You need to specify --trgsubject ico in mri_vol2surf
On 9/28/16 3:01 PM, Jared Zimmerman wrote: > Hi All, forwarding this message along again as I'm still having some trouble > getting this to work. Basically I would like to 1) project processed > residual time-series from the subject-space volume to the subject-space > surface, 2) smooth on the surface, 3) down-sample to FS4 space. > > To do this is have used bbregister to calculate the registration, then > mri_vol2surf to project to the surface, but I am not sure the output of > mri_vol2surf is what I should be expecting. The output file has dimensions > 112745 x 1 x 1 x 120 when I'm expecting ~40k vertices for FS6 space and ~3k > vertices for FS4 space, but changing the --icoorder flag seems to have no > effect on the number of vertices in the output. > > I have loaded the output surface functional image into Matlab to se that > there is real time-series data in there, but I have no way of knowing if it > has mapped the data appropriately. Additionally, I've tried to use > mri_surf2surf to downsample this data but have not ben able to successfully > get that to downsample the surface. The mri_surf2surf call I used is as > follows: > > mri_surf2surf --srcsubject subjID --srcsurfval > /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh --trgsubject subjID > --trgsurfval /mov_dir/filtered_func_residuals_fs4_lh_6mm_noreshape.mgh --hemi > lh --trgicoorder 4 > > Any advice on how to achieve my goal of projecting to subject surfaces, > smoothing and downsampling to FS4, as well as recommendations on how to > visualize the surface functional data and confirm that the projections has > worked properly would be much appreciated. Additionally, what should the > dimensions of a surface time series look like? I would have expected for > have an nVertices x nFrames x 1 array instead of the nVertices x 1 x 1 x > nFrames array, is this correct? > > > Thank you, > Jared > > ----- Forwarded Message ----- > From: "Jared Zimmerman" <jar...@mail.med.upenn.edu> > To: freesurfer@nmr.mgh.harvard.edu > Sent: Monday, September 19, 2016 8:46:17 PM > Subject: [Freesurfer] Projecting processed 4D functional data to individual > surfaces > > Hi All, > > I'm trying to project some processed resting-state data onto the surface to > run some surface based parcellations, and I'm running into a bit of > difficulty. Basically I'm using bbregister to register my functional to the > T1, then mri_vol2surf to project to the surface with the following pseudocode: > > bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \ > --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \ > --init-fsl --bold > > mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \ > --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \ > --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \ > --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh --noreshape > > > The registration looks pretty good after I run bbregister, but what I get out > from the mri_vol2surf seems weird. First of all, the dimensions are 112745 x > 1 x 1 x 120, which seems odd. I'm forcing no reshaping, and from the help > page it seems like the x-dim should be 40962 for icoorder=6. I have 120 > frames in my input data, so that seems to be right, but I'm not sure where > this dimension is coming from. I've also tried it with icoorder=4 and I get > the same x-dim=112745 when I'm expecting 2562. I've also run these commands > with various iterations e.g. reshaping, no smoothing, no projfrac, and I get > the same thing every time. > > I'm also wondering how I should view these files to confirm that the surface > projection has worked as I expect it if/when I am able to get the dimensions > to be correct. I cannot open any of the projected functional files in either > freeview or tksurfer, so it will be helpful to know how I might be able to > view these time-series on the surface after I've succeeded in projecting them > to that space. > > Any advice would be much appreciated > > > Thanks, > Jared > _______________________________________________ > 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. > _______________________________________________ > 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
