Yes I could save the file from my email into '/homes/8/hhe0/Documents'. Under 'Permissions' tab of this file, 'Allow executing file as program' option is checked.
I can try cd'ing into that folder then run the command as : >> mri_glmfit-sim --glmdir <ANALYSISPATH> --sim mc-z 10000 1.3 mcz10000_1.3 >> --sim-sign abs --cwpvalthresh .05 but I'm not sure if it will then use the new mri_glmfit-sim file you sent or the original file under '/usr/local/freesurfer/stable5_0_0/bin/'. Hamdi ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, September 10, 2014 4:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh Not sure what is wrong. Is it executable? Were you able to save the file from your email or did you cut and paste it into a file and save the file? On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote: > Hi Doug, > > Running it as you suggested didn't work either. I tried it as follows: > > 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir <ANALYSISPATH> --sim mc-z > 10000 1.3 mcz10000_1.3 --sim-sign abs --cwpvalthresh .05 > > It says: > > 'nknown option: `- > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. > > Then I thought maybe this is a c shell script so I need to use ./ before the > command. I tried that but it gave the same error as above. > > Any ideas? > > Thanks! > Hamdi > > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, September 09, 2014 6:14 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh > > Yes, you can just run > > /path/to/your/local/copy/mri_glmfit-sim > > > > On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote: >> Hi Doug, >> >> I don't seem to have the permission to change the contents of that folder. >> So I can't really copy it over. Is it possible to run this locally? I'm >> working on a linux workstation at Martinos and when I ask the source, it >> gives me that folder: >> >>>> which mri_glmfit-sim >> /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim >> >> >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Tuesday, September 09, 2014 5:24 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh >> >> You can just copy it over the old one (but make a backup of it first) >> >> On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote: >>> Hi Doug, >>> >>> Thanks for your reply. I can certainly test it. Could you tell me how I can >>> run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' >>> that I use is under '/usr/local/freesurfer/stable5_0_0/bin/' >>> >>> Best, >>> Hamdi >>> >>> >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >>> [gr...@nmr.mgh.harvard.edu] >>> Sent: Monday, September 08, 2014 11:48 AM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh >>> >>> That was an oversight. I've attached a version that should work. Can you >>> test it for me? Once I know it works I'll check it in to tree. >>> doug >>> >>> >>> >>> >>> On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote: >>>> Dear FS experts, >>>> >>>> I have a question about a MC output file. When I run the MC sim >>>> (using mri_glmfit-sim) on the surface, it generates a bunch of files >>>> including a 'sig.masked.mgh', which is nice for displaying the >>>> significance map limited to the clusters that survive the MC >>>> correction. However, when I run it on the volume, it doesn't generate >>>> this specific file. Does anyone know the reason for that? Is there an >>>> alternative way to display the significance map that show only the >>>> clusters that survive the MC correction? >>>> >>>> Many thanks! >>>> Hamdi >>>> >>>> >>>> -- >>>> >>>> Hamdi Eryilmaz, PhD >>>> >>>> Massachusetts General Hospital >>>> A.A. Martinos Center for Biomedical Imaging >>>> Psychiatric Neuroimaging Division >>>> 149 13th St, Charlestown, MA 02129 >>>> Phone: +1 617 643 7462 >>>> Email:heryil...@partners.org <mailto:heryil...@partners.org> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> 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 >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> 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 >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list 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.
