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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- 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> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/