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
<mailto: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
<mailto:jar...@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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.
