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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@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-bounces@nmr.mgh.harvard.edu [freesurfer- bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@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 greve@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
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@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-bounces@nmr.mgh.harvard.edu [freesurfer- bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@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 greve@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
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@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-bounces@nmr.mgh.harvard.edu [freesurfer- bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@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 greve@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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Krieger, Donald N.