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Freesurfer Wiki down?
by Caspar M. Schwiedrzik 29 Jul '13

29 Jul '13

not sure whether others are experiencing this as well, but the freesurfer wiki seems to be down. caspar

4 4

Fwd: infant atlas segmentation
by Mark Plantz 29 Jul '13

29 Jul '13

---------- Forwarded message ---------- From: Mark Plantz <markplantz2016(a)u.northwestern.edu> Date: Mon, Jul 29, 2013 at 11:33 AM Subject: Re: [Freesurfer] infant atlas segmentation To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Ahh, right. So it looks like the red regions appear to be averaged around 248. I am not sure why that is the case or if it has any significance. I attached a screen shot for reference. On Mon, Jul 29, 2013 at 11:29 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > it isn't a registration file. You should just specify it as a volume on > the freeview command line, the same as brainmask.mgz > > On Mon, 29 Jul 2013, Mark Plantz wrote: > > I actually tried to view the brainmask.mgz file with the segmentation >> file [Freeview calls it 'registration file' I believe]. >> For some reason, the file will load without segmentation, but when I >> attempt to add the registration file, I get an error >> message: >> "Failed to load MRI ~/.../../../brainmask.mgz >> >> Could this potentially be part of the problem? >> >> Thanks >> >> MP >> >> >> On Mon, Jul 29, 2013 at 10:57 AM, Mark Plantz <markplantz2016(a)u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> wrote: >> >> It looks like the values vary from 20-120 depending on which region >> I run the cursor over. However, aren't those the >> values that correspond to the brain.mgz regions? Is there another >> way to find the segmentation values? >> >> >> On Mon, Jul 29, 2013 at 10:37 AM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> wrote: >> I mean the segmentation values that give you the "out of bounds" >> message >> On Mon, 29 Jul 2013, Mark Plantz wrote: >> >> Hi Bruce, >> Do you mean the brainmask.mgz values? I'm not sure what the >> segmentation #'s exactly are. >> >> Thanks! >> >> MP >> >> >> On Mon, Jul 29, 2013 at 10:17 AM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Mark >> >> >> what #s are those segmentations? It should be trivial >> to just add them to the end of the >> LUT. I wouldn't let them be >> out of bounds as there might be code around that might >> ignore them then. >> >> cheers >> Bruce >> >> On Mon, 29 Jul 2013, Mark Plantz wrote: >> >> Hi Doug, >> Thanks for the reply. After doing some >> research, it looks like messing with the >> LUT might be a >> risky decision [and way >> out of my abilities!]. >> >> If I were to use this segmentation file to >> create a .gca atlas using the command >> mri_ca_train, do you >> think it would yield >> problems or be inaccurate? I guess what I am >> trying to figure out is if the color >> lookup values are even >> significant when using >> the segmentation file to create an atlas? >> >> Thanks for all of the help with this. >> >> Best, >> >> MP >> >> p.s. I attached the photo of the segmentation >> volume because this e-mail is sort of >> old >> >> >> On Wed, Jul 24, 2013 at 2:39 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu> wrote: >> you need a new LUT. See my comment from a >> few emails ago. >> On 07/24/2013 03:29 PM, Mark Plantz wrote: >> I'm not actually quite sure what it means >> either. When I use the command line: >> >> tkmedit $Subject brain.mgz -segmentation >> <seg.mgz>, >> >> I can run the cursor over various regions >> and the name of the region should pop >> up. For some >> reason, the red >> regions are simply labeled as "out of >> bounds." >> >> I'll keep messing with tkmedit and let you >> know if I find out what the problem >> is. >> >> Thanks guys! >> >> MP >> >> >> On Wed, Jul 24, 2013 at 2:26 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> wrote: >> >> what do you mean that they are out of bounds? >> >> On 07/24/2013 03:25 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 2:21 PM, Douglas >> N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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 >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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(a)u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> <mailto:markplantz2016@u. >> **northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>>> >> <mailto:markplantz2016@u. >> **northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> >> <mailto:markplantz2016@u. >> **northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)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(a)u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> <mailto:markplantz2016@u. >> **northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> >> <mailto:markplantz2016@u. >> **northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)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(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> <mailto:markplantz2016@u. >> **northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> >> <mailto:markplantz2016@u. >> **northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)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>> >> <tel:165-124-23-232 <tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232 >> >>> >> <tel:165-124-23-232 <tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>> >> <tel: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>> >> <tel:165-124-23-232 <tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232 >> >>> >> <tel:165-124-23-232 <tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>> >> <tel: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 >> < >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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-atlas…> >> ). >> 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 >> < >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> >> <mailto:greve@nmr.mgh.**harvard.edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> <mailto: >> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto: >> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)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 >> greve(a)nmr.mgh.harvard.edu <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:greve@nmr.mgh.**harvard.edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>>> >> >> Phone Number: >> 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel: >> 617-724-2358>> >> <tel:617-724-2358<tel: >> 617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>>> >> <tel:617-724-2358 <tel: >> 617-724-2358> <tel:617-724-2358 >> <tel:617-724-2358>> <tel: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>> >> <tel:617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 >> <tel:617-726-7422>>> >> <tel:617-726-7422<tel: >> 617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> <tel: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> >> > >> >> <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> >> > >> > >

