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Harvard Oxford Atlas

You are here: Home1 / Forums2 / Support Forum (ARCHIVED – Please use Slack Channel instead)3 / Harvard Oxford Atlas4
Viewing 9 posts - 1 through 9 (of 9 total)
  • Author
    Posts
  • 02/21/2017 at 10:24 PM #2113
    ada.sevillamu
    Participant

    I wanted to add Harvard Oxford atlas, so I used the scritp ea_labeling2atlas in this way: ea_labeling2atlas(‘Harvard Oxford Thr25 2mm Whole Brain (Makris 2006)’)
    My problem is that the atlas apppears on the drop-down menu of LEAD DBS, but when I selected it, the visulization 3D does not appear. The Command Windows is always showing these lines:

    SPM12: spm_write_sn (v4878) 21:22:21 – 21/02/2017
    ========================================================================
    Completed : 21:22:21 – 21/02/2017

    ————————————————————————
    Running job #1
    ————————————————————————
    Running ‘Image Calculator’

    SPM12: spm_imcalc (v6124) 21:22:22 – 21/02/2017
    ========================================================================
    Warning: The images do not all have the same dimensions. – using 1st image.
    Warning: The images do not all have same orientation and/or voxel sizes. – using 1st image.
    ImCalc Image: C:\Users\ADA\Documents\MATLAB\lead\lead\atlases\Harvard Oxford Thr25 2mm Whole Brain (Makris 2006)\gm_mask.nii
    Done ‘Image Calculator’
    Done

    Do I have to do something else before using the atlas?

    02/21/2017 at 10:28 PM #2114
    andreashorn
    Keymaster

    Hi Ada,

    the lines you wrote are just a warning and totally fine. There’s no real “error” in there.
    Maybe you just need to wait a bit longer?
    When visualizing an atlas for the first time, Lead-DBS needs to build several structures and files first.

    Best, Andy

    02/21/2017 at 10:28 PM #2115
    andreashorn
    Keymaster

    Hi Ada,

    the lines you wrote are just a warning and totally fine. There’s no real “error” in there.
    Maybe you just need to wait a bit longer?
    When visualizing an atlas for the first time, Lead-DBS needs to build several structures and files first.

    Best, Andy

    02/22/2017 at 1:29 PM #2117
    ada.sevillamu
    Participant

    Hi Andy,
    you were absolutely right. I have waited a bit longer, and the atlas has worked perfectly.
    Thank you.

    07/03/2018 at 8:58 PM #5024
    mar
    Participant

    Hi there!
    It happens to me exactly the same but then I got an error about memory.
    I run >> ea_labeling2atlas(‘Harvard Oxford Thr25 2mm Whole Brain (Makris 2006)’)
    and then try to visualize and I get this:

    Generating Atlas table (first run with new atlas only). This may take a while…
    Building atlas table…

    ————————————————————————
    Running job #1
    ————————————————————————
    Running ‘Image Calculator’

    SPM12: spm_imcalc (v6961) 21:26:20 – 03/07/2018
    ========================================================================
    Warning: The images do not all have the same dimensions. – using 1st image.
    Warning: The images do not all have same orientation and/or voxel sizes. – using 1st image.
    ImCalc Image: C:\Users\Documents\lead\templates\space\MNI_ICBM_2009b_NLIN_ASYM\atlases\Harvard Oxford Thr25 2mm Whole Brain (Makris 2006) – copia\gm_mask.nii
    Done ‘Image Calculator’
    Done
    Error using ea_smoothpatch_inversedistance_double
    Requested 18446744069414588570×1 (17179869184.0GB) array exceeds maximum array size preference. Creation of
    arrays greater than this limit may take a long time and cause MATLAB to become unresponsive. See array size
    limit or preference panel for more information.

    if I type memory I get this:
    >> memory
    Maximum possible array: 10349 MB (1.085e+10 bytes) *
    Memory available for all arrays: 10349 MB (1.085e+10 bytes) *
    Memory used by MATLAB: 2101 MB (2.203e+09 bytes)
    Physical Memory (RAM): 8071 MB (8.463e+09 bytes)

    I changed the preferences in matlab to the maximum
    But I don´t think I can run it in this laptop
    How can that be 17179869184.0GB? Is it normal? or is there something I´m doing wrong?

    Thanks a lot!

    07/03/2018 at 9:10 PM #5025
    andreashorn
    Keymaster

    Hi mar,

    no clue exactly what happened but it shouldn’t run into array size issues. What you can try:
    – Don’t rename the atlas folder to something with a dash (‘ – copia’) but try to avoid blanks and dashes in filepaths where you can
    – delete the gm_mask.nii and try again
    – check out each nifti image in the generated atlas folder. Any of them looking suspicious? These are just normal nifti files, so you can look at them and compare them to niftis of other atlases.
    – if not create the atlas manually (without the labeling2atlas script but e.g. only use selected items from the labeling file that you can e.g. export using the SPM imcalc.

    Best, Andy

    07/03/2018 at 11:48 PM #5029
    mar
    Participant

    Hi Andy,
    I tried what you sugested and same error.
    Actually I manually created the atlas using code in labeling2atlas function only selecting the labels I´m interested in: left and right hippocampus. The niftis generated look normal when I display them with spm. Then I tried to visualize the atlas in lead dbs and the same error after a while:

    Error using ea_smoothpatch_inversedistance_double
    Requested 8774618295792×1 (65376.0GB) array exceeds maximum array size preference. Creation of arrays greater than
    this limit may take a long time and cause MATLAB to become unresponsive. See array size limit or preference panel for
    more information.

    Is it possible to obtain the atlas folder to copy it directly in the atlases folder ready to load it in dbs?
    My best,
    Mar

    07/04/2018 at 7:43 AM #5031
    andreashorn
    Keymaster

    Mh, weird, I cannot reproduce it here. Maybe a clean install could be helpful.
    In any case, made the ready atlas for you: https://www.dropbox.com/s/lc7fx7kijyvs7wo/mar_atlas.zip?dl=0

    Best, Andy

    07/04/2018 at 11:43 AM #5033
    mar
    Participant

    Thank you very much! Now with your atlas it works! You are so kind.
    All the best,
    Mar

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