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