Problem with BSSR

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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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