Re: [Freesurfer] freesurfer trouble with FTLD subjects
sounds good Bruce On Mon, 27 Oct 2014, Adam Mezher wrote: Hi Bruce, I performed both cp and wm edits and was able to fix most of the subjects in the meantime. I’ll still see if I can get it ftp’d over to you guys to take a look for future reference. thanks! Adam Hi Adam it's impossible to say without seeing some examples. If you upload a problematic subject (the entire subject directory from recon-all) we will take a look cheers Bruce On Wed, 22 Oct 2014, Adam Mezher wrote: Hi All, I'm running a number of subjects who have FTLD and their surfarce/parcellation outputs are quite poor (especially in the frontal lo be obviously). Are there any expert commands that can be used to attempt to f ix this issue without having to do individual edits? Most of the subjects hav e underestimations in most frontal gyri and insula. Thanks a lot, Adam Adam Mezher USC Imaging Genetics Center Marina Del Rey, CA ___ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly 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] 7T reconstruction
Hello, I am interested in using functional data collected from 7t using freesurfer and fsfast. We would like to use EPI field maps to warp this data to 3T anatomical space. Can anyone guide me as to how to do this. Best, B ___ 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] Creating an ROI mask for Cortical Thickness Analysis
Hey Bruce, Never responded but this worked out great thanks for the help. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 23, 2014 9:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis Hi Michael you can use mri_annotation2label to extract a specific label from the aparc file and go from there. cheers Bruce On Thu, 23 Oct 2014, Smith, Michael wrote: I guess I'm not entirely sure how to do that? Are there any tutorials on how to extract an ROI from the aparc.stats file? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, October 22, 2014 4:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis Why not just get it from the ?h.aparc.stats file? On 10/22/2014 03:43 PM, Smith, Michael wrote: Hello Freesurfer's I am trying to look at the cortical thickness for a specific ROI on the cortical surface (Primary Auditory Cortex: transverse temporal gyri). I found a specific tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ) however the tutorial assumes I already have an ROI mask created. I was wondering if anyone had any tips on creating an ROI for the cortical surface from the parcellation/annotation files. I know you can hand-draw ROI's in tkmedit or freeview but I would prefer something less subjective that doesn't rely on my untrained eye and unsteady hand! Thanks in advance. Best, Michael S. ___ 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 ___ 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] Creating an ROI mask for Cortical Thickness Analysis
glad to hear it Bruce On Tue, 28 Oct 2014, Smith, Michael wrote: Hey Bruce, Never responded but this worked out great thanks for the help. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 23, 2014 9:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis Hi Michael you can use mri_annotation2label to extract a specific label from the aparc file and go from there. cheers Bruce On Thu, 23 Oct 2014, Smith, Michael wrote: I guess I'm not entirely sure how to do that? Are there any tutorials on how to extract an ROI from the aparc.stats file? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, October 22, 2014 4:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis Why not just get it from the ?h.aparc.stats file? On 10/22/2014 03:43 PM, Smith, Michael wrote: Hello Freesurfer's I am trying to look at the cortical thickness for a specific ROI on the cortical surface (Primary Auditory Cortex: transverse temporal gyri). I found a specific tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ) however the tutorial assumes I already have an ROI mask created. I was wondering if anyone had any tips on creating an ROI for the cortical surface from the parcellation/annotation files. I know you can hand-draw ROI's in tkmedit or freeview but I would prefer something less subjective that doesn't rely on my untrained eye and unsteady hand! Thanks in advance. Best, Michael S. ___ 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 ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] LGI fails for fsaverage
Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks cut. It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from. But in any case, I wouldn't advice to run the LGI on the fsaverage, as the pattern of cortical folding is lost from the averaging of the subjects. So I'm not even sure that the algorithm will work even if you get mris_fill to work. Can you tell us more precisely what you are trying to do? And why on the fsaverage rather than on your individual subject? Best, Marie On Oct 28, 2014, at 5:31 AM, Pierre Mégevand pierre.megev...@gmail.commailto:pierre.megev...@gmail.com wrote: Dear all, I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after a good while. More importantly for me, the lh.pial-outer-smoothed surface, which I am after, did not look right. It seems that the first step, mris_fill, produces a volume that does not look very much like a brain anymore (cf. attached screenshot). Any idea why that would happen? Thanks, Pierre -- Pierre Mégevand, MD, PhD PLOS Neuro Communityhttp://neuro.plos.org/ editor - Follow us on Twitterhttp://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitterhttp://twitter.com/pierre_vanmedge - Read my blog herehttp://neuroscimed.wordpress.com/ screenshot3.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] GI analysis of single subject
