[Freesurfer] Flux Satellite Conference
*UNC Chapel Hill, in association with The Flux Society, *will host a conference highlighting research using large, representative, or publicly available datasets to investigate developmental cognitive neuroscience. This conference will address the unique ability of larger, more representative datasets–and particularly those with multiple time points–to ask questions about brain development that have historically been impossible to address with the smaller, cross-sectional samples utilized in most neuroimaging research studies. The focus will be on research leveraging large datasets to understand functional and structural brain development in the context of connectomics, environmental influences on brain development, and typical and atypical trajectories of brain development. The conference will take place at UNC Chapel Hill May 6 – May 8, 2018. Abstract submission deadline: 1/22/18 Registration opens: 2/1/18 For more information and to submit your abstract, visit: http://fluxsatellite.web.unc.edu/ You may also sign up for the conference listserv on the site to receive future announcements. ___ 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] volumes in wmparc.stats vs. aparc.stats
Doug, et al., We ran a few subjects through recon1, 2, and 3 in an effort to get the volume of the hippocampus bilaterally. We emailed the list to find out if we should use aseg.stats or wmparc.stats. Doug wrote back saying that the hippocampus volumes should be the same. We went back & ran more subjects and they all appear to have a discrepancy between the number of voxels in aseg.stats and wmparc.stats for the hippocampus. Some of the stats are the same-- just the NVoxels and Volume_mm3 differ between the two stat files. we've attached a set of these aseg.stats vs wmparc.stats files. Does anyone have any idea why we might be getting this bug and how we could fix it? Thanks! Kathy & Margaret On Fri, Oct 24, 2008 at 3:32 PM, Doug Greve <[EMAIL PROTECTED]>wrote: > > They should be exactly the same. If not, it's a bug. I just looked at a few > of mine, and they are the same. > > doug > > Kathy Zhang wrote: > > Hello, I've recently started a project that involves measuring the volume > of the hippocampus and other subcortical structures, so I was also wondering > whether aseg.stats was more accurate or wmparc.stats. So far the difference > between them appears to be approximately a hundred voxels for each > right/left hippocampus. > > Thank you, > Kathy Zhang '09 > > On Wed, Oct 8, 2008 at 12:08 PM, Nurunisa Neyzi <[EMAIL PROTECTED]><[EMAIL > PROTECTED]>wrote: > >> Hi, for subcortical segmentations, is it then better to use the >> volumes in wmparc.stats than those in aseg.stats? >> >> >> >> On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve <[EMAIL PROTECTED]> >> wrote: >> > >> > Actually, the construction of aparc+aseg and wmparc do use info about >> where >> > the surface is to refine the aseg cortical boundaries. This information >> is >> > stored in ribbon.mgz (and it overrides the aseg definition). At some >> point, >> > we will use the surfaces to directly refine the aseg boundaries. >> > >> > doug >> > >> > >> > >> > >> > Michael Harms wrote: >> > >> > Hi Chris, >> > Doug, please correct me if I'm wrong, but the original gm/wm >> > segmentation contained in aseg.mgz is based on the 3D volume-based >> > tissue segmentation. This original segmentation then forms the basis >> > for all subsequent additional segmentations of either GM or WM in the 3D >> > volume. That is, aparc+aseg.mgz and wmparc.mgz make "use" of the >> > surface based parcellation, but only to decide the most appropriate >> > label to assign to GM/WM as defined in the already existing volume-based >> > segmentation that is contained in aseg.mgz. >> > >> > Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still based on >> > the 3D volume segmentation, there is no apriori reason that their >> > spatial extent will correspond precisely to the more accurate gray and >> > white mattes surfaces that come out of the surface-based processing >> > stream. (Although certainly we would hope that the discrepancies don't >> > become too large). >> > >> > cheers, >> > Mike H. >> > >> > On Thu, 2008-07-17 at 12:00 -0500, [EMAIL PROTECTED] wrote: >> > >> > >> > I have sent two images created with the following commands. >> > >> > tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white >> > -segmentation (aparc+aseg.mgz and wmparc.mgz) >> > $FREESURFER_HOME/FreesurferColorLUT.txt >> > >> > The wm segmenations go through the "main surface" and the "orig surface" >> > into the gray matter, for example in the rh-supramarginal and >> > rh-postcentral. From your last response I am unsure as to which pipeline >> > creates the wm parcellations, the volume-based pipeline (.i.e aseg.mgz) >> or >> > the surface-based pipeline (i.e. ribbon.mgz) or some combination of the >> > two. It seems to me that the gm/wm parcellations are created using the >> > surface pipeline and then transferred to the closest class-matched >> voxels >> > from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg >> > segmentations. I guess the question is how are we getting from the >> surface >> > parcellations back to volume space; is there a binary? >> > In a related vein, the value from aseg.stats "surface-based-volume mm3 >> > lh-cerebral-white-matter" seems to be created with mri_segstats or is it >> > from mris_wm_volume? Thanks for all your help! >> > >> > Chris Bell >> > >> > >> > >> > >> > >> > On Jul 17 2008, Doug Greve wrote: >> > >> > >> > >> > When the volume is created, a decision has to be made at each voxel as >> > to what to classify it as. This is used when the aseg.mgz and >> > ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from >> > these files. When using mri_segstats with --pv, it will take the >> > volume of a 1mm3 voxel and divide it up so that it can contribute to >> > more than one region. But there's not a way to put the partial volume >> > information into the segmentation itself. Not sure why that do not >> > appear alingned, but we've been recently looking into this for other >> > reasons. Can you send a p
Re: [Freesurfer] Volume Statistics
Alexa, et al., This also happend to our group (same volumes) Doug Greeve seemed to think they should be the same but my understanding is that they are calculated out of different processing streams so they shouldn't be the same. We posted to the list a week ago asking about this but haven't gotten a reply. Any more insight would be deeply welcome. Thanks, Margaret On Wed, Nov 19, 2008 at 12:19 PM, Alexa Nardelli <[EMAIL PROTECTED]> wrote: > Hi, I have performed subcorticol segmentation using freesurfer and I am now > interested in looking at the volume of the hippocampus and the amygdala; the > volume statistics under aseg.stats and those under wmparc.stats are > different. Is this normal and if so, which ones should I be using? > > Thanks > > Alexa > ___ > 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] brain orientation
Bruce, Yeah, I know about that danger. We are doing this on brains where we have a marker - a vitamin e capsule on the left side of the forehead. I'm most concerned about learning how to rotate the brains at all, right at the moment. Thanks (for the concern as well), Margaret On 8/20/08, Bruce Fischl <[EMAIL PROTECTED]> wrote: > > Hi Margaret and Kathy, > > you *really* don't want to be trying to guess the orientation yourself as > you are likely to get left/right wrong. Avi: have you moved data back and > forth into freesurfer? > cheers > Bruce > > > > On Wed, 20 Aug 2008, Margaret Sheridan wrote: > > We are new users of freesurfer (linux v 4.0.5) and have the following >> question: >> >> We have some .4dfp.img MPRAGE files which we are trying to use (from Wash >> U). When we run recon_all (1st step) or mri_convert on its own, the brain >> comes up upside down as if it was rotated 180 degrees around the sagital >> plane (see attached picture of the 4dfp.img file viewed in scuba). Since >> when we view the original 4dfp.img file or the orig.mgz file they are both >> in this orientation it appears that this is a problem with the original >> files. >> >> If we use tkmedit to rotate the brain around the sagital plane once we're >> in >> .mgz format the recon steps (including normalization which, obviously, >> would >> fail previously when the brain was upside down) would complete fine. >> However >> I'd prefer to rotate these brains using mri_convert (or another program) >> so >> I can rotate the original files; which is why I'm writing now. >> >> To determine what the current orientation for these images was I opened >> the >> original files in scuba & ran MRI convert like this: >> mri_convert --in_orientation ASL -i vcXXX.4dfp.img --out_orientation ASL >> -o >> vcXXX.4dfp.ASL.img >> >> until I found an orientation which matched the original. The orientation >> which matched the original was ASL. In this step I just converted from one >> form to the same form to reduce confusion. >> >> Next I ran several versions of the following: >> mri_convert --in_orientation ASL -i vcXXX.4dfp.img --out_orientation SAR >> -o >> vcXXX.4dfp.SAR.img >> >> however no mater how I changed the 'out orientation' when the files were >> viewed in scuba they all appeared to have the same orientation as the >> original (ASL or rotated around the sagital plane). >> >> Is there any more documentation on re-orienting in mri_convert or does >> anyone have any ideas/experience that can help? >> >> Thanks, >> Margaret Sheridan >> Kathy Zhang >> >> ___ > 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] Methodology Papers.
