[Freesurfer] difference in 001.mgz found
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 > > >
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/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
Re: [Freesurfer] difference in 001.mgz found
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
