Re: [Freesurfer] White Matter Edits: Removing White Matter from the WM Surface

Hi Arkadiy that's a bit strange looking. What does the orig surface look like? And the orig.nofix? If you upload this entire subject and tell us what voxel coords this spot is we will take a look cheers Bruce On Wed, 24 Jan 2018, Maksimovskiy, Arkadiy wrote: Dear Experts, I came across

Re: [Freesurfer] white matter edits not incorporated.

Dear All, I wanted to know if there is any take on the issue of white matter edits (specifically deleting unwanted voxels from wm.mgz). I sent a subject a week ago for your review. It seems this is a problem that I had with several scans, and by the message list, I am not the only one. Recent

[Freesurfer] White Matter Edits

Hello, I am a staff research associate for a group that specializes in MRI of Multiple Sclerosis. We use freesurfer's reconstruction approach, however the white matter masks are not very good for the MS disease population. We have combined the FreeSurfer algorithm with ANTS in order to get

Re: [Freesurfer] white matter edits not incorporated

yes, I think that's what V6 does I think On Thu, 21 Apr 2016, dgw wrote: Hi, I solved it (with help from a colleague) by just calling the individual mri_make_surfaces command separately (adjusting the nowhite), and the subsequent ones through the flair pial command. I am now running -make all,

Re: [Freesurfer] white matter edits not incorporated

Hi, I solved it (with help from a colleague) by just calling the individual mri_make_surfaces command separately (adjusting the nowhite), and the subsequent ones through the flair pial command. I am now running -make all, to finish the rest (note it did miss one step in the re-start: it didn't

Re: [Freesurfer] white matter edits not incorporated

Hi Mike yes, I think it is fixed. Daniel: can you try out dev and see if it fixes this for you? Bruce On Thu, 21 Apr 2016, Harms, Michael wrote: That looks very similar in principle to something I posted back in Oct. 2014 (“pial surface crossing white”). I think some of the subsequent

Re: [Freesurfer] white matter edits not incorporated

Hi Daniel I'm out if town , can you remind me next week? This is fixed in v6 I think if you want to just run the pial stuff in it Bruce > On Apr 21, 2016, at 10:41 AM, dgw wrote: > > Hi, > > I followed the advice, and the White Matter surface looks much better; >

Re: [Freesurfer] white matter edits not incorporated

That looks very similar in principle to something I posted back in Oct. 2014 (“pial surface crossing white”). I think some of the subsequent back-and-forth with Bruce and Nick was off the list, so I’ve included the key email (where Bruce diagnosed the problem) below. Has this been fixed in the

Re: [Freesurfer] white matter edits not incorporated

Hi, I followed the advice, and the White Matter surface looks much better; however, now the pial surface is crossing the white matter surface. I ran the following: /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8 for those at Martinos the new

Re: [Freesurfer] white matter edits not incorporated

Hi Bruce, Thanks! I'll give it a whirl. d On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl wrote: > Hi Daniel > > the problems isn't that it it's ignoring the wm edits, it is that it starts > the orig surface out there, but then retracts to the (same) visible >

Re: [Freesurfer] white matter edits not incorporated

Hi Daniel the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the

Re: [Freesurfer] white matter edits not incorporated

can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote: > Just to follow up, I have tried several different options with > recon-all to get the white matter edits to stick on this participant, > and it doesn't seem to be

Re: [Freesurfer] white matter edits not incorporated

Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working: re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all I can't seem to get any

[Freesurfer] white matter edits not incorporated

Hi, I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 none of the edits were incorporated. Is the

Re: [Freesurfer] White Matter Edits vs. Control Points, & third party software

Hi Alberto 1. No, this is not the same. The control points are used to estimate the bias field, which can affect an entire regions. Replacing a voxel in the brainmask with a 110 will only affect that voxel. 2. You can do this if you want but you have to be careful how you edit. When we turn

Re: [Freesurfer] White Matter Edits vs. Control Points, & third party software

Alberto, I included detailed replies below, but I have a question before you get to those. Why don't you want to follow the FreeSurfer techniques for reconstruction? You suggested several other ways, but I don't understand your motivation for not wanting to follow the instructions for

