Then you need to find a gray scale image/template that it does overlay properly on. We can't help you much until you do.
doug
kwa1@rice.edu wrote:
This one did not overlay correctly either (see attached). This is the same mov volume/gray scale/extracted mask volume that I used as well. What does this tell us?
Best, Kareem
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
OK, now check whether it overlays on the FSL template correctly in tkmedit:
tkmedit -f fslgrayscaleimage.nii.gz -overlay TP.nii.gz -fthresh 0.5
where fslgrayscaleimage.nii.gz is the gray scale image that you used as the mov volume in bbregister and also used as the gray scale image in fslview
doug
kwa1@rice.edu wrote:
Hmm, the label seems to be in the right area but larger and translated down (see attached picture). The bbregister I ran used the FS target to take the FSL standard space to and the registration looked fine. Any ideas why this happened?
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Sorry, I forgot that you were going to the surface, so dont use mri_label2vol. After #1, run tkmedit yoursubject orig.mgz -reg register.dat -overlay TP.nii.gz -fthresh 0.5 -surfs
you should see the mask in red. It should also intersect the surface. If not, then something is wrong.
doug
kwa1@rice.edu wrote:
Okay following that, here is what I did:
- bbregister the FSL anatomical contrast to the FS space of that
subject (using the 12 dof as suggested). Checking registration seemed to be fine.
- did mri_vol2surf of the FSL-derived mask (because when I
extract masks from fslview they are extracted into volumes), then I convert that surface to a label with mri_cor2label.
- I extracted the registration.dat file generated by bbregister
(with the 4x4 affine matrix) and ran the mri_label2vol using the registration matrix on the label developed in (2).
- Ran (2) again to get the registered label file.
When I mapped the label onto the subject's pial surface it did not map on. Any ideas why, though?
Additionally, if I wanted to extract an fsaverage TP mask using the mri_annotation2label, how would I convert that .label file to a subject's native space (for example to correspond with the labels I derive from each subject)?
Thank you, Kareem
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Don't use the temporal pole mask as the input to the registration. You need something with some anatomical contrast. The TP mask will basically be an empty image with a few 1s. Load a gray-scale image in fslview that matches the TP mask. Then bbregister to that gray scale image (with --12 for 12 dof). Check to make sure that the registration is ok. Then run mri_label2vol using the TP mask and the registration.
doug
kwa1@rice.edu wrote: > Hi Bruce, > > Thank you for your reply. The labels are coming from me > exporting the temporal pole label for a subject from fslview -- > so that would mean it's in standard space? All I would need is > that 4x4 affine matrix in order to calculate transformations but > I'm not sure how to calculate that kind of matrix between the > different spaces. However since I'm also trying to overlay the > converted label to individual subjects (e.g. tksurfer > visualization) do I need structural or native subject space > conversion? > > Specifically the label came from a t1 image and it should > register quite well, the scans were fine and we have no reason > to think they shouldn't register well (no abnormalities etc.). > > > Thank you very much, > Kareem > > Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu: > >> Hi Kareem, >> >> can you explain a bit more about where these atlas-derived >> labeling comes from? Is it in MNI space? Is there any reason to >> think it will register well to this subject? Or is it in this >> individual's space? If the latter, you probably want to give >> -t2 to bbregister since in your case as I understand it the >> gray matter is bright (e.g. 1) and the white matter is dark >> (0?). Is that correct? >> >> cheers >> Bruce >> >> >> On Mon, 30 May 2011 kwa1@rice.edu wrote: >> >>> Hi Doug, >>> >>> The bbregister didn't work out well, it didn't register >>> properly but I >>> must be putting in some erroneous argument: >>> >>> bbregister --s SUBJ1 --mov TP.nii.gz --reg register.dat >>> --init-fsl --t1 >>> >>> The final check with tkregister shows the temporal pole mask >>> several >>> slices off bilaterally and rotated about 30-40 degrees CW and >>> also >>> rotated spatially from frontal to posterior brain. >>> >>> I also tried a flirt command in FSL but couldn't not get a >>> proper 4x4 >>> affine matrix to use. Any ideas on why the registration isn't >>> working? >>> >>> Thank you, >>> Kareem >>> >>> >>> Quoting Douglas Greve greve@nmr.mgh.harvard.edu: >>> >>>> You use bbregister to compute the registration. You will need a >>>> template for your atlas (eg, an average anatomy). >>>> >>>> doug >>>> >>>> On 5/27/11 7:09 PM, kwa1@rice.edu wrote: >>>>> Do I feed the registration matrix into another FS command or >>>>> does >>>>> bbregister use the reg matrix to transform the atlas mask >>>>> into FS >>>>> anatomical space? I will try the bbregister with 12 DOF as you >>>>> recommend too. >>>>> >>>>> Thank you, >>>>> Kareem >>>>> >>>>> >>>>> Quoting Douglas N Greve greve@nmr.mgh.harvard.edu: >>>>> >>>>>> Yes, there's no other way for FS to know where data should >>>>>> go -- >>>>>> it has no idea how you derived the input. You can try using >>>>>> bbregister with 12 DOF to register the atlas template to >>>>>> the FS >>>>>> anatomical. This will give you a registration matrix. Check it >>>>>> visually to make sure that it is reasonably accurate. >>>>>> >>>>>> doug >>>>>> >>>>>> kwa1@rice.edu wrote: >>>>>>> Hmm, well I derived the volume from an FSL atlas which I >>>>>>> exported, binarized, then fed into the commands I listed >>>>>>> initially. Do I need to register the temporal pole volume >>>>>>> to some >>>>>>> FS space? And how would I so? >>>>>>> >>>>>>> Best, >>>>>>> Kareem >>>>>>> >>>>>>> >>>>>>> >>>>>>> Quoting Douglas N Greve greve@nmr.mgh.harvard.edu: >>>>>>> >>>>>>>> Then it means that the registration is incorrect. How did >>>>>>>> you >>>>>>>> create the reg? >>>>>>>> >>>>>>>> kwa1@rice.edu wrote: >>>>>>>>> No it doesn't look right. It is supposed to map on to the >>>>>>>>> temporal pole but doesn't do so. I don't think it's in the >>>>>>>>> right space. Is there a command we are perhaps missing >>>>>>>>> to bring >>>>>>>>> it to native FS space? >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Kareem >>>>>>>>> >>>>>>>>> >>>>>>>>> Quoting Douglas N Greve greve@nmr.mgh.harvard.edu: >>>>>>>>> >>>>>>>>>> It looks like your commands are correct. When you load >>>>>>>>>> mask.surf.nii.gz onto the surface, does it look ok? >>>>>>>>>> >>>>>>>>>> doug >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> kwa1@rice.edu wrote: >>>>>>>>>>> Hello, >>>>>>>>>>> >>>>>>>>>>> I've derived a .nii.gz atlas-based volume for a >>>>>>>>>>> specific part >>>>>>>>>>> of the cortical surface. I've binarized the volume >>>>>>>>>>> and now I >>>>>>>>>>> want to convert the file to a .label file that I can >>>>>>>>>>> use to >>>>>>>>>>> identify particular vertices in native FS space for that >>>>>>>>>>> same subject. >>>>>>>>>>> >>>>>>>>>>> This is what I have tried so far: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> mri_vol2surf --src mask.nii.gz --srcreg /tmp/reg.dat >>>>>>>>>>> --surf >>>>>>>>>>> pial --projfrac 0.5 --hemi lh --out mask.surf.nii.gz >>>>>>>>>>> >>>>>>>>>>> mri_cor2label --i mask.surf.nii.gz --id 1 --l mask.label >>>>>>>>>>> --surf SUBJ1 lh pial >>>>>>>>>>> >>>>>>>>>>> However when I overlayed the .label onto SUBJ1 the >>>>>>>>>>> vertices >>>>>>>>>>> did not match up and was completely off the region of >>>>>>>>>>> interest on the cortical surface. >>>>>>>>>>> >>>>>>>>>>> Does anyone know how to fix this or how to proceed with >>>>>>>>>>> conversion differently? >>>>>>>>>>> >>>>>>>>>>> Thank you very much, >>>>>>>>>>> Kareem >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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: >>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> 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. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> 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: >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> >>> >>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html