[David Shattuck]

hi Tod –

The binaries should have been included — I will repackage them later this week and upload a new version. We made a few final fixes right before release, and it looks like the code wasn’t recompiled before we packaged it.

What version of the MSVC compiler are you using? The strideiterator file would only affect BSE, and it compiles under MSVC2013 (I think it fails on MSVC2015 or later).

thanks,
David

[David Shattuck]

What T1 file are you expecting to see? Are you trying to load your own image?

We have tutorial data on our website. If you need data to use, you can start here:

http://brainsuite.org/tutorials/

perhaps with the Cortical Surface Extraction tutorial:

http://brainsuite.org/tutorials/cseexcercise/

thanks,
David Shattuck

[David Shattuck]

Hi Dayana –

There is a download button at the top of the page. Go there, or use this link:

Download

and select the correct version for your operating system.

thanks,
David Shattuck

[David Shattuck]

Hello –

There is also cortical_extraction.sh, which can be run from bash on Mac or Linux. It sets all of the parameters to be the same as the GUI. If necessary, you can copy it and edit it if you need to make any changes. If you do edit it, then you will want to make sure that BrainSuiteDir is set to the installation path. If it is not set, then the script will try to find the files based on location of the script.

thanks,
David

[David Shattuck]

Hi Gavin –

I think you are probably using either the build I sent you in August, or perhaps the current linux release version. In any case, I believe I have resolved this issue with the latest release of BrainSuite (16a1). I think it has to do with differences between the gcc compiler and the clang compiler. Clang didn’t report any errors compiling the 16a source code, but gcc did. I have fixed the few places where there were problems, and I have successfully compiled the source code under gcc 4.8. We still use clang for the official releases.

thanks,
David

[David Shattuck]

Hi Christian –

That’s great. One thing to make sure is that the order of the volumes is the same as is in your bvec/bval files. I’m not sure how best to do that. It might be safer to re-run dcm2nii on your original DICOM files, and make sure it outputs a 4D volume rather than individual 3D volumes. Are you using the latest version of dcm2nii?

We do have our own programs for merging DWI files (see here: http://neuroimage.usc.edu/neuro/Resources/BDPAddons#mergeDWIs), which is useful when a set of diffusion data is acquired as two different acquisitions. However, this program expects to have one bvec and one bval file per nii file. I think this would be different from how your data currently are stored.

thanks,
David

[David Shattuck]

Hi Cristian –

What tool did you use to convert them from DICOM to nifti? We typically use dcm2nii, which is included with MRIcron.

thanks,
David

[David Shattuck]

Hi Cristian –

How are you generating your .nii files in the first place? Do you have corresponding bvec and bval files already?

I don’t think we have a tool available from our site for doing this, but if you have FSL installed I believe you can do it with that. Let me know about the bvec/bval files, and I will see how we can help you with this.

thanks,
David Shattuck

[David Shattuck]

Hello –

Can you provide the specific command line call that you are making, including all arguments?

If that stage works in the GUI, the best thing to do is to use the cortical_extraction.cmd script. It is configured to have settings that match those in the GUI, and will produce identical results.

thanks,
David Shattuck

[David Shattuck]

Hi Michaela –

I have recently fixed a bug in the topology correction step, which caused the program to crash in certain cases. Can you download the latest version (16a1) and try again?

thanks,
David Shattuck

[David Shattuck]

Hello –

No, you do not need our permission to publish your results. The software is provided freely without any such restrictions. We do appreciate the citations, which help us document that the software is being used.

thanks,
David Shattuck

[David Shattuck]

Hello –

To run bse from the command line, you need to either specify the path to the bse command or add the path to your PATH variable. For example, if you unpacked the BrainSuite programs to your home directory, which I’ll call wwu94, then the path would be:

/home/wwu94/BrainSuite16a1/bin

In Linux BASH, you can type this command:

export PATH=/home/wwu94/BrainSuite16a1/bin:$PATH

to add BrainSuite’s program directory to the start of your path. Then, when you call bse, it should run.

You can also call the programs on the command line like this:

/home/wwu94/BrainSuite16a1/bin/bse

which tells the shell the precise location of the program.

Please give that a try.

thanks,
David Shattuck

[David Shattuck]

Hi Greg –

I was planning to put out an updated version of the code this week that fixes another bug. I’ll see if I can fix this as well.

Do you happen to remember which tools other than BFC failed on the 64-bit input?

thanks,
David

[David Shattuck]

Hi Gavin –

Can you provide some additional details about your compilation environment? Are you building this within Qt Creator? Which compiler are you using?

I do have a package that includes the GUI for linux, but we are still preparing it and packaging it for distribution. If you want to try it out and give us feedback, send me an email (dshattuck ucla edu) and I can provide it to you.

thanks,
David Shattuck

[David Shattuck]

The MathWorks download site for the MCR is on this page:

http://www.mathworks.com/products/compiler/mcr/

If you are using the newest version of BrainSuite (BrainSuite16a), then you will need to install the 2015b MCR. If you are using the older versions, then you will need 2012a.

I’ll update the links on our site. Thank you for pointing this out.

thanks,
David Shattuck

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