Re: [Freesurfer] Pial surface missing GM
Hi Bruce, Thanks for the response. I just uploaded the subject using the ftp file exchange. The issue is visible in the region close to voxel coordinate [172, 123 ,134]. the missing gyrus is capped between coronal slice 141 to 118. I forgot to mention in my first message that we used a T2 to improve pial surface after initial running with just the T1. Thanks again Jake Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl wrote: > Hi Jake > > usually that means that there is a topology defect that is being > incorrectly fixed. If you upload the subject and point us at the voxel > coords we will take a look > > cheers > Bruce > > On Wed, 26 Jul 2017, Jake Rieke wrote: > > > Hello surfers, > > > > I'm attempting to extend white and pial surfaces to encompass an > > unrecognized gyrus. The wm.mgz seems include the WM tissue, but the white > > surface does not extend to the WM boundary. I thought this might be > related > > to an intensity normalization error and tried using control points, but > that > > did not make a big difference in the resulting surfaces. I've attached > > pictures to better illustrate the problem. Thanks in advance for your > help! > > > > Best regards, > > Jake > > > > > > > ___ > 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 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.
Re: [Freesurfer] Pial surface missing GM
Thanks, Bruce and Douglas! Looking at the surface prior to the topology correction step has been very helpful. I can see the region you pointed out - where the wm.mgz connects to the body of the wm, disconnects, and then reconnects at a different spot. I'm having some trouble implementing the manual edits to the wm.mgz. Part of the problem is that I'm still training my eye to differentiate GM and WM (especially in cases with thin tracts or partial voluming), but this gives me a great place to start. I'm wondering, in general, is the idea to erase or add voxels in the wm.mgz where the defects are located? In other words, defects can be interpreted as areas of misclassified as WM? In this case, it seems that I need to focus on deleting voxels in the wm.mgz that are incorrectly segmented. Thanks, Jake Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com On Thu, Jul 27, 2017 at 1:09 PM, Bruce Fischl wrote: > Hi Jake > > there are voxels like 173, 112, 122 that are incorrectly segmented as wm > (that is, they have a value >=5 in the wm.mgz) that connect two adjenct > gyri. You can either change the intensity thresholds in mri_segment, or > manually erase some of them. The best way to see this is to look at the > surface prior to topology correction, and color it with defect numbers so > you can see where the defects are. Something like: > > cd $SUBJECTS_DIR//mri > freeview -v brain.mgz wm.mgz:colormap=heat:heatscale=1,100 \ > -f ../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels:overl > ay_threshold=1,255:edgecolor=overlay \ > -slice 172 123 134 > > > if you page through a few axial slices you will see that the wm.mgz is > connected to the body of the wm in slice 109, disconnecs in 110, then > reconnects to a different part in 115, which should never happen > > cheers > Bruce > On Thu, 27 Jul 2017, Jake Rieke wrote: > > Hi Bruce, >> >> Thanks for the response. I just uploaded the subject using the ftp file >> exchange. The issue is visible in the region close to voxel coordinate >> [172, >> 123 ,134]. the missing gyrus is capped between coronal slice 141 to 118. I >> forgot to mention in my first message that we used a T2 to improve pial >> surface after initial running with just the T1. >> >> Thanks again >> Jake >> >> Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall >> VA >> >> Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 >> Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com >> >> On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl > > >> wrote: >> Hi Jake >> >> usually that means that there is a topology defect that is being >> incorrectly fixed. If you upload the subject and point us at the >> voxel >> coords we will take a look >> >> cheers >> Bruce >> >> On Wed, 26 Jul 2017, Jake Rieke wrote: >> >> > Hello surfers, >> > >> > I'm attempting to extend white and pial surfaces to encompass >> an >> > unrecognized gyrus. The wm.mgz seems include the WM tissue, >> but the white >> > surface does not extend to the WM boundary. I thought this >> might be related >> > to an intensity normalization error and tried using control >> points, but that >> > did not make a big difference in the resulting surfaces. I've >> attached >> > pictures to better illustrate the problem. Thanks in advance >> for your help! >> > >> > Best regards, >> > Jake >> > >> > >> > >> ___ >> 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. >> >> >> >> >
