4 Mar
2014
4 Mar
'14
10:43 a.m.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 $FREESURFER_HOME/FreeSurferColorLUT.txt >> >> Any advice would be greatly appreciated! Attached is the >> recon-all.log for >> this subject. Let me know if I should cc the group. >> >> Thank you. >> Victor >> >> >> On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> wrote: >> Hi Victor >> >> for each subject I think you want to run: >> >> >> set mdir=$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 >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 >> >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@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, >> kovac081@umn.edu <mailto:kovac081@umn.edu> wrote: >> >> Hey! >> >> Victor >> Kovac >> (kovac081@umn.edu <mailto:kovac081@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> >> 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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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
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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Douglas N Greve