It contains the volumes of the white matter parcellation. You can make a table with asegstats2table and specifying --stats=wmparc.stats doug
On 03/05/2014 11:16 AM, Victor Kovac wrote: > So, I assume the aseg.mgz contains the values represented in the > asegstats2table, but what values does the wmparc.mgz contain? Is this > where the output for the aparcstats2table comes from? > > Thanks! > Victor > > > On Tue, Mar 4, 2014 at 9:43 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > The wmparc is off because the surfaces are incorrect. The aseg > does not > have to follow the surfaces, but wmparc does > doug > > > On 03/03/2014 03:10 PM, Victor Kovac wrote: > > Hi Bruce and Doug, > > > > "cp aseg.auto.mgz aseg.mgz" was my last step before running > > -autorecon2-cp -autorecon3, as suggested by Bruce before, so I > am not > > sure what the problem could be. Since there seem to be problems > > re-creating the pial/wm surfaces this way, would it be possible for > > you to send the entire subject folder to me via GoogleDrive or some > > other method? > > > > I also have another question: I have loaded a subject with tkmedit, > > but the segmentation looks drastically improved when the > -segmentation > > is aseg.auto_noCCseg.mgz instead of -wmparc.mgz (images attached), > > though the pial surface does not reflect this. > > > > Could you tell me why this is? And is it possible to get the pial/wm > > surfaces to follow along the lines of the aseg.auto_noCCseg.mgz > > segmentation? I am sorry if this is a naive question. > > > > Also: the images are from the original aseg.auto_noCCseg.mgz of this > > subject (MPS2002-3), not the updated one you sent me, Bruce. > > > > Thank you! > > Victor > > > > > > On Mon, Mar 3, 2014 at 10:53 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > I think that it should. To be safe, I would "cp aseg.auto.mgz > > aseg.mgz" > > otherwise aseg.mgz will not change (any differences will be > > interpreted > > as manual changes) > > doug > > > > > > On 03/02/2014 10:07 AM, Bruce Fischl wrote: > > > Hi Victor > > > > > > hmmm, I'm not sure why that didn't work. Perhaps someone > else can > > > comment? Doug or Nick: if the aseg.mgz is recreated and you > > start with > > > -autorecon2-cp shouldn't it propagate the effects of the > new aseg > > > forward? > > > > > > cheers > > > Bruce > > > > > > > > > On Thu, 27 Feb 2014, Victor Kovac wrote: > > > > > >> Dear Bruce, > > >> Have you had any time to try to analyze our subject > MPS2002-3? I > > >> believe you > > >> mentioned you would give it a shot in your free time a > couple of > > >> months ago. > > >> > > >> Also, you were kind enough to analyze a subject for me, > MPS1036-1, > > >> and sent > > >> me aseg.auto_noCCseg.new.mgz. I replaced the original > file and > > >> removed thee > > >> "new" within the title, and then, to re-create the pial > and wm > > >> surfaces, I > > >> ran: > > >> > > >> set mdir=$SUBJECTS_DIR/MPS1036-1/mri > > >> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ > > >> -lta $mdir/transforms/cc_up.lta MPS1036-1 > > >> cp aseg.auto.mgz aseg.mgz > > >> > > >> and then: recon-all -autorecon2-cp -autorecon3, which I > believe > > >> starts the > > >> recon-all pipeline at normalization2, as you suggested. > > However, this > > >> has > > >> yielded no effect that I can see when I visualize the > subject with > > >> > > >> tkmedit $proc brainmask.mgz lh.white -aux T1.mgz -aux-surface > > rh.white > > >> -segmentation wmparc.mgz > $FREESURFER_HOME/FreeSurferColorLUT.txt > > >> > > >> Any advice would be greatly appreciated! Attached is the > > >> recon-all.log for > > >> this subject. Let me know if I should cc the group. > > >> > > >> Thank you. > > >> Victor > > >> > > >> > > >> On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl > > >> <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> Hi Victor > > >> > > >> for each subject I think you want to run: > > >> > > >> > > >> set mdir=$SUBJECTS_DIR/$subject/mri > > >> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \ > > >> -lta $mdir/transforms/cc_up.lta $subject > > >> cp aseg.auto.mgz aseg.mgz > > >> > > >> > > >> then run recon-all from normalization2 forward > (check the > > >> recon-all -help for these steps) > > >> > > >> cheers > > >> Bruce > > >> > > >> On Tue, 7 Jan 2014, Victor Kovac wrote: > > >> > > >> Hi Bruce, > > >> > > >> I ran recon-all -autorecon2-cp -autorecon3 -s > > >> MPS1036-1 but, again, this did > > >> not affect the pial or wm surfaces. I have > attached > > >> the recon-all.log in > > >> case that would be helpful in diagnosing the > issue. > > >> > > >> Any advise would be greatly appreciated. > > >> > > >> Thanks! > > >> Victor > > >> > > >> > > >> On Thu, Jan 2, 2014 at 12:12 PM, Bruce Fischl > > >> <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> Hi Victor > > >> > > >> you can look in the recon-all -help and run > > >> the stages that are > > >> after mri_ca_label. Not sure why -make all > > >> didn't work, perhaps > > >> Zeke and/or Nick can comment? > > >> Bruce > > >> > > >> > > >> On Thu, 2 Jan 2014, Victor Kovac wrote: > > >> > > >> Dear Bruce, > > >> > > >> A few weeks ago you made code mods to > > >> mri_em_register and got recon-all to > > >> process a subject of mine, MPS1036-1. > > >> You sent me > > >> the new > > >> aseg.auto_noCCseg.mgz and told me to run > > >> recon-all > > >> -make all -s MPS1036-1. > > >> > > >> I did this but I get the message > > >> make: Nothing to be done for 'all' > > >> and when I visualize the segmentation > > >> with tkmedit, > > >> there appears to be no > > >> change to the pial or wm surfaces. > > >> > > >> Could you please advise? > > >> > > >> Thank you. > > >> Victor > > >> > > >> > > >> On Mon, Dec 9, 2013 at 2:11 PM, Bruce > > >> Fischl > > >> <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> if you rename > > >> aseg.auto_noCCseg.new.mgz to be > > >> aseg.auto_noCCseg.mgz > > >> > > >> then run: > > >> > > >> recon-all -make all -s MPS1036-1 > > >> > > >> you should be all set > > >> > > >> Bruce > > >> > > >> > > >> On Mon, 9 Dec 2013, Victor > Kovac > > >> wrote: > > >> > > >> I was hoping to > MPS1036-1. I > > >> only got > > >> aseg.auto_noCCseg.new.mgz. > > >> Thank you > > >> for looking into MPS2002-3 > > >> -- it is > > >> quite the brain. > > >> And somehow, with all > > >> those morphological > > >> abnormalities, this > > >> subject has > > >> an IQ of 130. Very > > >> strange. > > >> Thanks, > > >> Victor > > >> > > >> > > >> On Mon, Dec 9, 2013 > at 2:03 > > >> PM, Bruce > > >> Fischl > > >> <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> which one? I'm still > > >> messing with > > >> MPS2002-3 in > > >> my spare time > > >> On Mon, 9 Dec 2013, > > >> Victor Kovac > > >> wrote: > > >> > > >> Hi Bruce, > > >> Is there a way > > >> for you to > > >> send the > > >> subject(s) you > > >> analyzed to me? > > >> I know > > >> it's too big for > > >> email, but > > >> could you > > >> possibly > > >> upload it to > > >> GoogleDrive? > > >> > > >> Thanks! > > >> Victor > > >> > > >> > > >> On Wed, Dec 4, > > >> 2013 at 3:40 > > >> PM, Bruce > > >> Fischl > > >> > > >> <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > > >> wrote: > > >> p.s. the > > >> other thing I > > >> did was run > > >> the graph > > >> cut skull > > >> stripping, > > >> which > > >> removed a bunch > > >> of extraneous > > >> stuff > > >> On Wed, 4 > > >> Dec 2013, > > >> kovac...@umn.edu <mailto:kovac...@umn.edu> > <mailto:kovac...@umn.edu <mailto:kovac...@umn.edu>> wrote: > > >> > > >> Hey! > > >> > > >> Victor > > >> Kovac > > >> (kovac...@umn.edu > <mailto:kovac...@umn.edu> > > <mailto:kovac...@umn.edu <mailto:kovac...@umn.edu>>) > > >> has uploaded > > >> some files > > >> for you at > > >> the > > >> Martinos Center > > >> FileDrop: > > >> > > >> -> MPS2002-3.zip > > >> (292.12 > > >> MiB) > > >> > > >> > > >> > > >> > > > <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=55xjt9pflsi> > > >> -> MPS2017-1.zip > > >> (264.15 > > >> MiB) > > >> > > >> > > >> > > >> > > > <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep&f=ak4v31bzu4p> > > >> > > >> Also, they left > > >> this message > > >> for you: > > >> Hi Bruce, > > >> > > >> Here are the two > > >> subjects > > >> with > > >> ventriculomegaly that > > >> are causing > > >> the worst > > >> issues. The worst > > >> segmentation > > >> in > > >> MPS2002-3 is in > > >> the > > >> superior frontal > > >> (slices > > >> 150-180) and > > >> parietal > > >> (slices 50-95) > > >> cortical areas; > > >> this may be > > >> due to the > > >> numerous > > >> dilated > > >> Virchow-Robin > > >> spaces in his > > >> brain, which > > >> is another > > >> > > >> neuropathological feature of > > >> this > > >> disease. > > >> > > >> Thanks! > > >> Victor > > >> > > >> Please be aware, > > >> your upload > > >> will expire > > >> on December > > >> 31st. If > > >> you'd like to > > >> download these > > >> files, feel > > >> free to use > > >> the link > > >> below: > > >> > > >> > > >> > > >> > > >> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep > > >> > > >> Cheers, > > >> The NMR Team > > >> > > >> > > >> > > >> > > >> > > >> 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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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
