Problem with BSSR

Forums Forums BrainSuite Statistics toolbox (BSS) Problem with BSSR

This topic contains 8 replies, has 3 voices, and was last updated by  leonidastra86 3 months, 4 weeks ago.

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  • #897

    leonidastra86
    Participant

    I am trying to make a cortical thickness analysis with BSSR but it doesn’t really work.

    1)I made folder with the patients, smoothed atlas.pvc-thickness_0-6mm.smooth2.5mm.right/left.mid.cortex.dfs files for both sides.
    2)Smoothing for the abc.svreg.inv.jacobian.nii.gz files didn’t really work
    3)After installing R, R Suite and the BSSR through R Suite I am trying with the following path to start but comes always to an error :

    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)

    and the error:
    Error: unexpected ‘,’ in ” csv = “/Users/leonidastra86/Desktop/ICBM25/ABC_demographics_tbm.csv – sample_demographics_tbm.csv”,”

    Error: unexpected ‘/’ in:
    “bss_data <- load_bss_data (type=”cbm”,
    subjdir = /”

    I have no idea from programming and I need your help to analyse my data.

    Thank you in advance and thumbs up for your work on the program.

  • #898

    yeunkim
    Participant

    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

  • #901

    leonidastra86
    Participant

    Hi Yeun and thank you very much for your help.
    After some changes that you suggested and some mistakes that I found in my data, I could form the right pathway.
    It asks about the atlas, although I used the Brainsuite atlas.

    Error: Could not determine the BrainSuite atlas used for registration.
    Please check the log file /Users/leonidastra86/Desktop/ICBM25/1001/1001.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument.

    Any ideas?

  • #903

    yeunkim
    Participant

    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

  • #904

    leonidastra86
    Participant

    Oh God, I now know the problem. I analysed the Data with 2 Computers, half on a Windows computer (C:\Program Files\BrainSuite17a\svreg\BrainSuiteAtlas1\) and half with a MacOs Computer (so the path is not the same).
    Is there a solution for this? Do I need the svreg. files for all of the patients and edit the path every time or is it just for the first case? Because in the ICBM25 folder that I downloaded from the Brainsuite page was only on the first patient present.

  • #906

    leonidastra86
    Participant

    Problem was fixed, analysis was performed without any problems.
    Thank you all so much for your help!

  • #926

    leonidastra86
    Participant

    Could I make the same thing but without covariates?
    I am trying following command but without any success:
    bss_model <- bss_anova(main_effect= “disease”, bss_data)

    and I receive

    Error in bss_anova(main_effect = “tinnitus”, bss_data) :
    argument “bss_data” is missing, with no default

  • #1595

    fproessl
    Participant

    Hey leonidastra86 –

    I am running into a similar issue you did when trying to run the bssr:

    Error: Could not determine the BrainSuite atlas used for registration.
    Please check the log file C:/Users/Fproessl/Desktop/BACL_Visual/4010WK/4010WK.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument.

    Do you remember how you solved this? I tried to rename the filepath of the .log file but it did not work…

    Thanks,
    Felix

  • #1826

    leonidastra86
    Participant

    The path to the atlas is in the .svreg text file.

    However, I am trying to do the same analysis in windows and I get an error that the csv command is either wrong or not found.
    I am using exactly the same command as before and it used to work…
    What is the problem?

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