1 0

cvs_avg35
by SHAHIN NASR 29 Jul '13

29 Jul '13

Hi, Would you tell me where I can find cvs_avg35 brain template. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

Fwd: infant atlas segmentation
by Mark Plantz 29 Jul '13

29 Jul '13

It looks like the values vary from 20-120 depending on which region I run the cursor over. However, aren't those the values that correspond to the brain.mgz regions? Is there another way to find the segmentation values? On Mon, Jul 29, 2013 at 10:37 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > I mean the segmentation values that give you the "out of bounds" message > On Mon, 29 Jul 2013, Mark Plantz wrote: > > Hi Bruce, >> Do you mean the brainmask.mgz values? I'm not sure what the segmentation >> #'s exactly are. >> >> Thanks! >> >> MP >> >> >> On Mon, Jul 29, 2013 at 10:17 AM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Mark >> >> >> what #s are those segmentations? It should be trivial to just add >> them to the end of the LUT. I wouldn't let them be >> out of bounds as there might be code around that might ignore them >> then. >> >> cheers >> Bruce >> >> On Mon, 29 Jul 2013, Mark Plantz wrote: >> >> Hi Doug, >> Thanks for the reply. After doing some research, it >> looks like messing with the LUT might be a >> risky decision [and way >> out of my abilities!]. >> >> If I were to use this segmentation file to create a .gca >> atlas using the command mri_ca_train, do you >> think it would yield >> problems or be inaccurate? I guess what I am trying to figure >> out is if the color lookup values are even >> significant when using >> the segmentation file to create an atlas? >> >> Thanks for all of the help with this. >> >> Best, >> >> MP >> >> p.s. I attached the photo of the segmentation volume because >> this e-mail is sort of old >> >> >> On Wed, Jul 24, 2013 at 2:39 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu> wrote: >> you need a new LUT. See my comment from a few emails >> ago. >> On 07/24/2013 03:29 PM, Mark Plantz wrote: >> I'm not actually quite sure what it means either. When >> I use the command line: >> >> tkmedit $Subject brain.mgz -segmentation <seg.mgz>, >> >> I can run the cursor over various regions and the name >> of the region should pop up. For some >> reason, the red >> regions are simply labeled as "out of bounds." >> >> I'll keep messing with tkmedit and let you know if I >> find out what the problem is. >> >> Thanks guys! >> >> MP >> >> >> On Wed, Jul 24, 2013 at 2:26 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> wrote: >> >> what do you mean that they are out of bounds? >> >> On 07/24/2013 03:25 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 2:21 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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 >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> >> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)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(a)u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >>> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> >> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)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(a)u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> >> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)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>> >> <tel:165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>>> >> <tel:165-124-23-232 <tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>> >> <tel: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>> >> <tel:165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>>> >> <tel:165-124-23-232 <tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>> >> <tel: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 >> < >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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-atlas…> >> ). >> 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 >> < >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> <mailto: >> greve(a)nmr.mgh.**harvard.edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)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 >> greve(a)nmr.mgh.harvard.edu <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:greve@nmr.mgh.**harvard.edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>>> >> Phone Number: >> 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel:617-724-2358 <tel: >> 617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>>> >> <tel:617-724-2358 <tel:617-724-2358> <tel: >> 617-724-2358 >> <tel:617-724-2358>> <tel: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>> >> <tel:617-726-7422 <tel:617-726-7422> <tel: >> 617-726-7422 >> <tel:617-726-7422>>> >> <tel:617-726-7422 <tel: >> 617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> <tel: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>> >> < >> 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> >> > >> < >> 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(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)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 >> greve(a)nmr.mgh.harvard.edu <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> >> Phone Number: 617-724-2358 <tel: >> 617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel: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>> <tel: >> 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>> >> <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> >> > >> <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 >> greve(a)nmr.mgh.harvard.edu <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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/> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.* >> *edu <greve(a)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/> > >

