[David Shattuck]

Hi Fcuang –

We have a currently testing a fix for this. We will update you on this once it is ready for download.

thanks,
David Shattuck

[David Shattuck]

Hi Nuua –

Just to clarify what you are trying to do : do you basically want to sample the BrainSuite generated tracks into an image volume? Are you looking for a simple binary mask or a tract density map?

We do have some code to do these things. The first is in Matlab, and you can download the source code here:

http://neuroimage.usc.edu/neuro/Resources/TractConnect

Will that provide what you need?

We also have some additional C++ command line tools for this that we haven’t released it publicly yet. I expect we will have those available in the next two weeks.

thanks,
David Shattuck

[David Shattuck]

Hi Abujamea –

It looks like a processing error happened earlier in the cortical surface extraction routine. Without seeing all of your output, my best guess is that the skull-stripping step didn’t remove a sufficient amount of the scalp/neck, which then resulted in a misclassification of GM during the tissue classification step.

Can you step through the processing steps for cortical extraction and see where if it failed there?

thanks,
David Shattuck

[David Shattuck]

Hi Rachel –

There are a few other flags that need to be set to run cerebro. If you look at the cortical extraction script distributed with BrainSuite, which is probably located at /Applications/BrainSuite15b/bin/cortical_extraction.sh on your machine, there is a line for cerebro:

${BrainSuiteBin}cerebro $VERBOSE $ATLASES -i ${basename}.bfc.$EXT \
-l ${basename}.hemi.label.$EXT -m ${basename}.mask.$EXT -o ${basename}.cerebrum.mask.$EXT \
-c 2 –air ${basename}.air –warp ${basename}.warp ${CEREBROOPTIONS}

Replacing these with the arguments from your command and ignoring some empty variables yields:

cerebro –atlas ${workingdir}/inia19-t1-brain_16bit.img –atlaslabels ${workingdir}/inia-struct.img \
-i e3834_OxM130_AP.nii -o ${workingdir}/e3834_OxM130_AP.cerebrum.mask.nii.gz \
-l ${basename}.hemi.label.$EXT -m ${basename}.mask.$EXT \
-c 2 –air ${basename}.air –warp ${basename}.warp

The -c 2 flag is the one that should fix your issue (it controls the cost function used by AIR during the linear registration step).

You will need the other flags to complete the cortical extraction and SVReg labeling process.-l and -m save the hemisphere labels and cerebrum mask, which are used later for hemisphere splitting and pial surface expansion. The .air and .warp files save the transformation files and are used to initialize parts of the SVReg registration.

You could also edit the cortical extraction script to change the atlas files. These lines (38-40) are where it is specified.

ATLAS=”${BrainSuiteDir}/atlas/brainsuite.icbm452.lpi.v08a.img”
ATLASLABELS=”${BrainSuiteDir}/atlas/brainsuite.icbm452.v15a.label.img”
ATLASES=”–atlas ${ATLAS} –atlaslabels ${ATLASLABELS}”

Let us know if this solves your issue.

thanks,
David

[David Shattuck]

Hi Stefan –

I’m glad to hear it is working now. My best guess is that the file was uncompressed at some point, but retained the .gz extension. The file readers that I use in the GUI and command line tools will open files whether they are compressed or not, regardless of the extension, but the readers used in BDP will explicitly decompress .gz files before processing them. If you are curious and still have the original file, you could check whether or not the files is the same size as your uncompressed volume.

thanks,
David Shattuck

[David Shattuck]

Hi Steso –

The slow startup is due to MCR. It takes some time to load all of the Matlab libraries, unfortunately. I am not aware of a way to get around it, but we will look into it.

What did you use to try to unzip it?

It is possible that the file is corrupt. Does the BrainSuite gui open it correctly?

thanks,
David Shattuck

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