Brain Mapping

This topic contains 5 replies, has 3 voices, and was last updated by  Anand Joshi 12 months ago.

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  • #960


    A probably stupid question but although in the label description file are many ROIs mentioned, not all of them are included in my analysed patients.

    Did I do something false or does it have to do with the (Brainsuite-)atlas that I used?

    For example Corpus Callosum, transverse temporal gyrus and so on.

  • #1202

    Anand Joshi

    If the *.roiwise.stats.txt file reports the volumes of then ROIs then these ROIs should be generated by BrainSuite. If the ROI volumes are not reported in the .txt file, then it is likely that something in the cortical extraction or registration sequence has not worked well. Please check the outputs at each stage to figure out.

  • #1526


    I`m a little bit confused on how to use the command.
    Where do I find the requested param_nii_file?
    If I try this:
    /opt/BrainSuite18a/svreg/bin/ SUBJECT -v2
    It says that the *.label.nii.gz file is missing. But its there!
    I need Help!

    Full massage:

    root@voltool:/home/flo/DATA/Files/RAD-2010-261829# /opt/BrainSuite18a/svreg/bin/ /home/flo/DATA/Files/RAD-2010-261829 -v2
    Error using generate_vol_param_stats_xls (line 57)
    SVREG label file missing: SVREG volume labels file not found. Please check if <name>.svreg.corr.label.nii.gz or <name>.svreg.label.nii.gz or <name>.svreg.corr.manual.label.nii.gz exists.
    root@voltool:/home/flo/DATA/Files/RAD-2010-261829# ls -l | grep *.svreg.label*
    -rwxrwxrwx 1 root   root      343194 Okt 20 15:23 RAD-2010-261829.svreg.label.nii.gz
  • #1527

    Anand Joshi

    Can you please explain what you are trying to do? I want to have a better idea of what you are doing so that I have a better idea and suggest the correct command.

  • #1528


    I´m trying to get the more detailed Volumes. In the GUI i can get them at
    DelineationToolbox->ROI Details->Compute Volumes and then I can save them as a *csv.
    But how to do this on the cmdline? (Linux)

  • #1529

    Anand Joshi

    If you ran the full BrainSuite and SVReg sequence, the volumes are already computed. You can find them in {subject}.roiwise.stats.txt file. Just load this in excel and you can see the table of all the statistics. Please let me know if there is any issue.

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