Creating xls files

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This topic contains 6 replies, has 3 voices, and was last updated by  JB 4 months, 1 week ago.

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  • #21225 Reply

    Ismail

    Dear all,

    First of all, congratulations on this new tool that looks very promising.
    In order to use BRAPH, i was wondering how can I create these xls files for each of my subjects from my nifti time series ?

    Thank you in advance,

    Ismail

    #21228 Reply

    JB
    Participant

    Dear Ismail,

    You will need to preprocess your nifti fMRI images with SPM, FSL or any other software.

    After preprocessing, you should extract the time series for each region of a brain atlas (whichever you like).

    These time series should be included in a file (xls, mat, txt) for each subject, where each column corresponds to a brain region and each row corresponds to a time point.

    Check our videos online, some of them show how these files should look like.

    Good luck with the analyses.

    Best wishes,

    Joana

    #21237 Reply

    Ismail

    Dear Joana,

    Thank you for your answer.
    I’m familiar with the preprocessing of fMRI with these softwares, however I just don’t see how I can extract these time series for each region in the xls file ? Is there a script or a software for that ?

    Thank you again,

    Best,

    Ismail

    #21242 Reply

    Joana
    Participant

    Dear Ismail,

    You could try using fslmeants or mri_segstats and concatenate the ROI signals into a single file. I believe the option –avgwf of mri_segstats saves directly your ROI time series into a text file. Check the forum/websites of FSL and FreeSurfer.

    Best wishes,

    Joana

    #21244 Reply

    Ismail

    Dear Joana,

    Thank you very much for your help, it works perfectly.

    Best,

    Ismail

    #22152 Reply

    Adam

    Hello,
    I am a novice in this field, and my colleagues and I find your tool very suitable for our objectives. The problem is that we are finding it hard to understand the conversion of subjects & atlases data to BRAPH required formats.

    We would love it if you can make a video tutorial that illustrated the procedure in detail.

    Regards,
    Adam Zubair.

    #22182 Reply

    JB
    Participant

    Hi Adam,

    I understand your concern.
    The problem is the procedure you mention will vary depending on the software you use for image preprocessing and there are quite a few out there.

    But it all comes down to:
    1) preprocessing your images using fsl, spm, freesurfer or any other software
    2) selecting a brain atlas
    3) extracting the values of your images (volumes, fmri signals, etc) from each region of the atlas
    4) including these values in an excel or .mat file

    If you have specific questions on how to carry out the previous steps you can send an email to the support forums of the software you are using. We have experience with some but not all softwares.

    Hope this helps,

    Joana

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