Hi Maria, Here are the responses: 1. Can you send us a screenshot of what you mean with it doesn't hug the contours of the brain mask? You can use: tkmedit SUBJ T1.mgz lh.pial -aux-surface lh.pial-outer-smoothed (or the corresponding in freeview) and it should give you what correspond to the top image in the wiki page. 2. The color code including many colors as you see in the wiki was created using scuba. With free view / tksurfer you'll rather have a binary color scale. You have to set the minimum at 1, and you will see minimum values around the medial prefrontal regions, and maximal ones around the insula. You can use the following command: tksurfer SUBJ ?h pial -overlay /surf/?h.pial_lgi -fthresh 1. See as well the jove video explaining the process here: http://www.jove.com/video/3417 (subscription required) 3. Yes you can get all of that: numerical values for each vertex are stored in the ?h.pial_lgi (curv format). Otherwise, average lGI over the entire hemisphere should be written at the end of the lGI process in your command line (or in your log). And you can get statistics in ROI using: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats Hope it helps, Marie On Oct 27, 2014, at 10:02 PM, Maria Holland mho...@stanford.edumailto:mho...@stanford.edu wrote: Hi all, I'm trying to get gyrification information about a single subject. I've run the -localGI process but I have a few questions about the results: 1. When I try to plot the smoothed out pial surface over the brainmask in freeview, I use the command freeview -v subject/mri/brainmask.mgz -f subject/surf/lh.pial-outer-smoothed but it appears to be an inflated surface of some sort. It doesn't hug the contours of the brain mask as I expected (or as shown in the top image here: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI). How can I see that surface? 2. I see very little variation in the local GI. I'm wondering if the third image in the link above is typical, and also how to get the blue to red color scale as shown? I can only get red to yellow, which doesn't show as much variation. 3. There is information on how to run analysis on a group of subjects, but I'm wondering if it's possible to get numerical data on a single subject. For instance: average GI in a given ROI, global GI, distribution (min, max, std dev, etc.). If nothing else, can I get the numerical values for each vertex? Thanks for your help! ~ Maria Holland Stanford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] LGI fails for fsaverage
It does not surprise me that it fails on the fsaverage surface. I agree with Marie that it is not good idea to use LGI on fsaverage for anything. Definitely not its intended purpose. doug On 10/28/2014 03:06 PM, Marie Schaer wrote: Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks cut. It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from. But in any case, I wouldn't advice to run the LGI on the fsaverage, as the pattern of cortical folding is lost from the averaging of the subjects. So I'm not even sure that the algorithm will work even if you get mris_fill to work. Can you tell us more precisely what you are trying to do? And why on the fsaverage rather than on your individual subject? Best, Marie On Oct 28, 2014, at 5:31 AM, Pierre Mégevand pierre.megev...@gmail.com mailto:pierre.megev...@gmail.com wrote: Dear all, I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after a good while. More importantly for me, the lh.pial-outer-smoothed surface, which I am after, did not look right. It seems that the first step, mris_fill, produces a volume that does not look very much like a brain anymore (cf. attached screenshot). Any idea why that would happen? Thanks, Pierre -- Pierre Mégevand, MD, PhD PLOS Neuro Community http://neuro.plos.org/ editor - Follow us on Twitter http://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter http://twitter.com/pierre_vanmedge- Read my blog here http://neuroscimed.wordpress.com/ screenshot3.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 -- 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
[Freesurfer] Corpus Callosum segmentation
Is the corpus callosum segmentation based on the Hofer and Frahm functional parcellation, a mathematical formula, or, as listed on the website, 5 equal subdivision roughly along the long axis? What is the preferred citation for this? Thanks. ___ 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] LGI fails for fsaverage
Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage. Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to localize the electrodes, and a pre-implant MR scan to which we co-register the post-op exams and to whose smoothed outer pial surface we then snap the electrodes to, in order to account for the brain shift caused by the implantation procedure (Dykstra et al., 2012). Now, for one of our patients, the pre-op MRI was acquired with a lot of gadolinium, and we can't get Freesurfer to compute the pial surface. So I thought I would co-register the post-op exams to the fsaverage brain, and then snap the electrodes to fsaverage's outer smoothed pial surface as an approximation. Any idea how else I could do this? Thanks, Pierre On Oct 28, 2014 3:06 PM, Marie Schaer marie.sch...@unige.ch wrote: Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks cut. It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from. But in any case, I wouldn't advice to run the LGI on the fsaverage, as the pattern of cortical folding is lost from the averaging of the subjects. So I'm not even sure that the algorithm will work even if you get mris_fill to work. Can you tell us more precisely what you are trying to do? And why on the fsaverage rather than on your individual subject? Best, Marie On Oct 28, 2014, at 5:31 AM, Pierre Mégevand pierre.megev...@gmail.com wrote: Dear all, I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after a good while. More importantly for me, the lh.pial-outer-smoothed surface, which I am after, did not look right. It seems that the first step, mris_fill, produces a volume that does not look very much like a brain anymore (cf. attached screenshot). Any idea why that would happen? Thanks, Pierre -- Pierre Mégevand, MD, PhD PLOS Neuro Community http://neuro.plos.org/ editor - Follow us on Twitter http://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter http://twitter.com/pierre_vanmedge - Read my blog here http://neuroscimed.wordpress.com/ screenshot3.png___ 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] LGI fails for fsaverage
