On Thu, Sep 26, 2013 at 12:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Ye, can you run the command like this:

mri_glmfit-sim --glmdir lh.meditation_age.glmdir --sim mc-z 500 4 mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --overwrite >&terminal.txt

Note the "&" after the ">". This will cause all the terminal output to go to terminal.txt which will help me figure out exactly what is going wrong

doug

On 09/24/2013 08:39 PM, ye tian wrote:

Dear Doug,

The command line is
mri_glmfit-sim --glmdir lh.meditation_age.glmdir --sim mc-z 500 4 mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --overwrite > terminal.txt
Most output goes into terminal.txt except the following (which is not important anyways)
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortabel_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortabel_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortabel_desikan_killiany.txt)
*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2ff05b10 ***
Please see terminal output and log file in attachment.
PS: if you ever wonder, the time on my virtualbox is 1hr ahead of my host.

Thank you so much for your patience.

Sincerely,
Ye

On Tue, Sep 24, 2013 at 6:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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