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 greve@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" jaredz@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

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I want to project to the native subject surfaces though, not fsaverage. If I use —trgsubject subjID would that work with the —icoorder flag? Alternatively I guess I could project to fsaverage and then use mri_surf2surf to move back to the subject surface, but that seems like a roundabout way to do it and will probably add some unnecessary interpolation.

Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder flags and I did successfully get output with 112745 vertices (is this FS7 space? I would have expected ~164k vertices, is this with medial wall masked?) and I could try to resample that with mri_surf2surf. I wasn’t able to do this before, but I didn’t use the flag —trgsubject or —trgicoorder flags, though I suspect I will run into the same problem trying doing this. I’m not at my computer now but can try this later this afternoon though.

Thanks, Jared

On Sep 29, 2016, at 12:00 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

you can actually skip the ico thing and just use --trgsubject fsaverage6

On 9/28/16 7:06 PM, Jared P Zimmerman wrote:

...

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 <greve@nmr.mgh.harvard.edu mailto:greve@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" <jaredz@mail.med.upenn.edu mailto:jaredz@mail.med.upenn.edu> To: freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ahh, thanks Bruce. Is there a way to downsample the subject meshes?

-jared

On Sep 29, 2016, at 10:18 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Jared

the icosahedra are only used to represent average space surface (fsaverage[4-7]), not individual subjects.

cheers Bruce On Thu, 29 Sep 2016, Jared P Zimmerman wrote:

...

I want to project to the native subject surfaces though, not fsaverage. If I use —trgsubject subjID would that work with the —icoorder flag? Alternatively I guess I could project to fsaverage and then use mri_surf2surf to move back to the subject surface, but that seems like a roundabout way to do it and will probably add some unnecessary interpolation. Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder flags and I did successfully get output with 112745 vertices (is this FS7 space? I would have expected ~164k vertices, is this with medial wall masked?) and I could try to resample that with mri_surf2surf. I wasn’t able to do this before, but I didn’t use the flag —trgsubject or —trgicoorder flags, though I suspect I will run into the same problem trying doing this. I’m not at my computer now but can try this later this afternoon though. Thanks, Jared

 On Sep 29, 2016, at 12:00 AM, Douglas Greve
 <greve@nmr.mgh.harvard.edu> wrote:

you can actually skip the ico thing and just use --trgsubject fsaverage6 On 9/28/16 7:06 PM, Jared P Zimmerman wrote: 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
 <greve@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"
 <jaredz@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

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Yeah, I think I misunderstood what was happening with the ico registration. I thought it was using the ico to downsample the subject surface, but I see that this is an atlas space and I can do w/e calculations I need I this space and then register back to subject space after.

Thanks for the help, I got it to work by doing mri_vol2surf to register to my subject surface and then mri_surf2surf to downsample.

-jared

On Sep 29, 2016, at 12:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

I don't understand what you mean. When you use ico (when it used to work), it always went to fsaverage space. Do you want to decimate the native space surfaces?

On 09/29/2016 10:15 AM, Jared P Zimmerman wrote:

...

I want to project to the native subject surfaces though, not fsaverage. If I use —trgsubject subjID would that work with the —icoorder flag? Alternatively I guess I could project to fsaverage and then use mri_surf2surf to move back to the subject surface, but that seems like a roundabout way to do it and will probably add some unnecessary interpolation.

Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder flags and I did successfully get output with 112745 vertices (is this FS7 space? I would have expected ~164k vertices, is this with medial wall masked?) and I could try to resample that with mri_surf2surf. I wasn’t able to do this before, but I didn’t use the flag —trgsubject or —trgicoorder flags, though I suspect I will run into the same problem trying doing this. I’m not at my computer now but can try this later this afternoon though.

Thanks, Jared

...

On Sep 29, 2016, at 12:00 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote:

you can actually skip the ico thing and just use --trgsubject fsaverage6

On 9/28/16 7:06 PM, Jared P Zimmerman wrote:

...

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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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" <jaredz@mail.med.upenn.edu mailto:jaredz@mail.med.upenn.edu <mailto:jaredz@mail.med.upenn.edu mailto:jaredz@mail.med.upenn.edu>> To: 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, September 19, 2016 8:46:17 PM Subject: [Freesurfer] Projecting processed 4D functional data to individualsurfaces

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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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 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.

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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