can you send the command, terminal output, and log file?

On 09/24/2013 06:04 PM, ye tian wrote:

Dear Doug,
Thank you! I tried 500 iterations (I am aware that people usually do >10,000), but the program threw a "memory corruption" error. I have freesurfer 5.3. My ram is 4.0GB and the virtual memory is 7.8GB.
Would you please shine some light on what's going on? I can't seem to find an executable solution from the archive.
Thank you very much!
Sincerely,
Ye

On Tue, Sep 24, 2013 at 3:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:


    You need much more than 5 iterations! If you are doing whole
    hemisphere
    analysis, then you can use the precomputed tables.

    doug


    On 09/24/2013 01:46 PM, ye tian wrote:
    > Dear Freesurfers,
    > Sorry for having posted an incorrect question. I basically ran
    > *mri_glmfit-sim *on both hemispheres and tried both *--sim-sign neg
    > *and *--sim-sign pos*. Although I only had 5 iterations, I found no
    > significant clusters on any case. Does that mean that I accept the
    > null hypothesis?
    > PS: I found in
    >
    http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23324.html
    > that 10,000 iterations are commonly used.
    > Thank you very much!
    >
    >
    > On Mon, Sep 23, 2013 at 9:47 PM, ye tian <tianye730@gmail.com
    <mailto:tianye730@gmail.com>

    > <mailto:tianye730@gmail.com <mailto:tianye730@gmail.com>>> wrote:
    >
    >     Dear Freesurfers,
    >     I used the following command line to find significant clusters
    >     after glm analysis (before MC clusters attached)
    >     mri_glmfit-sim \
    >       --glmdir lh.meditation_age.glmdir \
    >       --sim mc-z 5 4 mc-z.negative \
    >       --sim-sign neg --cwpvalthresh 0.05\
    >       --overwrite
    >     I didn't find any, i.e., there are no clusters listed in file
    >     mc-z.negative.sig.cluster.summary. Does this mean that I should
    >     accept the null hypothesis for the whole cortex?
    >     Also, how many iterations of mc do people typically perform? I
    >     guess it doesn't make a difference if I do 1000 iterations
    instead
    >     of 5 anyways.
    >     Thank you very much!
    >     Sincerely,
    >     Ye
    >
    >
    >
    >
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    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center

    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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