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
<gr...@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
<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
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The information in this e-mail is intended only for the person to whom
it is
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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