Hi Longchuan, I'm still not sure I understand what you are trying to do ultimately. Do you just want a binary map of the surface in the DTI space so that you can use each cortex voxel as a seed? Or do you want to use one of the surface-based ROIs as the seed? This should be possible without re-running recon-all at 1mm. doug
On 11/20/2012 06:01 PM, Longchuan Li wrote: > Hi, Doug > > Thank you very much for the information. What I want to do is to use > the white and pial surfaces in the FreeSurfer space as the seeds for > surface-based tractography implemented in FSL. In order to do that, I > need a transformation between the white matter surface and diffusion > MR data. For some reason, the space of the white matter surface in my > monkey data is not the same as that of the other volumetric data, such > as filled.mgz, orig.mgz. This is however not the case for humans, > which are processed using the standard FreeSurfer pipeline. > > To make things worse, I used "cm" option in recon-all and processed > the data in their original resolution(0.5mm isotropic). When I used > "mris_fill" without "-c" option, the left and right white volumes will > have different dimensions, making it difficult to combine them for > registering with filled.mgz. If I use "-c" option, I can combine them > since they now have the same dimension. However, they would be > "conformed" to 1mm isotropic (originally 0.5m isotropic), which is > severely downsampled. I am afraid that this downsampling from 0.5mm to > 1mm will affect the registration results. Do you have any suggestions > on solving the issue? > > I am planning to change the resolution of the image from 0.5mm to 1mm > without downsampling before I feed the image to recon-all. I noticed > that there are two options in mri_convert (-vs, -cs) that are supposed > to be related to this. However, I found both of them downsample the > images. Is there any way that I could change the resolution of the > images from 0.5mm to 1mm and in the mean time, magnifying the images > so that the partial volume effect of the image will not change? > > Thank you ! > > Longchuan > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* Longchuan Li <leonad...@yahoo.com> > *Cc:* "freesurfer@nmr.mgh.harvard.edu" > <freesurfer@nmr.mgh.harvard.edu>; Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > *Sent:* Tuesday, November 20, 2012 3:19 PM > *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and > the brain.mgz > > > Hi Longchuan, mris_fill create a volume with a different geometry than > orig.mgz (though it is in the same space). What do you want to do > exactly? Map the output of mris_fill into the DTI space? The transform > from the output of mris_fill to orig.mgz is easy to obtain: > > tkregister2 --noedit --mov mris_fill.mgz --s subject --regheader > --reg mris_fill.reg.dat > > this will be in "register.dat" format/space. > > doug > > > > On 11/19/2012 03:35 PM, Longchuan Li wrote: > > Hi, Doug > > > > I tried bbregister and checked the registration using tkregister2. > It seems that this program registers the diffusion image with the > anatomical *volume* images in FreeSurfer, such as brain.mgz. My > problem is a little unique: I am working on monkey data and I found > that my ?h.white surfaces do not have the identical sto_xyz > coordinates as those of the anatomical volume images, such as > brain.mgz. That is, when I use "mris_fill" to write the ?h.white to a > volume file, I find that the center of the images in the header file > is not identical to that of the anatomical volume images. In my human > data processed using FreeSurfer standard recon-all pipeline, they are > identical. Since I am working on monkey data, I used "-notalairach" > and "-notal-check" in recon-all to have the piepline work. I suspect > this may be related to these options. > > > > So my questions are: > > (1) what do you think are the reasons causing the inconsistent > sto_xyz values between the surface files (?h.white) and voluem files > in the non-human data. > > > > (2) Is there any way that I could find a transformation matrix > between the ?h.white and my FreeSurfer volume images (such as brain.mgz)? > > > > thank you! > > > > Longchuan > > > > PS: I also used "-cm" option in recon-all as suggested by Bruce. I > just got the results and the problem is still there. > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > *To:* freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > *Sent:* Monday, November 19, 2012 10:43 AM > > *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and > the brain.mgz > > > > use bbregister, something like > > bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg > register.dat > > where lowb is the low b (usually b=0) volume from your DTI, the one that > > you used as the template for motion correction. > > doug > > > > On 11/19/2012 10:30 AM, Bruce Fischl wrote: > > > Hi Longchuan > > > > > > yes, I think you can do this with tkregister2. Doug can give you the > > > details > > > Bruce > > > On Mon, 19 Nov 2012, Longchuan Li wrote: > > > > > >> Hi, Bruce > > >> > > >> Thank you for the information. I will re-run recon-all using "-cm" > > >> option to > > >> see if the problem will be solved. In the mean time, do you have any > > >> suggestions regarding finding a transformation between the mismatched > > >> surfaces and the volume? > > >> > > >> Thanks again. > > >> > > >> Longchuan > > >> > > >> > > >> > ____________________________________________________________________________ > > > >> > > >> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > > >> To: Longchuan Li <leonad...@yahoo.com > <mailto:leonad...@yahoo.com> <mailto:leonad...@yahoo.com > <mailto:leonad...@yahoo.com>>> > > >> Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > >> Sent: Monday, November 19, 2012 8:57 AM > > >> Subject: Re: [Freesurfer] the positions of white/pial surfaces > and the > > >> brain.mgz > > >> > > >> Hi Longchuan > > >> > > >> have you tried the -cm (conform to min) option in recon-all? > > >> > > >> cheers > > >> Bruce > > >> > > >> > > >> On Sun, 18 Nov > > >> 2012, Longchuan Li wrote: > > >> > > >> > Hi, FreeSurfer experts > > >> > > > >> > I have a question regarding coregistering white and pial surfaces > > >> with the > > >> brain.mgz and would appreciate your help on this. I > > >> > am working on non-human primates and noticed that my white and pial > > >> surfaces do not have identical positions as brain.mgz. For > > >> > example, when I used "mris_fill" to write white and pial > surfaces into > > >> volume files, they do not have same sto_xyz and qto_xyz > > >> > values as these in the brain.mgz. This is not the case for human > > >> data. So > > >> my questions are: > > >> > > > >> > (1) how could I find a transformation matrix between the two, so > > >> that when > > >> I am using surface-based tractography in the future, > > >> > the program can find the correspondence between the points on the > > >> surfaces > > >> and those in the volumetric diffusion MRI data? > > >> > > > >> > (2) How in the future, can I avoid such misregistrations in > generating > > >> non-human primate surface files in FreeSurfer? > > >> > > > >> > Thank you very much in advance! > > >> > > > >> > Longchuan > > >> > > > >> > > > >> > > >> > > >> 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 mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > > 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> > <mailto: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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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