Hi Pierre, Tricky question. So you can't really use the post-op cortical surface for this participant, right? Otherwise I would simply use the outer smoothed pial for this subject directly, which would be much more similar to the pre-op than the outer surface from the fsaverage (?). Otherwise, with the gadolinium MRI, maybe you can still get an adequate white surface, but I'm not sure that it would help you. The other option is to use the brain mask volume (which may work even with gadolinium if you are lucky, otherwise you can play with the watershed parameters), and tesselate a surface directly on this volume. But you'll get the two hemispheres at once (and probably the cerebellum as well), which may not be what you want? Best, Marie On Oct 28, 2014, at 2:10 PM, Pierre Mégevand pierre.megev...@gmail.commailto:pierre.megev...@gmail.com wrote: Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage. Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to localize the electrodes, and a pre-implant MR scan to which we co-register the post-op exams and to whose smoothed outer pial surface we then snap the electrodes to, in order to account for the brain shift caused by the implantation procedure (Dykstra et al., 2012). Now, for one of our patients, the pre-op MRI was acquired with a lot of gadolinium, and we can't get Freesurfer to compute the pial surface. So I thought I would co-register the post-op exams to the fsaverage brain, and then snap the electrodes to fsaverage's outer smoothed pial surface as an approximation. Any idea how else I could do this? Thanks, Pierre On Oct 28, 2014 3:06 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks cut. It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from. But in any case, I wouldn't advice to run the LGI on the fsaverage, as the pattern of cortical folding is lost from the averaging of the subjects. So I'm not even sure that the algorithm will work even if you get mris_fill to work. Can you tell us more precisely what you are trying to do? And why on the fsaverage rather than on your individual subject? Best, Marie On Oct 28, 2014, at 5:31 AM, Pierre Mégevand pierre.megev...@gmail.commailto:pierre.megev...@gmail.com wrote: Dear all, I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after a good while. More importantly for me, the lh.pial-outer-smoothed surface, which I am after, did not look right. It seems that the first step, mris_fill, produces a volume that does not look very much like a brain anymore (cf. attached screenshot). Any idea why that would happen? Thanks, Pierre -- Pierre Mégevand, MD, PhD PLOS Neuro Communityhttp://neuro.plos.org/ editor - Follow us on Twitterhttp://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitterhttp://twitter.com/pierre_vanmedge - Read my blog herehttp://neuroscimed.wordpress.com/ screenshot3.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] LGI fails for fsaverage
You're right, we can't use the post-op surface because of the deformation caused by surgery and the electrode artifacts. Getting a surface right from the brainmask would be OK, if we can't get anything better, but the nice thing about using the fsaverage surface is that you can plot and compare electrode locations from multiple patients. Just in case we have nothing better, though, how would you do it? Thanks again! -- Pierre Mégevand, MD, PhD PLOS Neuro Community http://neuro.plos.org editor - Follow us on Twitter http://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter http://twitter.com/pierre_vanmedge - Read my blog here http://neuroscimed.wordpress.com On Tue, Oct 28, 2014 at 5:23 PM, Marie Schaer marie.sch...@unige.ch wrote: Hi Pierre, Tricky question. So you can't really use the post-op cortical surface for this participant, right? Otherwise I would simply use the outer smoothed pial for this subject directly, which would be much more similar to the pre-op than the outer surface from the fsaverage (?). Otherwise, with the gadolinium MRI, maybe you can still get an adequate white surface, but I'm not sure that it would help you. The other option is to use the brain mask volume (which may work even with gadolinium if you are lucky, otherwise you can play with the watershed parameters), and tesselate a surface directly on this volume. But you'll get the two hemispheres at once (and probably the cerebellum as well), which may not be what you want? Best, Marie On Oct 28, 2014, at 2:10 PM, Pierre Mégevand pierre.megev...@gmail.com wrote: Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage. Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to localize the electrodes, and a pre-implant MR scan to which we co-register the post-op exams and to whose smoothed outer pial surface we then snap the electrodes to, in order to account for the brain shift caused by the implantation procedure (Dykstra et al., 2012). Now, for one of our patients, the pre-op MRI was acquired with a lot of gadolinium, and we can't get Freesurfer to compute the pial surface. So I thought I would co-register the post-op exams to the fsaverage brain, and then snap the electrodes to fsaverage's outer smoothed pial surface as an approximation. Any idea how else I could do this? Thanks, Pierre On Oct 28, 2014 3:06 PM, Marie Schaer marie.sch...