2 2

Error "Cannot allocate memory"
by Annemarie Brandhofe 29 Jul '13

29 Jul '13

Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-5.1.0 and have been experiencing some problems with the automatic recognition of the control points. For several subjects, we run the recon-all command and after about 40 hours of computations, we receive the error message “Excessive topologic defect encountered: could not allocate 171060256 edges for retessellation Cannot allocate memory”. After the occurrence of the error message, the computation is stopped. Below, we provide the details of our setup and the exact error message for one subject. Feel free to ask for more information. Thank you very much for your help! Yours sincerely, Annemarie $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-5.1.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39-1-ql-beowulf i686 $ which freesurfer -> /apps/prod/i486/freesurfer-5.1.0/bin/freesurfer Used command: recon-all –autorecon2-cp –subjid IB34_mdeft. Error message: CORRECTING DEFECT 0 (vertices=72621, convex hull=6983) Excessive topologic defect encountered: could not allocate 171060256 edges for retessellation Cannot allocate memory Linux beo-08 2.6.27.39-1-ql-beowulf #1 SMP Mon Nov 23 10:55:10 CET 2009 i686 GNU/Linux recon-all -s IB34_mdeft. exited with ERRORS at Sat Jul 27 00:01:52 CEST 2013

2 1

Re: [Freesurfer] infant atlas segmentation
by Mark Plantz 29 Jul '13

29 Jul '13

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 <greve(a)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 < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)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(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)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(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)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 >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)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-atlas…> >> ). >> 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 >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)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 >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)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 >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)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 > greve(a)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/> > >

3 7

displaying labels from old session onto new session
by Bianca van Kemenade 29 Jul '13

29 Jul '13

Hi Freesurfers, I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A. However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine. Data from the newer session were coregistered to the older session, so that can't be the problem. I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'? Thanks, Bianca

3 17

Processing Multiple Subjects
by Michael Kranz 29 Jul '13

29 Jul '13

Hi all, If I process more subjects than the recommended amount given my number of cores and memory, will this affect the stats/surfaces or just slow the process down? I'm asking due to the sensitivity of workstations and also I seem to be getting slightly different stats sometimes when I re-submit to recon-all but haven't pin pointed the reason yet. Thanks, Mike

2 1

function that do the same step like qcache?
by fatma zribi 29 Jul '13

29 Jul '13

Dear Bruce, Would you mind tell me if there is a function of freesurfer that I can use to do the same step of qcache to smooth and interpolate in the fsaverage one subject with mri_surf2surf I can smooth only or align one subject with an average. thank you for you help. with best regards, Fatma

2 3

Error
by Muhammad Naveed Iqbal Qureshi 29 Jul '13

29 Jul '13

Dear Community, I got the following error every time I try to calculate the cortical thickness of my MRI data: bmssa-desktop:~> recon-all -i /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm -subject sub02 -all -qcache & WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/bmssa/freesurfer/subjects Actual FREESURFER_HOME /home/bmssa/freesurfer Linux bmssa-desktop 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/bmssa/freesurfer/subjects/sub02 mri_convert /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm /home/bmssa/freesurfer/subjects/sub02/mri/orig/001.mgz mri_convert /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm /home/bmssa/freesurfer/subjects/sub02/mri/orig/001.mgz ERROR: cannot determine file type for /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm Linux bmssa-desktop 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub02 exited with ERRORS at Mon Jul 29 14:10:40 KST 2013 For more details, see the log file /home/bmssa/freesurfer/subjects/sub02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Please guide me how to rectify this error. I have used the same command for another dataset and it was working perfectly fine. Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi(a)hotmail.com URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to

2 1

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