Hi Sabrina, Just wanted to update you on my progress.
I tried editing the wm.mgz and filling in the hole to see if that might help things. If we can get the wm surface accurate then there is a good chance the pial surf (which grows from the white) will follow suit. After I edited the wm surf I ran this command to quickly generate the next step and check prelim surfaces
recon-all -fill -tessellate -s SUBJECT01_wmedit
I made a copy of your subject to keep track of my edits, that's why the name is a bit different. But basically I generated the filled volume (from the wm.mgz) and then made the surfaces ?h.orig.nofix. These are prelim surfaces to what will eventually become the wm surfaces. If they look good then there is hope that this edit might do the trick!
I've attached a screenshot and you can see that it did help push the surfs out a bit more. I obviously did not edit the wm.mgz as carefully or accurately as I could have but if this works then you can try it yourself with more knowledge of the stroke region.
So! The next step is to see what the ?h.white surfs look like and to do that I ran this command:
recon-all -smooth1 -inflate1 -qshpere -fix -white -s SUBJECT01_wmedit
I am getting these commands here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable This is a really helpful table that lists the FS pipeline and all the different steps so you can pick and choose which ones to run if you want to see a result quickly.
I didn't check which version of FS you were using. I'm running the dev version of 6.0 so some things might be a bit different but overall the major steps should be the same enough to make a comparison. To see a list of your recon-all steps you can always use the -dontrun flag with your subject and it will just print out all the commands to the logfile without actually running them. It's a really good way to get a list of the steps and then you can look into what they do!
Anyways, when this is done I will update you on the white surfs. If they look good then I will try the next step which will be generating the pial!
Hope all is well and thank you again for being so patient during this busy time. -Ani
On 06/02/2016 02:15 PM, Ani Varjabedian wrote:
Hi Sabrina,
I'm not entirely sure about that, but if my manual edits don't work I'll let Bruce know and we can discuss other workarounds.
-Ani
On 06/02/2016 12:55 PM, Sabrina Yu wrote:
Hi Ani,
Thanks so much for your explanation, it makes sense that the brain is too deformed for one continuous surface. If we are not able to find a workaround that creates a continuous surface, can I create a separate surface just for the stroke region? And generate average voxel intensity for that region?
Thanks, Sabrina
On Jun 2, 2016, at 6:21 PM, Ani Varjabedian aniv@nmr.mgh.harvard.edu wrote:
Hi Sabrina,
Usually we don't add voxels in the brainmask. We usually add to the wm.mgz which pushes the white surf out and ultimately the pial surf out (because it grows from the white). If the area around the stroke on both sides looks good but there is a hole in the middle where there is no information or labels, then the surfaces will not connect all the way around it. They treat it like two separate pieces. Does this make sense? I'll try to play around with some different things (like adding to the wm.mgz) and see if I can get the surfaces to be continuous around this region.
Like Bruce said, it might end up being that the brain is too different from what freesurfer assumes a brain to look like, but I will try some work arounds and get back to you.
Thank you, Ani
On 06/02/2016 08:18 AM, Sabrina Yu wrote:
Hi Ani,
Thanks for looking into this for me. I'm actually out of town right now, so cannot access the subject in front of me.
Yes, it is. As I am trying to generate the stats on intensity over an ROI, I am hoping to be able to generate good surfaces. To me, the aseg looks pretty good. The brain matter around the stroke area is recognized, but is not in the surfaces.
I only edited the brainmask.mgz. I unfortunately cannot tell you the exact slices that I edited until I am back, but I tried to recon edit and add in voxels in the stroke area. I did not notice major problems with the surface including dura or skull, so I did not really remove voxels. I'm not sure if how I did it is correct, but I tried to follow the wiki page on pial surface edits. The command I used to try to regenerate the surface was: recon-all -subjid <SUBJECT> -autorecon2-pial
Thanks, Sabrina
On Jun 1, 2016, at 4:39 PM, Ani Varjabedian aniv@nmr.mgh.harvard.edu wrote:
Hello Sabrina,
I have received the subject and am looking at it now. I've attached a screenshot that is similar to the one you sent. At [158, 115, 124] I see a hole in the aseg, wm mask, so it makes sense that the brainmask does not cross over the area. Is this the area you wish to include? I just want to make sure I'm looking at the correct region.
What have you done so far to edit? I know you mentioned brainmask editing, but what specifically did you do?
Thank you, Ani
On 05/25/2016 08:47 AM, Ani Varjabedian wrote:
Hi Sabrina,
Could you upload the whole subject folder to the FTP or to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ I can play around with the data a bit to see if we can improve surfaces. If that doesn't work then we can discuss other options for how to get the information you need.
Thanks!
-Ani
On 05/23/2016 05:47 PM, Sabrina Yu wrote: > Thank you for your explanation. Would it be possible to find a workaround? I want to generate stats on intensity over an ROI for these stroke subjects. For the brain matter not included in the surface, can I create a volume label file in freeview instead of trying to edit the surfaces? > > Thank you, > Sabrina > ________________________________________ > From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischlfischl@nmr.mgh.harvard.edu > Sent: Monday, May 23, 2016 12:30:30 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Brainmask edit error > > because it violates too many of our assumptions about the topology and > geometry of the brain. > > cheers > Bruce > On Mon, 23 May 2016, Sabrina Yu > wrote: > >> Hi Bruce, >> >> Thank you for your reply. I've uploaded the .mgz and surfaces using FTP to FreeSurfer. Why is it that it may not be possible to get good surfaces with extensive strokes? >> >> Thank you, >> Sabrina >> ________________________________________ >> From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischlfischl@nmr.mgh.harvard.edu >> Sent: Thursday, May 19, 2016 11:24:51 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Brainmask edit error >> >> Hi Sabrina >> >> it's tough to tell from just the 2 slices. If you upload the subject one >> of us will take a look, but it may not be possible to get good surfaces >> with that extensive a stroke >> >> cheers >> Bruce >> On Wed, 18 May 2016, Sabrina Yu wrote: >> >>> Hello, >>> >>> >>> I'm having problems with regenerating the surfaces for stroke cases after >>> editing the brainmask.mgz file. In the aseg.mgz file, the brain matter >>> around lesion area is correctly classified as brain matter. In the pial >>> surface, this brain matter is not included. >>> >>> >>> I've tried to edit the brainmask.mgz file to include this region, but when I >>> run: recon-all -subjid <SUBJECT> -autorecon2-pial, the surfaces generated >>> are not changed at all. >>> >>> >>> I have attached some images to this email. I'm new to Freesurfer, so any >>> help would be greatly appreciated. >>> >>> >>> Thank you. >>> >>> >>> >>> >>> >> _______________________________________________ >> 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 > > > 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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