Thanks Doug! It seems to be working this time. I will keep you posted on the results.
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: Thursday, September 11, 2014 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh I think it must have gotten contaminated as an attachement. Try using this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim On 09/10/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote: > 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 > > -- 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 . 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