Re: [Freesurfer] brainmask volume disappearing in certain planes in freeview
Hi Rachel, This appears to be some kind of openGL rendering artifact that we are not able to reproduce nor find a definitive solution, unfortunately. It happened to some of us over the years but very very rarely and we were never able to replicate it. It may be a hardware/system glitch. Would it be possible for you to reboot your machine (to flush opengl cache)? or even update your graphics driver? Best, Ruopeng On 05/31/2018 02:06 PM, Rachel Smallwood Shoukry wrote: Hello FreeSurfer developers, I'm having an odd problem using freeview. When I open a set of volumes (wm and brainmask) and surfaces (both pial and white), everything seems to work fine. However, when I turn off the volumes to look at the 3D view and then turn them back on when switching back to 2D, the situation in Screenshot1 happens. The brainmask volume disappears in the coronal and axial planes but is still there in the sagittal. Also, it looks like a coordinate appears in large text written backwards superimposed over the surface outlines (mirrored, not just in reverse order), but it's not the coordinate from the current slice. For instance, this coronal slice says R 97.66 and the axial slice says R 147.65. If I zoom in or out, the numbers get larger and smaller. The white matter volume is not affected. Everything works normally if I keep the volumes for viewing 3D rendering. I have a similar thing happen when adding control points (it first happened when creating a new set, but if I load an existing set it happens also). The image is fine until I get to a specific coronal slice (usually just a few slices away from where I put the first control point), then the brainmask volume disappears in the coronal view but is still there in sagittal and axial. This time the displayed number is A 58.73 (mirrored), which is actually the label on the exact slice where brainmask disappears for this subject, but this number does change sometimes when scrolling through slices, but not on most slices and it doesn't change to match the current label. If I close and re-open freeview with the same set of volumes and surfaces, they come up the way they should and remain as they should unless I turn off the volumes while looking at the 3D rendering or open the control point file again. This has happened for multiple subjects/sets of files, and no messages appear in the terminal when this happens. I'm using a Linux with CentOS 6.9. Any idea what could be causing this and/or how to fix it? Thanks! Rachel ___ 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.
Re: [Freesurfer] Brainmask Shifted
what is your freeview command? On 6/14/17 3:51 PM, KALEY E ELLIS wrote: Dear FreeSurfer Developers, We are using FreeSurfer v6.0 and our operating system is OS X El Capitan version 10.11.6. We are going through the manual editing process and are checking the brainmask by following these instructions: http://freesurfer.net/fswiki/FsTutorial/SkullStripFixV6.0 We have two subjects who appear to have brainmasks that are shifted up considerably (see attached image). The recon-all.log file indicates that it finished without errors: reading volume /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz... reading input surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... reading input pial surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial... reading input white surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 277 173970 3.493 0.659 0.107 0.0393 0.4 ./rh.entorhinal_exvivo.label #-- Started at Thu Jun 8 10:50:24 CDT 2017 Ended at Fri Jun 9 00:06:58 CDT 2017 #@#%# recon-all-run-time-hours 13.276 recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58 CDT 2017 Could you please advise me on how to correct this issue? We have run all of these subjects the same way, but only two have had this problem. Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison ___ 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.
Re: [Freesurfer] Brainmask edit error
Hi Sabrina, I talked to Bruce and he said we can improve the surfaces further if we try labeling the lesion as "Left_Lesion" in the aseg and then running recon-all from that point onward. It should freeze the white surface exactly where you draw voxels (so be careful with it) but still let the pial deform outwards. Right now, labeling the wm.mgz helps improve things but the ?h.white surf still ignores the edits in some places. If you directly edit the aseg then the surfaces will follow those boundaries exactly. I'll try it on a few slices of the data and let you know the results, but you can also do it if you like. -Ani On 06/07/2016 04:46 PM, Sabrina Yu wrote: Hi Ani, I really appreciate the time and effort you are putting in to help me find a solution to this problem. The surface does look much more promising. Following your instructions in the email, I have been playing around with editing the wm.mgz and have been able to generate better wm surfaces. With these edits, will I also be able to improve the aparc.mgz and aparc+aseg.mgz? Thanks so much, Sabrina *From:* freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ani Varjabedian <a...@nmr.mgh.harvard.edu> *Sent:* Tuesday, June 7, 2016 5:45:43 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Brainmask edit error 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 <a...@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
Re: [Freesurfer] Brainmask edit error
Hi Ani, I really appreciate the time and effort you are putting in to help me find a solution to this problem. The surface does look much more promising. Following your instructions in the email, I have been playing around with editing the wm.mgz and have been able to generate better wm surfaces. With these edits, will I also be able to improve the aparc.mgz and aparc+aseg.mgz? Thanks so much, Sabrina From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ani Varjabedian <a...@nmr.mgh.harvard.edu> Sent: Tuesday, June 7, 2016 5:45:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainmask edit error 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 <<mailto:a...@nmr.mgh.harvard.edu>a...@nmr.mgh.harvard.edu<mailto:a...@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
