Bruce, I tried mris_fill, but it gives me a filled white matter volume (I already have that in the mri directory. I need the contour only.
Douglas, Looking into the --help gave me a few ideas. I think the help page (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol ) should include this information. I was able to create the volume by adding --identity, --template, and --mkmask. The required surfval and volreg, are taken from the -mkmask and identity respectively. The surface is created using the template from T1.mgz,, -mkmask works for me. However the orientation is wrong (and thus the registration). I wonder which file contains the correct registration (to give it as input to volreg. I tried using fstal 1 (this sets the template to mni305.cor.subfov1res.mgz and registration from mni305.cor.subfov1res.reg: That also gave me an unregistered output. [image: Inline image 2] [image: Inline image 1] I guess the only piece of the puzzle I am missing is which registration file to use, so that the final volume is registered to the T1.mgz. This file must be there, as when loading the images into tkmedit they are registered. here is the output of the execution. The reg files comes from using --identity. I wonder which reg file can I use. test@ubuntudev12:~/Desktop/surftovol/user_id$ mri_surf2vol --mkmask --surf white --hemi lh --o out.nii.gz --template mri/T1.mgz --sd /home/test/Desktop/surftovol/ --subject user_id --identity user_id gdiagno = -1 Using identity matrix for registration Overriding reg subject user_id with user_id Qa2v: SurfXYZ to VolCRS: ------------------------------ -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; -------------------------------------------------- subjects dir /home/test/Desktop/surftovol/ hemi lh mksurfmask 1 projfrac 0 outvol path out.nii.gz template path mri/T1.mgz ------- Anat2Vol Registration (TkReg)---- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ----------------------------------------- height = 256 width = 256 depth = 256 xsize = 1.000000 ysize = 1.000000 zsize = 1.000000 cdc = -1.000000 0.000000 0.000000 rdc = 0.000000 0.000000 -1.000000 sdc = 0.000000 1.000000 -0.000000 xyz0 = -8.411377 8.796127 -0.092697 Gdiag_no -1 Reading surface /home/test/Desktop/surftovol//user_id/surf/lh.white Done reading source surface surf nframes = 1 INFO: mapping vertices to closest voxel INFO: resampling surface to volume INFO: sampled 61045 voxels in the volume INFO: writing output volume to out.nii.gz done test@ubuntudev12:~/Desktop/surftovol/user_id$ mri_surf2vol --mkmask --surf white --hemi lh --o out.nii.gz --template mri/T1.mgz --sd /home/test/Desktop/surftovol/ --subject user_id --identity user_id On Tue, May 16, 2017 at 11:08 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > If you run it with --help, it will print out examples. Did you try that? > > On 5/16/17 9:26 AM, Bruce Fischl wrote: > > Hi gAbE > > you could try using mris_fill, or even mris_compute_volume_fractions > > cheers > Bruce > On Mon, 15 May 2017, Gamaliz wrote: > > > My idea is to convert the registered white surface into a volume, so it > can be shown in a volume viewer (not a surface viewer). I need to display a > DTI image and mark the edges of the white matter as a line on top if it. > This is not the exact command, I am not sitting in front of my station, > but it goes something like it. I tried many combinations, the general error > was related to the template files not on the correct format (it could have > been they couldn't be found to be opened too, the error seemed generic). > mri_surf2vol --surfval white --hemi lh --outvol test.mgz --template > T1.mgz > --volreg T1.mgz --sd /home/user/Desktop/sf/sub1 > I am at a loss for the --volreg flag. > The sd seems to indicate the directory of freesurfer (but then how is the > co > mmand aware of the specficic subject I am trying to process? I tried > using: --identity subject no luck. > 'sub1' us my subject, located not in the default freesurfer directory. > There are no examples or a lot of help using it > https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol > > If this is not enough I can get back to you with the specific error > tomorrow > . > On Mon, May 15, 2017 at 10:02 PM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu> <gr...@nmr.mgh.harvard.edu> > > wrote: > > what was your mri_surf2vol cmd line? And what was the terminal > output? > > > On 5/15/17 9:59 PM, Gamaliz wrote: > I looked at the ribbon.mgz, but it is a pial surface, not > really delineated white matter the way I need it. There is > a command called mri_sur2vol, I have tried to use it, but > unsuccessfully, no idea if that is the solution to my > problem. > > On Mon, May 15, 2017 at 9:57 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu> <gr...@nmr.mgh.harvard.edu> wrote: > > not sure what you mean. Have you looked at the > ribbon.mgz file? > > > On 5/15/17 5:20 PM, Gamaliz wrote: > I need to create an image which overlaps the > T1/mgz and the outer surface of the white > matter. How do I convert the surface into a > mgz volume? > > > -- > gAbE > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ 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. > > -- gAbE > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > 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. > > > > > -- > gAbE > > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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. > > -- gAbE
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