Pedro, That was a really helpful organizational tool for the rest of us - Matt, I also hope you found it helpful. Thanks! Margaret On Sun, Sep 14, 2008 at 2:48 PM, Pedro Paulo de Magalhães Oliveira Junior < [EMAIL PROTECTED]> wrote: > Matt, > I have a table I use sometimes. It contains 12 references I believe are the > most important and their role in recon-all process. > > Regards, > > PPJ > > 2008/9/12 Bruce Fischl <[EMAIL PROTECTED]> > > Hi Matt, >> >> the Segonne paper is the current skull stripping (the hybrid one), >> although it's evolved somewhat since then (unpublished). The segmentation is >> both those papers (the first one is the segmentation methodology, the 2nd is >> the addition of a nonlinear warp), plus the more recent one with Han as the >> 1st author describing how we reestimate the atlas to account for sequence >> differences. The surface stuff is similar in that the 93 paper is still >> relevant as are the two 99 papers, then the parcellation, spherical >> morphing, topology correction and more recent (Desikan) parcellation. >> >> cheers, >> >> Bruce >> >> >> On Fri, 12 Sep 2008, Matt Clarkson wrote: >> >> Hi Bruce, >>> >>> for sure, I didnt expect it to all be in one place! >>> >>> For example, what I believe are the original papers (Neuroimage 9 1999, >>> and the 1993 Cognitive Neuroscience paper), describe the first method, then >>> we have all the other subsequent papers. So for example, does the current >>> methodology use the brain stripping from Neuroimage 22 (2004), (i believe it >>> does, but I'm a newbie.), and is the volume segmentation best described in >>> the 2002 Neurotechnique paper "Whole brain segmentation"? Or has it >>> been superceded by the methodology in Neuroimage 23 (2004) >>> "Sequence-independent segmentation of magnetic resonance imaging". >>> >>> I suppose, another way of phrasing the question is simply, which >>> methodology papers are in the current software version, which ones have been >>> superseded, and which ones are totally cutting edge research, and not part >>> of the software package? >>> I just wondered if anyone had a view on this, or compiled a handy list >>> that they would be willing to share? >>> >>> Many thanks in advance. >>> >>> Matt >>> >>> Matt Clarkson >>> Senior Research Associate >>> Dementia Research Centre >>> UCL >>> Institute Of Neurology >>> Queen Square >>> London WC1N 3BG >>> >>> [EMAIL PROTECTED] >>> Tel: 08451 555 000 ext. 723653 >>> Fax: 020 7676 2066 >>> >>> >>> >>> Bruce Fischl wrote: >>> Hi Matt, the methodologies are described in those papers. Sorry, I don't think there's any one or two paper summary - it's just too much stuff over the years (topology correction, segmentation, surface analysis, morphing, etc). Bruce On Fri, 12 Sep 2008, Matt Clarkson wrote: Dear everyone, > > Hopefully someone can help me. If I do "recon-all --help" i can see a > list of 31 steps for the main cortical thickness pipeline. Does anyone > have > a list that links each of the 31 steps to the most current methodology > paper? > > I've been reading most of the methodology papers referenced in the > wiki, but the software has clearly evolved over the years, and even though > you can read the wiki, and trawl through log files, I want to be > absolutely > sure that for each step, I know exactly what algorithm is applied. Has > anyone gone through this before? > > Thanks in advance, > > Matt > > Matt Clarkson > Senior Research Associate > Dementia Research Centre > UCL > Institute Of Neurology > Queen Square > London WC1N 3BG > > [EMAIL PROTECTED] > Tel: 08451 555 000 ext. 723653 > Fax: 020 7676 2066 > > > ___ > 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 >> > > > > -- > --- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > > > ___ > 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
