[wy]

Any help?

[wy]

How do i delete this post? Just saw that i already asked this few month back and got no answer!

[wy]

an*

[Anand Joshi]

Hi Wy, I will try to help you with this.
Can you try running /Applications/BrainSuite18a/svreg/bin/svreg_label_surf_hemi.sh
from the command line and let me know what message you get?

[wy]

Thank you very much.

Here is the output.

surface registration and labeling (svreg)
This is the main program for surface registration. First, the surface is
smoothed to create a multiresolution representation of the surface. An
initial registration is performed by aligning the 3D coordinates of this
smoothed surface. This is followed by p-harmonic mapping to a square and
curvature-based registration.
For more information, please see http://brainsuite.org
Authored by Anand A. Joshi, Signal and Image Processing Institute
Department of Electrical Engineering, Viterbi School of Engineering, USC

usage: svreg_label_surf_hemi.sh [subject fileprefix] [atlas fileprefix]
[hemi] [flags]

required input:
subject fileprefix path and filename prefix of the subject’s output
from BrainSuite’s Cortical Surface Extraction
Sequence
atlas fileprefix path and filename prefix of atlas files and labels
to which the subject will be registered
hemi the hemisphere to refine; either left or right

optional flags:
-v# Controls the verbosity of output messages (# is 0, 1, or 2)
-t display timestamps along with output messages

Here is one of the errors i am getting from the run..

Using Executable /Applications/BrainSuite18a/svreg/bin/warp_points_mac
A matrix with a negative or zero determinant was encountered. (AIR_NON_POSITIVE_DETERMINANT_ERROR)
SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
Error using readdfs (line 61)
Unable to read:~/study/BS_SPGR/A11/A11.svreg.tmp/A11.target.left.mid.cortex_smooth10_smooth10.dfs
Error in surf_align_autocorrect_with_AIR (line 159)
Error in align_surf_curves (line 62)
Error in surf_flatten_newbs (line 32)
Error in svreg_label_surf_hemi (line 163)

another is the pial line. While brainsuite is running, i can see that it was too much inside the brain, sometimes including the inner temporal!!!

[Anand Joshi]

Ok thanks. From the BrainSuite GUI, goto Cortex->Select SVReg directory.
Then from the dialog box, goto BrainSuite installation folder and select directory named svreg.
After this, try running the whole sequence for your subject data and it should work.

The next error is something else. It is due to some errors in surface extraction. Please make sure that the cortical surface you get look reasonable, as shown on brainsuite website.

[ASD]

Sir,
I am also getting the same error
Registration Process Error
could not launch Label Left Hemisphere Surface
please check that the executable /home/alphin/Downloads/BrainSuite19a/svreg/bin/svreg_label_surf_hemi.sh exists and that /home/alphin/Downloads is a valid directory.

Please see log window for process output

I selected the SVReg directory and still facing the same issue.

[Anand Joshi]

Does the /home/alphin/Downloads/BrainSuite19a/svreg/bin/svreg_label_surf_hemi.sh
file exist on your computer?

[Author]

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