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@nmr.mgh.harvard.eduwrote:
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@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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<markplantz2016@u.northwestern.edu> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016@u.northwestern.edu><mailto:markplantz2016@u.**northwestern.edu<markplantz2016@u.northwestern.edu> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016@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<markplantz2016@u.northwestern.edu> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016@u.northwestern.edu><mailto:markplantz2016@u.**northwestern.edu<markplantz2016@u.northwestern.edu> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016@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<markplantz2016@u.northwestern.edu> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016@u.northwestern.edu><mailto:markplantz2016@u.**northwestern.edu<markplantz2016@u.northwestern.edu> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016@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@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@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-atlaseshttp://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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu<greve@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:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@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
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