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/MRN_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
