well after my attempt. But I'll take your advice and give it another try. Thank you! On Fri, Jan 31, 2020 at 5:11 PM Douglas N. Greve wrote: > It is hard to say from that image because of the aseg, but it looks like > the white surface is not extending far enough and so the pial surface > starts too far away to get all the way out. You might need some control > points in the WM in that area > > On 1/28/2020 7:56 PM, Monica Bondy wrote: > > External Email - Use Caution > Sorry for the very late reply and not explaining the problem well in the > first place. I would still appreciate your assistance if possible. > Like some other threads that are on the archive, I was experiencing the > problem where the pial surface wasn't getting all of the gray matter. None > of the threads have seem to been resolved so I hope I could get some help. > Would it be alright if I sent the subject directory for you to take a > look? > Thank you. > > On Fri, Dec 13, 2019 at 4:56 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> Can you be clearer as to what the problem is? If it is that the cortical >> segmentation (red voxels) don't seem to follow the white/pial surfaces, >> then there is nothing to worry about because the aseg is not expected to >> have a good cortical segmentation (see aparc+aseg.mgz instead). >> >> On 12/13/2019 12:12 PM, Monica Bondy wrote: >> >> External Email - Use Caution >> Hello FreeSurfer experts, >> >> I am trying to figure out how to fix the segmentation so that the cortex >> is properly included. >> I have had this problem with several subjects, especially in the temporal >> lobe regions. >> >> I have tried tkmregister but it unfortunately didn't change anything. I >> am in the middle of using control points to try to fix this problem but it >> hasn't been ideal as it is requiring a lot of control points. Do you have >> any ideas on how to fix this? >> >> I have attached an image of what the problem looks like below. Please let >> me know if you need anything else. >> >> Thank you! >> >> 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514 >> 2. Platform: macOS Mojave (version 10.14.6) >> 3. uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat >> Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64 >> >> [image: Screen Shot 2019-12-13 at 9.56.46 AM.png] >> >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Pial surface not including parts of cortex
External Email - Use Caution Hi, I just wanted to check in on the progress of this thread. Could you let me know if you had the chance to take a look at the scan I sent? I'm unfortunately having the same problem with multiple scans so if I could get some help, I'd really appreciate it. If I somehow failed to send the files please let me know as well. Thank you! Monica On Fri, Jan 31, 2020 at 11:37 AM Monica Bondy wrote: > Thank you so much! I just sent the gzipped subject directory > *subjectdir.gz. * > My main concern is that a lot of the lateral gray matter isn't included. > Here are some Talairach coordinates that illustrate the areas I'm concerned > about: (-67 -27 -9) (-65 -33 22). > > Let me know if it didn't send properly or if I can do anything else. > > Thanks again, > Monica > > On Fri, Jan 31, 2020 at 10:34 AM Bruce Fischl > wrote: > >> Hi Monica >> >> sure, if you tar and gzip the entire subject dir and ftp it to us, then >> send us a description that includes the voxel coords of where you think >> things should be more accurate we will take a look >> >> cheers >> Bruce >> On Fri, 31 Jan 2020, >> Monica Bondy wrote: >> >> > >> > External Email - Use Caution >> > >> > Dear Freesurfer experts, >> > I was wondering if I could get some help with a problem that I keep >> > experiencing. For some of the patients, their gray matter is not >> properly >> > included in the pial surface. I have tried tkmregister and using control >> > points but neither have been successful. >> > I have read on a separate thread that editing the wm.mgz may be helpful >> but >> > could I have some guidance on this please? Also, I know it can be >> difficult >> > to tell the problem based on the description so please let me know if I >> can >> > send something over to help. I'm still very much learning how to work >> > freesurfer so I really appreciate your help. >> > (Note: I am using version 5.3) >> > >> > Thank you, >> > Monica >> > >> >___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extending the pial surface
External Email - Use Caution Hi Freesurfer Developers, I was hoping to get some advice on fixing pial surface error so we can calculate cortical thickness. In several patients, although the aseg is fine, the red outline for the pial surface is missing parts of the cortex (not the subcortical areas, those are alright). Unfortunately, we cannot use control points to edit the pial surface because there is no white matter in those parts of the brain. Is it possible to manually extend the pial surface to include the excluded cortex? Also, I looked through the archive and found a similar question and read that overriding the intensity statistics that mris_make_surfaces computes automatically may solve my issue. If this is possible could I have some advice on how to do this? Otherwise, if you have any advice to fix this problem we would greatly appreciate it. Thanks, Monica ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
