[yeunkim]

Hi,

I apologize, I missed this post.
Just to clarify, you are unable to run BrainSuite BIDS App on HCP data because they are not in BIDS format? And so you need BIDS converters?

If so, here are some websites that lists available programs for BIDS conversion:
https://bids.neuroimaging.io/benefits
https://andysbrainbook.readthedocs.io/en/latest/OpenScience/OS/BIDS_Overview.html

If this is not the issue, could you paste the error message you are getting when you try to run the diffusion and fMRI data?

Thank you,
Yeun

[yeunkim]

Hi,

It looks like there may be a folder or file path error. Could you please provide the following information?

* Path to your output files (the path of your output folder that has the processed outputs)
* The exact command you ran (e.g., if it was using the docker version, it would be something like “docker run -ti –rm …”; if it was singularity, then it would be “singularity run …”)

Thank you,
Yeun

[yeunkim]

Hi,

Could you try putting two dashes in front of nii? i.e. --nii

So the command line would be:
/Applications/BrainSuite18a/bdp/bdp.sh A01.bfc.nii.gz –tensor –FRT –FRACT –nii /Users/BS_SPGR/A01/data.nii -g bvec -b bval

[yeunkim]

Hi,

Could you open the /Users/leonidastra86/Desktop/ICBM25/1001/1001.svreg.log file and look at the second line and see if the path to your atlas exists? You may have to edit the path to the atlas folder in the *.svreg.log files.

I hope this made sense.

Best,
Yeun

[yeunkim]

Hi,

In this command:

bss_data <- load_bss_data (type=”cbm”,
subjdir = /Users/leonidastra86/Desktop/ICBM25
csv = “/Users/leonidastra86/Desktop/ICBM25/ABC_demographics_tbm.csv – sample_demographics_tbm.csv”, hemi=”left”, smooth=2,5)

Could you try putting quotation marks around:
/Users/leonidastra86/Desktop/ICBM25

Could you also put just one csv file for the csv argument?
“/Users/leonidastra86/Desktop/ICBM25/sample_demographics_tbm.csv”

And use “.” for 2.5 for the smoothing level.

So the command would be something like:
bss_data <- load_bss_data (type=”cbm”,
subjdir = “/Users/leonidastra86/Desktop/ICBM25”,
csv = “/Users/leonidastra86/Desktop/ICBM25/sample_demographics_tbm.csv”, hemi=”left”, smooth=2.5)

Hope this helps.

Best,
Yeun

[yeunkim]

Hi,

Which version of BrainSuite are you using? And which OS are you running BrainSuite on?

Best,
Yeun

[yeunkim]

Hi,

Do you happen to have error logs from the crash? The log can be found in the Console log window in the BrainSuite GUI.

Best,
Yeun

[yeunkim]

Hi,

The method for pial surface generation is described here:

http://brainsuite.org/processing/surfaceextraction/pial/

Please let us know if you have more questions.

Best,
Yeun

[yeunkim]

Hi,

Could you try this?

1. Open BrainSuite
2. Go to Cortex (located on the top menu bar) -> Select SVReg Directory
3. Navigate to svreg directory (try going to /Applications/BrainSuite16a1/svreg)
4. Select Open

Thanks,
Yeun

[yeunkim]

Hi,

If you did not specify the atlas in your SVReg command line, the default atlas, BrainSuiteAtlas1, is used.

Best,
Yeun

[yeunkim]

Hi Zafarneyaz,

You can mask out the lesion using our Mask tool and then generate a surface of the lesion by clicking “Make Surface” under the Surface Generator in the Delineation Toolbox sidebar (under Mask Tool tab). Information on masking can be found here.

After, you can load in the labelled cortical surfaces and the lesion surfaces onto BrainSuite.

Best,
Yeun

[yeunkim]

Hi,

Skull threshold is the lower threshold hold and scalp threshold is the upper threshold.

The label values represent an arbitrary numerical value that a specified voxel will take on. For example, any voxel that has a label value of 16 will be considered/labeled as scalp in BrainSuite. You have the option to set this integer value.

To save out the surface files, you have to run the Skull and scalp step in the Cortical Surface Extraction Sequence dialog (Cortex -> Cortical Surface Extraction Sequence dialog). Make sure that the “save output of each stage automatically” box is checked (autosave is default). If you already have the structural file and brain mask (fileprefix.mask.nii.gz) loaded, then you can uncheck the Skull stripping step and just run the the Skull and scalp stage.

You can also run this via command line, with an additional -s flag to have the surface outputs as described here.

Best,
Yeun

[yeunkim]

Hi,

Have you tried switching/redirecting your SVReg directory? If you go to your main tool bar and click on “Cortex”, then select “Select SVReg Directory” in the drop down menu, you are able to switch the directory.

But, if possible, I would suggest that you download the latest version of BrainSuite (v16a1).

Best,
Yeun

[yeunkim]

Hi,

Are you able to get Matlab? Unfortunately, the matlab files for eig2nifti can’t run just with the Matlab compiler as of right now.

Best,
Yeun

[yeunkim]

Could you try loading up the *pvc.label.nii.gz (label volume of tissue types) file superimposed over your brain image? (Load either the unprocessed brain image or the bias field corrected (*bfc.nii.gz image) as Volume and load *pvc.label.nii.gz file as Label). From here, you can visually check the quality of the tissue segmentation. As you move your cursor around in the images, the bottom bar of your window will tell you which tissue type it has been labeled.

If your image has been poorly segmented, you may want to try editing your brain mask (Skull Stripping) or bias field correction (Nonuniformity Correction) parameters. I hope this helps!

Best,
Yeun

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