Thanks for the confirmation, Bruce. I've looked at the other files I spot checked which failed to match. A bunch of the files in directory surf contain a line at the top like "Created by nobody on Mon Feb 8 15:13:58 2016" The mri/transforms/talairach.m3z.inv.?.mgz files contain the pathname of a .xfm file. I'm pretty confident now that we are getting the same results from all the runs but I want write something to check systematically.
Best - Don > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, February 10, 2016 8:15 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] difference in 001.mgz found > > yes, we store the command lines used to generate a .mgz in the header, so that > makes sense Bruce On Thu, 11 Feb 2016, Krieger, Donald N. wrote: > > > These runs were executed on the Open Science Grid. > > So the data file, the scan, was uploaded to grid worker machine, placed in a > transitory directory, and processed. > > The full pathname of the file is included in 001.mgz. > > I got it by: zcat mri/orig/001.mgz | strings Here are the input and > > output file names for 2 of the runs: > > /var/lib/condor/execute/dir_31034/MRN_1_defaced.mgz > > /scratch/tmp.FFTGBhmgp8/MRN_1/mri/orig/001.mgz > > > > /var/lib/condor/execute/dir_3734674/glide_HRFaAm/execute/dir_3741395/M > > RN_1_defaced.mgz /scratch/tmp.ghJfB4leGR/MRN_1/mri/orig/001.mgz > > > > Best - Don > > > > > >> -----Original Message----- > >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > >> boun...@nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N. > >> Sent: Wednesday, February 10, 2016 6:38 PM > >> To: Freesurfer support list > >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan > >> > >> It looks like they do give the same results. > >> I have to write something to go through everything systematically > >> which I may not get to till tomorrow. > >> Also I am checking to see whether there was some difference in how > >> 001.mgz was created. > >> The source image file on which we are running freesurfer is a defaced.mgz . > >> It's possible that it was sitting in a different directory for the > >> different runs since the runs were executed by a work flow management > >> system (Pegasus) on the Open Science Grid. > >> > >> Don > >> > >> ________________________________________ > >> 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, February 10, 2016 6:13 PM > >> To: freesurfer@nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan > >> > >> That probably means that there is something in the header that is > >> different. It should print a report to the terminal. Do they not give the > >> same > results? > >> > >> On 02/10/2016 04:36 PM, Krieger, Donald N. wrote: > >>> mri_diff finds no differences in the mri/orig/001.mgz's but the > >>> checksums are > >> different. > >>> In fact, their sizes are slightly different. > >>> > >>> > >>> > >>>> -----Original Message----- > >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > >>>> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > >>>> Sent: Wednesday, February 10, 2016 3:45 PM > >>>> To: Freesurfer support list > >>>> Subject: Re: [Freesurfer] comparing multiple runs on the same scan > >>>> > >>>> Hi Don > >>>> > >>>> are you saying the 001.mgz is different when created from the same > >>>> dicom data? Can you run mri_diff on it to see what the difference is? > >>>> > >>>> cheers > >>>> Bruce > >>>> On Wed, 10 > >>>> Feb 2016, Krieger, Donald N. wrote: > >>>> > >>>>> We would like to confirm that we are getting identical results > >>>>> from multiple freesurfer runs on the same data set. > >>>>> > >>>>> To do so we are comparing identically named files using md5sum and > >>>>> would very much appreciate your thoughts on our results. For > >>>>> multiple files, we concatenate them and pipe the output into md5sum. > >>>>> Below is a table showing what we’ve found so far. I take hope > >>>>> from the positive matches we get from all of the .annot files and > >>>>> from the fact that 001.mgz does not match. This latter suggests > >>>>> that there is a date or something embedded in some of the files > >>>>> from separate runs which > >>>> defeats the match. > >>>>> > >>>>> > >>>>> Please let us know what you know about this and thanks. > >>>>> > >>>>> > >>>>> > >>>>> file(s) > >>>>> > >>>>> md5sum result > >>>>> > >>>>> label/*.annot > >>>>> > >>>>> match > >>>>> > >>>>> label/*.label > >>>>> > >>>>> match > >>>>> > >>>>> mri/wmparc.mgz > >>>>> > >>>>> mismatch > >>>>> > >>>>> surf/qsphere.nofix > >>>>> > >>>>> surf/rh.sphere > >>>>> > >>>>> mismatch > >>>>> > >>>>> mri/orig/001.mgz > >>>>> > >>>>> mismatch > >>>>> > >>>>> mri/transforms/talairach.m3z > >>>>> > >>>>> match > >>>>> > >>>>> mri/transforms/talairach.m3z.inv.x.mgz > >>>>> > >>>>> mri/transforms/talairach.m3z.inv.y.mgz > >>>>> > >>>>> mri/transforms/talairach.m3z.inv.z.mgz > >>>>> > >>>>> mismatch > >>>>> > >>>>> mismatch > >>>>> > >>>>> mismatch > >>>>> > >>>>> > >>>>> > >>>>> Best - Don > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> Don Krieger, Ph.D. > >>>>> > >>>>> Department of Neurological Surgery > >>>>> > >>>>> University of Pittsburgh > >>>>> > >>>>> > >>>>> > >>> _______________________________________________ > >>> 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 > >> > >> > >> 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. > >> > >> _______________________________________________ > >> 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 > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
