I guess the problem is that those regions should not be out of bounds. Maybe I need to create a new Lookup Table for the infant mri's? Is that possible to do?
On Wed, Jul 24, 2013 at 2:21 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Hi Mark, please post to the list and not to me. > thanks > doug > > On 07/24/2013 03:21 PM, Mark Plantz wrote: > >> I guess the problem is that those regions should not be out of bounds. >> Maybe I need to create a new Lookup Table for the infant mri's? Is that >> possible to do? >> >> >> On Wed, Jul 24, 2013 at 2:15 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> >> what is the problem exactly? The fact that there are red regions >> or that that the red regions are labeled as "Out of Bounds"? If >> the latter, you will need to create a LUT that matches your >> regions. the out of bounds means that the index in the volume does >> not match an index in the LUT. >> doug >> >> >> >> On 07/24/2013 01:26 PM, Mark Plantz wrote: >> >> Finally got the registration to work. However, it looks like >> the out of bounds regions (in red) are still present (even >> though the regions are well within our boundaries). Is that >> expected since they were labeled in the original segmentation >> volume? Is there anyway to correct those? >> >> Thanks for all of the help! >> >> - Mark >> p.s. I attached a picture of the original brain.mgz file >> viewed with the corrected segmentation volume >> >> >> On Wed, Jul 24, 2013 at 12:22 PM, Mark Plantz >> >> <markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu> >> > >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu> >> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu>>>> >> wrote: >> >> Finally got the registration to work. However, it looks >> like the >> out of bound regions (in red) are still prevalent. Is that >> expected since they were present in the original segmentation >> volume? Would there be anyway to correct those? >> >> Thanks for all the help! >> >> - MP >> >> >> On Wed, Jul 24, 2013 at 11:11 AM, Mark Plantz >> >> <markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu> >> > >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu> >> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu>>>> >> wrote: >> >> Nevermind, it turned out to be a permissions issue. >> Thanks! >> >> >> On Wed, Jul 24, 2013 at 10:12 AM, Mark Plantz >> >> <markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu> >> > >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu> >> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2...@u.northwestern.edu>>>> >> wrote: >> >> Thanks for the reply Doug. I recently ran the >> bbregister >> command and attempted to view the results using >> tkregister2. I received the following error: >> >> dhcp-165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>>:Desktop >> >> >> IngvalsonLab$ tkregister2 --mov >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/ >> **infant-1yr-mgz/mri/avgseg.mgz >> --reg /Users/IngvalsonLab/Desktop/**register.dat >> --surf >> >> tkregister_tcl >> /Applications/freesurfer/**tktools/tkregister2.tcl >> INFO: no target volume specified, assuming >> FreeSurfer orig >> volume. >> target volume orig >> movable volume >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/ >> **infant-1yr-mgz/mri/avgseg.mgz >> reg file /Users/IngvalsonLab/Desktop/**register.dat >> LoadVol 1 >> ZeroCRAS 0 >> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 >> greve Exp $ >> Diagnostic Level -1 >> regio_read_register(): Undefined error: 0 >> Error reading subject from >> /Users/IngvalsonLab/Desktop/**register.dat >> ERROR: reading >> /Users/IngvalsonLab/Desktop/**register.dat >> dhcp-165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>>:Desktop >> >> >> IngvalsonLab$ >> >> I do not believe it is a permissions issue? >> >> Could it simply be that the register was bad? Is >> there an >> easy way to open up the register.dat.mincost file >> to check >> the registration? >> >> Thanks again, >> >> MP >> >> >> On Tue, Jul 23, 2013 at 9:32 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> >> >> You can try using bbregister. Normally, you >> don't use >> bbregister on a segmentation, but the segmentation >> index numbers just happen to be "T1-weighted". >> doug >> ps. Please remember to copy the list when >> responding. >> thanks! >> >> >> >> On 7/23/13 9:51 AM, Mark Plantz wrote: >> >> Hi Doug, >> >> Sorry about that vague explanation. So >> I received >> a series of infant brain atlases from a >> UNC medical >> research group >> (http://www.med.unc.edu/bric/** >> ideagroup/free-softwares/unc-**infant-0-1-2-atlases<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases> >> ). >> I have a series of infant MRI's that I >> would like to >> segment (using the infant atlases, instead >> of the >> default adult atlas in FreeSurfer). >> >> As a preliminary step, I was attempting >> to check >> the alignment of one of the atlas files >> ('avgseg.mgz') with one of the input brains >> ('brain.mgz'). [I attached these two >> files, just in >> case]. >> >> So my command line would be: >> >> tkmedit $Subject brain.mgz -segmentation >> avgseg.mgz >> $FREESURFER_HOME/**FreeSurferColorLUT.txt >> >> The result was the previously attached >> image. I was >> just wondering if there is any way to >> shift the two >> images manually so the alignment is >> better? Or maybe >> the two files are simply not compatible >> with one another? >> >> Thanks for all the help! >> >> Best, >> >> Mark >> >> >> >> >> On Mon, Jul 22, 2013 at 3:53 PM, Douglas N >> Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> >> >> Hi Mark, I have no idea what you are >> doing. Can >> you send a command line? >> Are either of the images generated by FS? >> doug >> >> >> >> >> On 07/22/2013 03:56 PM, Mark Plantz wrote: >> > Hello FreeSurfers, >> > >> > I recently obtained a set of infant >> templates. Out of curiousity, >> > I decided to view one of the input >> brains with >> the provided segmented >> > volume file. It appears that there >> is some >> misalignment. I wouldn't >> > expect the alignment to be perfect, >> since I am >> basically overlaying an >> > average of multiple brains onto one. >> However, >> it looks like this >> > misalignment may be caused by >> either: 1.) the >> segmentation volume file >> > being shifted down or 2.) the slices >> not lining >> up properly (i.e. one >> > file starts before the other). >> > >> > Any ideas what could cause a >> problem like >> this? Could it be that >> > the segmented files are simply not >> compatible >> with FreeSurfer? >> > >> > Thanks for the help, >> > >> > Mark >> > >> > >> > >> > >> ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <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<gr...@nmr.mgh.harvard.edu> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<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<http://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<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 <http://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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________ >> **_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <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<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. >> >> >> >> >> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<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> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<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/ <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.
