[Anand Joshi]

The curve adding/editing is currently disabled in version 17a, but you can use earlier versions (13a4) of BrainSuite for drawing the curves. The versions are available from here:

Download

[Anand Joshi]

For smoothing volumetrically, you can use
svreg_smooth_vol_function.sh

Please type it on the command line without any arguments to see the usage.

svreg_smooth_vol_function : This script performs 3d vol news
Authored by Anand A. Joshi, Signal and Image Processing Institute
Department of Electrical Engineering, Viterbi School of Engineering, USC

usage: svreg_smooth_vol_function.sh in_file stdx stdy stdz out_file

required input:
in_file: input vol file
stdx,stdy,stdz: std dev (in mm) in 3 directions
out_vol: output vol file

[Anand Joshi]

subject file contains cortical thickness on the subject’s surface whereas
atlas file contains subjects cortical thickness coregistered to the atlas.
If you want to perform multisubject or across scan comparison then you can use atlas file as input, whereas if you want to look at only one scan then you can use the subject file.

[Anand Joshi]

I read your command, I think you are specifying 2 files as inputs.
There should be 3 files. If you are smoothing cortical thickness, then you should specify the input file twice and then the output file.
first file contains geometry
second file contains the function that needs to be smoothed
third file if the output file
fourth argument is the amount of smoothing.

If that doesn’t work, can you share one file with me using dropbox and share the exact command that you are trying so that I can try to reproduce the error?

[Anand Joshi]

can you try the following in the terminal
ls /Users/leonidastra86/Desktop/AAA/Pre/xxx/Normalised/abc.pvc-thickness_0-6mm.left.mid.cortex.dfs

Is there any space in the path? If yes, then you should use double quotes around the file name.

[Anand Joshi]

Can you check if the input files exist by typing ls <filename> exactly as in the input command?

[Anand Joshi]

You can use –auto flag to do automatic parameter tuning.
Invoke bse in the terminal without any arguments to see the usage.

[Anand Joshi]

I assume you are referring to BrainSuite_Workshop_2017_GUI_David_Shattuck.pdf, right?
You can obtain the screen shown in slide 45 by following the instructions above. If that is not what you are looking for, can you please let me know the slide number?

[Anand Joshi]

You can try using gksudo to run the installer as root with gui.
gksudo ./install

[Anand Joshi]

The MAC and Linux versions of BrainSuite17a have all the binaries included. Would you be able to use them by any chance? In the meantime we will check about the Windows build.

[Anand Joshi]

Are you trying to visualize the cross section of surface and slices?
In order to see the pial surface on the cross section of the volume, you can load:
1. Load brain image and pial surfaces in BrainSuite.
2. Move the green cross hair to where you want to see the cross section in the image.
3. Go to surface view and press x, y or z depending on which cross section you want to see. You can try these keys multiple times to toggle cross sections.

As mentioned earlier, there is no volumetric mask for the pial surface since it is at much higher resolution than the WM surface. Can you please let me know what you want to do so that we can figure out how to best do it within BrainSuite.

[Anand Joshi]

Hi BrainSuite does not currently store a mask corresponding to the pial surface, since at voxel resolution, such a mask does not retain sulcal depths in the pial surface. Can you please explain a bit more on what you are trying to do, so that we can see if there an output that will serve the purpose? thanks,

[Anand Joshi]

Great! The latest version of BrainSuite (17a) contains automatic skull extraction. You can give it a try.

[Anand Joshi]

We don’t have a Monkey atlas that is integrated into BrainSuite, but you can create your own using the instructions below
http://brainsuite.org/processing/svreg/creating-custom-atlases
video tutorial:
http://brainsuite.org/video-tutorials/custom-atlas/

[Anand Joshi]

The white matter mask after topology correction is stored in subject.dewisp.mask.nii.gz files.
The WM GM and CSF tissue types are stored in subject.pvc.label.nii.gz. Since at MR resolution, most voxels contains a mixture of tissues. The partial tissue fractrions are stored in subject.pvc.frac.nii.gz. These are before topology correction, but depending on your application, these might serve the purpose. Please refer to the following link for more information.
http://brainsuite.org/processing/surfaceextraction/pvc/

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