Thanks Doug, This does seem like it will do the right thing, but it’s failing because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to have an ico subject in my subjects_dir
Should this normally be in the subjects_dir? I don’t recall ever seeing this made when I’ve run recon-all in the past. Thanks, Jared Here’s the full terminal output when I run the command: mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 --interp trilinear --noreshape --trgsubject ico --icoorder 6 --out_type mgh --surf-fwhm 6 IcoOrder = 6, nIcoVtxs = 40962 srcvol = /func_test/filtered_func_residuals.nii.gz srcreg = func_test/coreg/fs_ep2struct_fsl.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ico surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /subjdir_test//subID/surf/lh.white Done reading source surface Reading thickness /subjdir_test//subID/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11345 Reading source surface registration subjdir_test//subID/surf/lh.sphere.reg Done loading source registration surface Reading icosahedron, order = 6, radius = 100 Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri Done loading target registration surface Mapping Surfaces (subID -> ico) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (40962) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (112745) Reverse Loop had 72236 hits > On Sep 28, 2016, at 3:34 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 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
_______________________________________________ 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.