Re: [Freesurfer] Brainmask edit error
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 <a...@nmr.mgh.harvard.edu <mailto:a...@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 -autorecon2-pial Thanks, Sabrina On Jun 1, 2016, at 4:39 PM, Ani Varjabedian <a...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl<fis...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl<fis...@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 fi
Re: [Freesurfer] Brainmask edit error
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 -autorecon2-pial Thanks, Sabrina On Jun 1, 2016, at 4:39 PM, Ani Varjabedian <a...@nmr.mgh.harvard.edu <mailto:a...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl<fis...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl<fis...@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 -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.har
Re: [Freesurfer] Brainmask edit error
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 -autorecon2-pial Thanks, Sabrina > On Jun 1, 2016, at 4:39 PM, Ani Varjabedian <a...@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-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl >>> <fis...@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-boun...@nmr.mgh.harvard.edu >>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl >>>> <fis...@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 -autorecon2-pial, the sur
Re: [Freesurfer] Brainmask edit error
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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@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 -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 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] Brainmask edit error
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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@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 -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 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] brainmask error
Hi Bruce (and the rest of the list), It looks better (see attached) but it still look like it removed too much. cheers for the point though, Mads On 21/08/14 16:22, Bruce Fischl wrote: Hi Mads what does it look like if you move off the mideline? Or check a coronal view? Sagittal views of the midline are notoriously bad for judging skull stripping accuracy cheers Bruce On Tue, 19 Aug 2014, Mads Jensen wrote: Dear list, I have problem with the brainmask from a subject where there is removed to much of the gray matter. So, I would like to hear if someone has a good idea where I should start to fix this issue? I have attached a jpgs of the brainmask and orig, and a link to the recon-all.log best regards, mads https://dl.dropboxusercontent.com/u/915037/recon-all.log ___ 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] brainmask error
Are you sure? Did you flip back and forth between this and a volume with the skull? On Aug 25, 2014, at 7:13 AM, Mads Jensen mje.m...@gmail.com wrote: Hi Bruce (and the rest of the list), It looks better (see attached) but it still look like it removed too much. cheers for the point though, Mads On 21/08/14 16:22, Bruce Fischl wrote: Hi Mads what does it look like if you move off the mideline? Or check a coronal view? Sagittal views of the midline are notoriously bad for judging skull stripping accuracy cheers Bruce On Tue, 19 Aug 2014, Mads Jensen wrote: Dear list, I have problem with the brainmask from a subject where there is removed to much of the gray matter. So, I would like to hear if someone has a good idea where I should start to fix this issue? I have attached a jpgs of the brainmask and orig, and a link to the recon-all.log best regards, mads https://dl.dropboxusercontent.com/u/915037/recon-all.log ___ 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. coronal.jpg ___ 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] brainmask error
Hi Mads what does it look like if you move off the mideline? Or check a coronal view? Sagittal views of the midline are notoriously bad for judging skull stripping accuracy cheers Bruce On Tue, 19 Aug 2014, Mads Jensen wrote: Dear list, I have problem with the brainmask from a subject where there is removed to much of the gray matter. So, I would like to hear if someone has a good idea where I should start to fix this issue? I have attached a jpgs of the brainmask and orig, and a link to the recon-all.log best regards, mads https://dl.dropboxusercontent.com/u/915037/recon-all.log ___ 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] BrainMask Edits
Question regarding the use of skull stripping errors. I am wondering if it is possible to correct (use the -wsthresh or -gcut) in longitudinal processed data or would these types of edits be required in the earlier processing steps (initial FreeSurfer recon-all)? Thanks in advance for any help with this. David F. Tate, Ph.D. ___ 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] brainmask VS wm correction
Hi Elisa it's tough to tell from just the wm.mgz image. Are the voxels excluded from the pial brain or are they dura? What does the orig surface show? If the orig doesn't follow the wm.mgz and you think it should, that means there is a topological defect that was inaccurately corrected and you need to fix that cheers Bruce On Fri, 31 Jan 2014, elisa veronese wrote: Dear all, I am trying to manually correct the segmentation result in one subject. My problem is that I am not sure if in the area highlighted with the green circle (see attached file) the volume I should correct is the brainmask.mgz or the wm.mgz. The pial boundary looks uncorrect, so I'd correct the brainmask. But those voxels seem to belong to the wm.mgz volume, as well... Thank you. Best, Elisa -- Elisa Veronese - PhD Research Unit on Brain Imaging and Neuropsychology (RUBIN) Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php ___ 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] brainmask and wm correction
