sychoi

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Viewing 15 posts - 1 through 15 (of 32 total)
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  • in reply to: Co-registration #1557

    sychoi
    Participant

    BDP (BrainSuite Diffusion Pipeline) is a commandline tool only.

    sorry about that.
    flags: http://brainsuite.org/processing/diffusion/flags/
    overview: http://brainsuite.org/processing/diffusion/
    usage: http://brainsuite.org/processing/diffusion/pipeline/

  • in reply to: Co-registration #1549

    sychoi
    Participant

    This can be done using BDP using the following flags

    –custom-t1-label
    –output-diffusion-coordinate

    you can find documentation for these flags here:

    Let us know if this works for you.

  • in reply to: Cerebrum Labeling Problem #1420

    sychoi
    Participant

    you’re correct in that you need t1 images to run svreg since you need to first run CSE

    There’s no way to do automated segmentation on diffusion images alone on brainsuite. If you have label files made elsewhere as long as you have the correct file format, you can load the label file and create a connectivity graph that way.

    If you have further questions on the connectivity graph, please open up a new topic.

    Good luck!

  • in reply to: Cerebrum Labeling Problem #1403

    sychoi
    Participant

    Unfortunately, you can only perform cortical extraction on T1 weighted images.

    If you do not have T1 weighted images, you can still process your diffusion data through BDP. http://brainsuite.org/processing/diffusion/

    make sure to use the flag –no-structural-registration

  • in reply to: Cerebrum Labeling Problem #1401

    sychoi
    Participant

    quick question, are you running the cortical surface extraction sequence on T1 or diffusion images?

  • in reply to: nube; how2: access/use brain atlas #1291

    sychoi
    Participant

    The surfaces we generate do not include subcortical nor extratentorial structures.
    You can generate surfaces from any mask or label.

    If you have the svreg.label.nii.gz file loaded, open up the tools–> mask tool–> label mask tool
    then click “update list”
    you can then select any ROI (subcortical structures are in the 600s) and then click “make surfaces for each label”
    These surfaces can be saved using the surface display toolbox (hit “s” and it will appear or Surface->Show Surface Display Properties Toolbox)

    Your question on saving views was answered here: http://forums.brainsuite.org/forums/topic/bci-dni_brain_atlas-how2-save-retrieve-different-views/

    you can remove the slices from the surface viewer by hitting ctrl+v or cmd+v
    you can also unclick “slow slices” option in the surface display toolbox. Specific orientations can also optionally be turned off.

    You can view your surface as a solid color by going to the surface display toolbox.
    select your surface then select “solid color”
    unclick that and your colorized surfaces will be reappear

    Good luck. Glad you’re enjoying our interface


  • sychoi
    Participant

    you can create a .bst file that you can drag and drop onto brainsuite and will load a specified set of files.
    instructions found here: http://brainsuite.org/formats/formatsbst/

  • in reply to: atlas: how2 'deform' (open) a sulcus? #1289

    sychoi
    Participant

    Hi Dan,

    you can try cutting through the surfaces by pressing keys “x” “y” or “z” on the surface viewer.
    x : sagittal
    y : coronal
    z : axial
    The surface will cut through where ever your crosshairs are located on the volume slices.

  • in reply to: nube; how2: access/use brain atlas #1248

    sychoi
    Participant

    Hi Dan, our atlases will be found with your installation files. for example

    for windows:
    C:\Program Files\BrainSuite18a\svreg

    for mac
    /Applications/BrainSuite18a/svreg

    you will see a directory for the BCI-DNI_brain atlas and BrainSuiteAtlas1. I recommend the BCI-DNI_brain atlas.

    drag and drop files ending in:
    .bfc.nii.gz (or BCI-DNI_brain.nii.gz for inclusion of skull and scalp)
    .left.mid.cortex.dfs
    .right.mid.cortex.dfs
    .all.dfc (right and left will only load one at a time)
    and under File–>open–>label volume
    select the “BCI-DNI_brain.label.nii.gz” file

    To give you a few tips:
    you can learn about navigation controls here: http://brainsuite.org/interface/
    you can click anywhere on the volume slices or double click anywhere on the surface and the name of the region will appear on the bottom of the interface. There’s also some fun things you can do for visualization by opening up the mask toolbox.
    You can see the names and description of the sulcal curves (.dfc files) by opening up the sulcal toolbox

    click around, experiment and have fun. Let us know if you have any other questions.

  • in reply to: Extraction of single anatomical Surfaces #1174

    sychoi
    Participant

    I think what you’ve tried so far is great.
    It seems for a closed surface, rendering a surface using the svreg labels are your best bet so far.
    Can you specify what was inaccurate about your surfaces?

    Note also that your svreg labels will be subdelineated by GM and WM labels for each individual cortical label. ROI ID labels for GM starts with “1” and for WM “2”
    example: 1120: R. Superior frontal gyrus (WM) 2120: L. Superior frontal gyrus (WM)

    I’m not sure how we can help you more with the given information. What are you trying to calculate exactly?

  • in reply to: load fail #1173

    sychoi
    Participant

    Sorry I didn’t completely understand your question but are you asking how to load your .nii file?

    You can simply open brainsuite and drag and drop the file directly onto the gui.
    Or you can go to File–> Open volume.

  • in reply to: full segmentation #802

    sychoi
    Participant

    the subject.pvc.label.nii.gz will have GM/WM/CSF labels only.
    Then the subject.skull.label.nii.gz will have skull, scalp, space and brain labeled.

    detailed information can be found here: http://brainsuite.org/processing/surfaceextraction/skull-and-scalp/


  • sychoi
    Participant

    There is a number of different ways to do this interactively on the GUI or automated using matlab.

    Are you trying to add ROIs already created in subject or atlas space?
    or are you trying to add new ROIs by manually drawing them in the GUI?

  • in reply to: BDP running error message #761

    sychoi
    Participant

    It looks like the bvec file is not in the format that can be read by BDP
    Here is a sample of what BDP looks for: http://brainsuite.org/examples/siemens_20.txt

    You might have to reformat it to this or I would suggest using dcm2nii to convert your dicoms to nifti

  • in reply to: Grey matter and white matter volumes 2523412.nii.gz #745

    sychoi
    Participant

    The hemi.label file is an intermediate file that we use to roughly identify regions of the brain. If you load the hemi.label.nii.gz file in brainsuite, you will see that it labels the right and left brainstem, cerebrum, and a general subcortical area.

    You can take a look at your tissue classification results by opening the pvc.label.nii.gz or pvc.frac.nii.gz
    Here’s a video where I explain the brainsuite outputs: http://brainsuite.org/video-tutorials/checking-outputs/

    In order to get calculations of GM/WM/CSF and total volume, run your subject through SVReg which can be run on the GUI or command line. (instructions found here: http://brainsuite.org/processing/svreg/)
    it will output a roi.stats.txt file which outputs volume measurements which you can open in excel. the 1st line will give you total CSF volume, 2nd: GM Vol and 3rd WM Vol.
    It will also list regional measurements and you can find the description of the ROI IDs by opening the brainsuite_labeldescription.xml

    It looks like for this subject I get
    CSF: 272.569
    GM: 682.809
    WM:521.965
    GM+WM: 1204.774

    BrainSuite uses partial volume tissue classification which considers that some voxels are composed of mixed tissue and assigns it that way. So a single voxel can be calculated as 40% GM and 60% WM which is why you get voxels labeled as GM/WM or GM/CSF. This can give you more accurate measurements.

Viewing 15 posts - 1 through 15 (of 32 total)