[Anand Joshi]

If the *.roiwise.stats.txt file reports the volumes of then ROIs then these ROIs should be generated by BrainSuite. If the ROI volumes are not reported in the .txt file, then it is likely that something in the cortical extraction or registration sequence has not worked well. Please check the outputs at each stage to figure out.

[Anand Joshi]

Thank you for using BrainSuite.
When you run the full brainsuite sequence, it generates *.roiwise.stats.txt file that has ROIwise volumes. You can open this file in excel and check the volumes of the ROIs.

[Anand Joshi]

Is your windows system 32 bit o 64 bit?
Is the pial surface generated correctly?

[Anand Joshi]

The source code mentioned above has functionality to remove tiny patches of voxels that you can seen in the surfaces. It can be done in Matlab as follows, using the svreg source code from the brainsuite website.

s=readdfs(surfacefile);
s=myclean_patch_cc(s);
sm=smooth_cortex_fast(s,.1,1000);
view_patch(sm);

We don’t have a command line utility for doing this, but the above mentioned matlab code should work.

[Anand Joshi]

Please inspect the quality of cortical surfaces. It is likely that the surfaces are not extracted properly. Do they look realistic?

[Anand Joshi]

You can drag and drop dfc files in brainsuite interface to see the sulci.

[Anand Joshi]

If the thickness looks ok, then don’t worry about the warning. Usually, it does not cause any problems, it is just a precaution.

[Anand Joshi]

Hi Louise, For some reason, I can’t see the image you posted.
You can smooth the surface in matlab using svreg code.
First, save the surface as a dfs file using BrainSuite.
1. Generate the surface in BrainSuite
2. Goto Surface->Surface Display properties, select the surface that you want to save and press save button under the surface properties bar.
3. Download svreg source code from downloads section on BrainSuite website. Add path to the code in matlab.

s=readdfs(surfacefile);
sm=smooth_cortex_fast(s,.1,1000);
view_patch(sm);

You can also save it back to dfs file using writedfs function.

Additionally, you can compute vertexwise curvature using patchcurvature function available here:
https://www.mathworks.com/matlabcentral/fileexchange/32573-patch-curvature

[Anand Joshi]

Can you please type the error log here?

[Anand Joshi]

For combining
v.img(v.img==l1|v.img==l2)=l1;
should work. What happens when you do that?

[Anand Joshi]

Thanks, Mike for your feedback. With the current release, you can use the Matlab functions from SVReg source code to load the label nifti files in Matlab, delete and combine the labels you want, and then save the file.

Here is a pseudocode

v=load_nii_BIG_Lab(labelfilename);
v.img(v.img==l1||v.img==l2)=l1; %combine labels l1 and l2
v.img(v.img==l3)=0; %delete label l3
save_untouch_nii(out_file, v)

[Anand Joshi]

You can ignore the warning. The output should be correct.

[Anand Joshi]

Instead of std2 try just 2

[Anand Joshi]

What’s the command line that you tried?

[Anand Joshi]

svreg_smooth_vol_function.sh uses 3D Gaussian smoothing. The parameters specify standard deviation, in mm, of the Gaussian kernel for the smoothing. One can specify the std dev in three directions separately.
Please make sure to svreg_smooth_vol_function.sh for nii.gz volume files, and svreg_smooth_surf_function.sh for .dfs files for surface based smoothing.

[Author]

Posts