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>> 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 
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
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The information in this e-mail is intended only for the person to 
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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 
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MGH-NMR Center
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