---------- Forwarded message ---------- From: Mark Plantz markplantz2016@u.northwestern.edu Date: Mon, Jul 29, 2013 at 11:33 AM Subject: Re: [Freesurfer] infant atlas segmentation To: Bruce Fischl fischl@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@nmr.mgh.harvard.eduwrote:
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@u.** northwestern.edu markplantz2016@u.northwestern.edu> wrote:
It looks like the values vary from 20-120 depending on which regionI 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@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 thesegmentation #'s exactly are.
Thanks! MP On Mon, Jul 29, 2013 at 10:17 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Mark
what #s are those segmentations? It should be trivialto 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 someresearch, 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 tocreate 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 segmentationvolume because this e-mail is sort of old
On Wed, Jul 24, 2013 at 2:39 PM, Douglas N Greve <greve@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 regionsand 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 youknow if I find out what the problem is.
Thanks guys! MP On Wed, Jul 24, 2013 at 2:26 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 regionsshould 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, DouglasN Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>>> wrote:
Hi Mark, please post to the list andnot to me. thanks doug
On 07/24/2013 03:21 PM, Mark Plantzwrote:
I guess the problem is that thoseregions 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
<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 <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu 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, MarkPlantz wrote:
Finally got theregistration 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 thehelp!
- Mark p.s. I attached a pictureof the original brain.mgz file viewed with the corrected segmentation volume
On Wed, Jul 24, 2013 at12:22 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>> <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 <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> <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 <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 theregistration 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 thehelp!
- MP On Wed, Jul 24, 2013at 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>> <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 <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> <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 <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, itturned 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>> <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 <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> <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 <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 forthe 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:165-124-23-232tel: 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:165-124-23-232tel: 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 notbelieve it is a permissions issue?
Could itsimply 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, Jul23, 2013 at 9:32 PM, Douglas Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>>>>> wrote:
You cantry 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!
On7/23/13 9:51 AM, Mark Plantz wrote:
HiDoug,
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).
Asa 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 mycommand line would be:
tkmedit $Subject brain.mgz -segmentation avgseg.mgz $FREESURFER_HOME/** FreeSurferColorLUT.txt
Theresult 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 OnMon, Jul 22, 2013 at 3:53 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.**harvard.edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 > > > >
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