Re: [Freesurfer] Pial surface missing GM
Okay, understood. Thanks again for your help. Best regards, Jake On Fri, Jul 28, 2017 at 11:20 AM, Bruce Fischl wrote: > it depends. In this case you want to erase as it creates an incorrect > connection. In others you want to add if there is an incorrect break > On Fri, 28 Jul 2017, Jake Rieke wrote: > > Thanks, Bruce and Douglas! Looking at the surface prior to the topology >> correction step has been very helpful. I can see the region you pointed >> out >> - where the wm.mgz connects to the body of the wm, disconnects, and then >> reconnects at a different spot. I'm having some trouble implementing the >> manual edits to the wm.mgz. >> Part of the problem is that I'm still training my eye to differentiate GM >> and WM (especially in cases with thin tracts or partial voluming), but >> this >> gives me a great place to start. >> >> I'm wondering, in general, is the idea to erase or add voxels in the >> wm.mgz >> where the defects are located? In other words, defects can be interpreted >> as >> areas of misclassified as WM? In this case, it seems that I need to focus >> on >> deleting voxels in the wm.mgz that are incorrectly segmented. >> >> Thanks, >> Jake >> >> Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall >> VA >> Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 >> Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com >> >> On Thu, Jul 27, 2017 at 1:09 PM, Bruce Fischl > > >> wrote: >> Hi Jake >> >> there are voxels like 173, 112, 122 that are incorrectly >> segmented as wm (that is, they have a value >=5 in the wm.mgz) >> that connect two adjenct gyri. You can either change the >> intensity thresholds in mri_segment, or manually erase some of >> them. The best way to see this is to look at the surface prior >> to topology correction, and color it with defect numbers so you >> can see where the defects are. Something like: >> >> cd $SUBJECTS_DIR//mri >> freeview -v brain.mgz wm.mgz:colormap=heat:heatscale=1,100 \ >> -f../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels: >> overlay_threshold=1, >> 255:edgecolor=overlay \ >> -slice 172 123 134 >> >> >> if you page through a few axial slices you will see that the >> wm.mgz is connected to the body of the wm in slice 109, >> disconnecs in 110, then reconnects to a different part in 115, >> which should never happen >> >> cheers >> Bruce >>On Thu, 27 Jul 2017, Jake Rieke wrote: >> >> Hi Bruce, >> >> Thanks for the response. I just uploaded the subject >> using the ftp file >> exchange. The issue is visible in the region close >> to voxel coordinate [172, >> 123 ,134]. the missing gyrus is capped between >> coronal slice 141 to 118. I >> forgot to mention in my first message that we used a >> T2 to improve pial >> surface after initial running with just the T1. >> >> Thanks again >> Jake >> >> Biomedical Engineer, Brain Rehabilitation Research >> CenterMalcolm Randall VA >> Medical Center, 1601 SW Archer Road, Gainesville, FL >> 32608 >> Phone: 1-352-376-1611 ext. 5249, E-mail: >> jakeri...@gmail.com >> >> On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl >> >> wrote: >> Hi Jake >> >> usually that means that there is a topology >> defect that is being >> incorrectly fixed. If you upload the subject >> and point us at the >> voxel >> coords we will take a look >> >> cheers >> Bruce >> >> On Wed, 26 Jul 2017, Jake Rieke wrote: >> >> > Hello surfers, >> > >> > I'm attempting to extend white and pial >> surfaces to encompass >> an >> > unrecognized gyrus. The wm.mgz seems include >> the WM tiss
Re: [Freesurfer] Unknown regions in cortical parcellation
We are using Freesurfer v6.0 Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve wrote: > what version of FS are you using? > > > On 09/07/2017 03:19 PM, Aidan Murphy wrote: > > > > We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the > > aparc volume we're noticing fairly large unknown regions in what > > should be entorhinal cortex, specifically where it comes up against > > the hippocampus and amygdala. The aseg volumes label these unknown > > regions as cortex. I've searched the archives and haven't been able to > > find anything similar from recent years. > > > > I've attached some axial screenshots of the raw T1, the aseg and the > > aparc+aseg. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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 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] Edits to aparc+aseg
Hi FreeSurfers, I have a group of subjects with manual edits to the aparc+aseg volume. These edits were made to re-label unknown regions of cortex. I am wondering what recon-all flags I could use to implement the changes and re-generate cortical stats based on these edits. Thanks in advance. Best regards, Jake ___ 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.