Hello all, I am new to FreeSurfer and still trying to understand how things work. I am currently trying to understand how the manual correction works. Following the online tutorials I was able to fix the brainmask and wm.mgz, and also add control points in the wm so that low intensity wm is also included in the segmentation. In the tutorials it is suggested to run the FreeSurfer after doing the brainmask correction by recon-all -autorecon2 -subjid subject name After the wm control point addition, the tutorial says that run the program with -autorecon2-cp Is it possible to do brainmask correction, white matter edits and control points in one session and run the FreeSurfer again to fix all this at once? Is there a different command for this? I apologize if this has been answered before. Thanks a lot. Deniz. ___ 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] brainmask and wm correction
Yes, you would just run the command for the fix that happens earliest on in the processing stream. The order these fixes occur in the processing stream is: control points wm edits pial edits So if you've done all 3, you only need to run recon-all -autorecon2-cp -autorecon3 -s subjid and it will take care of all those edits for you. Allison -- On Tue, 25 May 2010, Deniz Ozgen wrote: Hello all, I am new to FreeSurfer and still trying to understand how things work. I am currently trying to understand how the manual correction works. Following the online tutorials I was able to fix the brainmask and wm.mgz, and also add control points in the wm so that low intensity wm is also included in the segmentation. In the tutorials it is suggested to run the FreeSurfer after doing the brainmask correction by recon-all -autorecon2 -subjid subject name After the wm control point addition, the tutorial says that run the program with -autorecon2-cp Is it possible to do brainmask correction, white matter edits and control points in one session and run the FreeSurfer again to fix all this at once? Is there a different command for this? I apologize if this has been answered before. Thanks a lot. Deniz. ___ 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] brainmask/wm edits
Hi, I have a similar questionto the one listed below. After I edit brainmask.mgz and wm.mgz, my understanding was that I could run autorecon2-wm and would not have to run autorecon2-pial because -wm will run everything else through the end of -autorecon2. However, if brainmask.mgz is run at the end of autorecon1, don't I need to run autorecon1 again, since wm or contol point edits would alter the brainmask?? Thanks for help, Helen Hi Dana, you can do autorecon2-cp and it will do both things (the wm comes after it in the stream anyway) cheers Bruce On Tue, 9 Mar 2010, Dana W. Moore wrote: Hello everyone, There is an image that needs white matter edits (editing voxels) as well as control points. I know the two commands I need to re-run are autorecon2-cp and autorecon2-wm. Can I do both kinds of edits and somehow combine the -cp and -wm commands, or do I need to do the control points first, re-run, and then do further white matter edits? Thanks, Dana -- Helen L. Keefe Mental Health Clinical Research Center Image Processing Lab University of Iowa 319-353-8586 ___ 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] brainmask/wm edits
Hi Helen, That's a good question. You don't have to start at autorecon1, however. When you run -autorecon2-wm or -autorecon2-pial one of the first steps is: mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz which is changing the brain.finalsurfs.mgz to take into account the changes you made to the brainmask.mgz. Your edits are not lost. Allison -- On Thu, 11 Mar 2010, Helen Keefe wrote: Hi, I have a similar questionto the one listed below. After I edit brainmask.mgz and wm.mgz, my understanding was that I could run autorecon2-wm and would not have to run autorecon2-pial because -wm will run everything else through the end of -autorecon2. However, if brainmask.mgz is run at the end of autorecon1, don't I need to run autorecon1 again, since wm or contol point edits would alter the brainmask?? Thanks for help, Helen Hi Dana, you can do autorecon2-cp and it will do both things (the wm comes after it in the stream anyway) cheers Bruce On Tue, 9 Mar 2010, Dana W. Moore wrote: Hello everyone, There is an image that needs white matter edits (editing voxels) as well as control points. I know the two commands I need to re-run are autorecon2-cp and autorecon2-wm. Can I do both kinds of edits and somehow combine the -cp and -wm commands, or do I need to do the control points first, re-run, and then do further white matter edits? Thanks, Dana ___ 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] brainmask
if one wants to get at the brain only (similar to bet), is brainmask.mgz the best file to use? on some of our data, we are noticing a lot of eyeball. i presume one can use aseg as an alternative. is this more recommended than brainmask.mgz? also, is the total brain volume computation based on aseg or some other file? cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] brainmask
aparc+aseg.mgz is probably better. See surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume for the answer to your question. Satrajit Ghosh wrote: if one wants to get at the brain only (similar to bet), is brainmask.mgz the best file to use? on some of our data, we are noticing a lot of eyeball. i presume one can use aseg as an alternative. is this more recommended than brainmask.mgz? also, is the total brain volume computation based on aseg or some other file? cheers, satra ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] brainmask volume greater than ICV
Hi, I am running FS-4.3.0 and after recon-all -all, I am finding in aseg.stats of quite a few of my subjects that brain mask volume (1735600 mm^3) is greater than ICV (1701891 mm^3). The talairach failure detection passed fine: talairach.xfm OK (p=0.7556, pval=0.6675 = threshold 0.005 ). The segstat step passed fine, with atlas_icv (eTIV) = 1701891 mm^3 (det: 1.144671). However, the mris_volmask, which followed right after the segstat exited with errors and dumped the core. I see this on about 30% of my analyzes. :( I can provide the data, if that could help. Thanks, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