@unige.ch wrote: Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks cut. It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from. But in any case, I wouldn't advice to run the LGI on the fsaverage, as the pattern of cortical folding is lost from the averaging of the subjects. So I'm not even sure that the algorithm will work even if you get mris_fill to work. Can you tell us more precisely what you are trying to do? And why on the fsaverage rather than on your individual subject? Best, Marie On Oct 28, 2014, at 5:31 AM, Pierre Mégevand pierre.megev...@gmail.com wrote: Dear all, I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after a good while. More importantly for me, the lh.pial-outer-smoothed surface, which I am after, did not look right. It seems that the first step, mris_fill, produces a volume that does not look very much like a brain anymore (cf. attached screenshot). Any idea why that would happen? Thanks, Pierre -- Pierre Mégevand, MD, PhD PLOS Neuro Community http://neuro.plos.org/ editor - Follow us on Twitter http://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter http://twitter.com/pierre_vanmedge - Read my blog here http://neuroscimed.wordpress.com/ screenshot3.png___ 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
Re: [Freesurfer] LGI fails for fsaverage
So what I don't get in your pipeline is how you'll register the post-op brain to fsaverage if you don't have any cortical surface in the post-op? If I were you, if you want precise registration that includes the sulci, I'd go with the white surface from the pre-op gadolinium scan. And if you just want a rough registration of the skull shape, then you can probably find a way to create the outer surface directly on the gadolinium scan: if your brain mask is good, then mris_fill should work (maybe you need to binarize the data first (in any case a few lines of code in matlab should do the trick). If the brain mask is not good due to gadolinium, then either playing with mri_watershed (and maybe try mri_fill to separate the hemispheres / pons and cerebellum) and then mris_fill for the tessellation. Or if it doesn't work with mri_watershed, playing a bit with threshold with another skull-stripping program (e.g. MRIcro), then importing the volume back in FreeSurfer and use mris_fill to get a good tessellation. Both solutions will need you to play a bit, but I guess you cannot really afford to simply throw these data and take another subject! Good luck, Marie On Oct 28, 2014, at 2:57 PM, Pierre Mégevand pierre.megev...@gmail.commailto:pierre.megev...@gmail.com wrote: You're right, we can't use the post-op surface because of the deformation caused by surgery and the electrode artifacts. Getting a surface right from the brainmask would be OK, if we can't get anything better, but the nice thing about using the fsaverage surface is that you can plot and compare electrode locations from multiple patients. Just in case we have nothing better, though, how would you do it? Thanks again! -- Pierre Mégevand, MD, PhD PLOS Neuro Communityhttp://neuro.plos.org/ editor - Follow us on Twitterhttp://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitterhttp://twitter.com/pierre_vanmedge - Read my blog herehttp://neuroscimed.wordpress.com/ On Tue, Oct 28, 2014 at 5:23 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Pierre, Tricky question. So you can't really use the post-op cortical surface for this participant, right? Otherwise I would simply use the outer smoothed pial for this subject directly, which would be much more similar to the pre-op than the outer surface from the fsaverage (?). Otherwise, with the gadolinium MRI, maybe you can still get an adequate white surface, but I'm not sure that it would help you. The other option is to use the brain mask volume (which may work even with gadolinium if you are lucky, otherwise you can play with the watershed parameters), and tesselate a surface directly on this volume. But you'll get the two hemispheres at once (and probably the cerebellum as well), which may not be what you want? Best, Marie On Oct 28, 2014, at 2:10 PM, Pierre Mégevand pierre.megev...@gmail.commailto:pierre.megev...@gmail.com wrote: Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage. Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to localize the electrodes, and a pre-implant MR scan to which we co-register the post-op exams and to whose smoothed outer pial surface we then snap the electrodes to, in order to account for the brain shift caused by the implantation procedure (Dykstra et al., 2012). Now, for one of our patients, the pre-op MRI was acquired with a lot of gadolinium, and we can't get Freesurfer to compute the pial surface. So I thought I would co-register the post-op exams to the fsaverage brain, and then snap the electrodes to fsaverage's outer smoothed pial surface as an approximation. Any idea how else I could do this? Thanks, Pierre On Oct 28, 2014 3:06 PM, Marie Schaer marie.sch...@unige.chmailto:marie.sch...@unige.ch wrote: Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks cut. It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from. But in any case, I wouldn't advice to run the LGI on the fsaverage, as the pattern of cortical folding is lost from the averaging of the subjects. So I'm not even sure that the algorithm will work even if you get mris_fill to work. Can you tell us more precisely what you are trying to do? And why on the fsaverage rather than on your individual subject? Best, Marie On Oct 28, 2014, at 5:31 AM, Pierre Mégevand pierre.megev...@gmail.commailto:pierre.megev...@gmail.com wrote: Dear all, I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after
