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-atlase...). 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> 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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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: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: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.eduwrote:
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 infantbrain atlases from a UNC medical research group ( http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlase...). 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 oneof 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> 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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> 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: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: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.eduwrote:
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 infantbrain atlases from a UNC medical research group ( http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlase...). 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 ofone 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> 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
does that file exist? Did bbregister exit with errors? On 07/24/2013 11:12 AM, Mark Plantz 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: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: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> 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). 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>> 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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Mark Plantz