[Freesurfer] White Matter Edits vs. Control Points, & third party software

I have some questions about how to manually correct the white matter regions . It's the same manually edit the volume "brainmask.mgz" and use control points? Would I get the same result? My intention is not to use control points, but directly replace the voxels that have not been classified as

[Freesurfer] White matter edits

Hello, I am visually checking wm.mgz after running recon-all. There seems to be a pattern where I'm seeing white matter bleed past the (correct) white matter surface and into gray matter or appear in the sagittal sinus/dura. However, when I look at wmparc.mgz, the problem is no longer there and

Re: [Freesurfer] White matter edits

nope, that's why we usually trust the surfaces more than the volume segmentations. cheers Bruce On Wed, 26 Mar 2014, Eleanor Stahura wrote: Hello, I am visually checking wm.mgz after running recon-all. There seems to be a pattern where I'm seeing white matter bleed past the (correct) white

Re: [Freesurfer] White matter edits

Hi Alexarae it's pretty much impossible for us to diagnose the problem from a single slice of the wm.mgz. If you upload the subject and send us some voxel coords of where the problem is we will take a look. cheers Bruce p.s. in general you don't need nearly that many control points. You

Re: [Freesurfer] white matter edits

Vincent, Some may look like holes but as you mention are just sulci being cut through by that plane. A way to check if it is the above is to put the cursor on the surface that creates this hole and then toggle to the other views (sagittal, axial, coronal). It will become clearer whether it is

[Freesurfer] white matter edits

According to the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, we should be looking for these holes in the white surface, but when I looked at my processed data using tkmedit SUBJECT brainmask.mgz -aux wm.mgz -surfs, I saw many such holes. They seem to be

Re: [Freesurfer] White matter edits and talairach.xfm

Hi Jesse, I doubt these have anything to do with talairach. Have you added control points? If not, I don't understand the cause of the local brightening that your images show in both the cerebellum and cortex in what is either the end of a white matter strand or in the gray matter itself.

Re: [Freesurfer] White matter edits and talairach.xfm

yes, I do think it's causing the bumps, and also leading to inaccuracy in the surface locations. Usually these are associated with susceptibility artifacts, but not usually in those locations, so I'm not sure what's going on Bruce On Sun, 24 Jan 2010, Jesse Bledsoe wrote: Hi Bruce, I have

Re: [Freesurfer] white matter edits

It's a little bumpier than usual but ultimately you would have to look at the surfaces in tkmedit to determine whether these are errors. Allison -- On Fri, 4 Dec 2009, Jesse Bledsoe wrote: Hi experts, Should I be concerned about the number of white matter errors in the attached tif? Is

Re: [Freesurfer] white matter edits

Hi Jesse, you can't tell from an inflated surface what wm needs editing. You need to look at the surface overlaid on the volume in tkmedit for that. cheers Bruce On Fri, 4 Dec 2009, Jesse Bledsoe wrote: Hi experts, Should I be concerned about the number of white matter errors in the

Re: [Freesurfer] white matter edits

Thank you. I did have the tkmedit and tksurfer windows open at the same time and the surfaces do not seem to be pulling in any non-white matter/dura. When I use the save point/open point and view the wm in tkmedit, I do not see any glaring wm inconsistencies. The brains I am using have been

Re: [Freesurfer] white matter edits

Hi Jesse, we don't find that ac/pc aligning helps. Bruce On Fri, 4 Dec 2009, Jesse Bledsoe wrote: Thank you. I did have the tkmedit and tksurfer windows open at the same time and the surfaces do not seem to be pulling in any non-white matter/dura. When I use the save point/open point and

Re: [Freesurfer] White matter edits - when to do manual corrections?

1. No, if the surface is correct you are fine. 2. Not positive what you mean, but it looks fine to me. 3. The green is usually the orig surface, not the ?h.white one. This is also a non-cortical region, so I wouldn't worry about it cheers Bruce On Wed, 18 Nov 2009, Lena Palaniyappan wrote: