Re: [Freesurfer] comparing multiple runs on the same scan

2016-02-10 Thread dgw 
Doug responded to your previous mail with this:

Even on the same operating system they will be different because there
is stuff in the header that will change. Use mri_diff (volumes,
segmentations, and surface overlays) or mris_diff for surfaces to check
whether they are different.


hth
d


On Wed, Feb 10, 2016 at 2:14 PM, 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
>
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Re: [Freesurfer] comparing multiple runs on the same scan

2016-02-10 Thread Krieger, Donald N. 
Thanks very much for getting back so quickly.
Please pardon.
I’m sure this answer must be in lots of other places.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of dgw
Sent: Wednesday, February 10, 2016 3:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] comparing multiple runs on the same scan

Doug responded to your previous mail with this:

Even on the same operating system they will be different because there
is stuff in the header that will change. Use mri_diff (volumes,
segmentations, and surface overlays) or mris_diff for surfaces to check
whether they are different.
[Image removed by sender.]
hth
d


On Wed, Feb 10, 2016 at 2:14 PM, Krieger, Donald N. 
<krieg...@upmc.edu<mailto:krieg...@upmc.edu>> 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

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Re: [Freesurfer] comparing multiple runs on the same scan

2016-02-10 Thread Bruce Fischl 

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


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Re: [Freesurfer] comparing multiple runs on the same scan

2016-02-10 Thread Krieger, Donald N. 
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
> >
> >
> >

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Re: [Freesurfer] comparing multiple runs on the same scan

2016-02-10 Thread Bruce Fischl 

what is the difference in how you created them?
On Wed, 10 Feb 2016, 
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





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Re: [Freesurfer] comparing multiple runs on the same scan

2016-02-10 Thread Krieger, Donald N. 
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
>>>
>>>
>>>
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> 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/

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Re: [Freesurfer] comparing multiple runs on the same scan

2016-02-10 Thread Douglas N Greve 
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
>>>
>>>
>>>
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>
>

-- 
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/

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