[Freesurfer] mni/bin/nu_correct: Exec format error. Binary file not executable.

[Bill Taylor]

I have cruised the mailing list for 5.3 specific causes. Some runs work and 
some hit this error.recon-all -autorecon1 -skullstrip -gcut -subjid  1217_1

We are crunching a set of over 300 and I have checked the obvious. This is what 
I downloaded:  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

We are running scientific linux 6.3 in our cluster and the one machine I 
checked did indeed have perl in /usr/bin and we are all x86_64.

I recently upgraded our pipeline from 5.1 to 5.3 but this is the first time 
running with these exact options.

I am not the one doing the research, I only automated it to run in our HTCondor 
cluster.

If it helps stdout for that one job is:

Linux glow-c112.cs.wisc.edu 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 
14:18:09 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux
#
#@# MotionCor Fri Jun 13 19:00:45 CDT 2014
Found 1 runs
/var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

  cp /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig/001.mgz 
/var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz

/var/lib/condor/execute/slot1/dir_4596/1217_1

  mri_convert /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz 
/var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz --conform

mri_convert /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz 
/var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz...

  mri_add_xform_to_header -c 
/var/lib/condor/execute/slot1/dir_4596/1217_1/mri/transforms/talairach.xfm 
/var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz 
/var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz

INFO: extension is mgz
#
#@# Talairach Fri Jun 13 19:01:08 CDT 2014
/var/lib/condor/execute/slot1/dir_4596/1217_1/mri

  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

Linux glow-c112.cs.wisc.edu 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 
14:18:09 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 1217_1 exited with ERRORS at Fri Jun 13 19:01:11 CDT 2014

For more details, see the log file 
/var/lib/condor/execute/slot1/dir_4596/1217_1/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Command requested is  
finished with result<256>
Non-zero recon-all -autorecon1 -skullstrip -gcut -subjid  1217_1
Changing to 1217_1 to read  scripts/recon-all.log
...
Finished WITH freesurfer errors<<<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>>
Tar up subject directory before leaving
1217_1/
1217_1/mri/
1217_1/mri/orig/
1217_1/mri/orig/001.mgz
1217_1/mri/transforms/
1217_1/mri/transforms/bak/
1217_1/mri/rawavg.mgz
1217_1/mri/orig.mgz
1217_1/mri/orig_nu.log
1217_1/mri/mri_nu_correct.mni.log
1217_1/mri/tmp.mri_nu_correct.mni.5252/
1217_1/mri/tmp.mri_nu_correct.mni.5252/nu0.mnc
1217_1/scripts/
1217_1/scripts/build-stamp.txt
1217_1/scripts/recon-all.env
1217_1/scripts/recon-all.log
1217_1/scripts/csurfdir
1217_1/scripts/recon-all-status.log
1217_1/scripts/recon-all.local-copy
1217_1/scripts/recon-all.cmd
1217_1/scripts/recon-all.error
1217_1/surf/
1217_1/tmp/
1217_1/label/
1217_1/touch/
1217_1/touch/conform.touch
1217_1/stats/
1217_1/src/
1217_1/trash/
1217_1/bem/
total 152

-- 
Bill Taylor 608-263-2656 (608-219-4430)
Center for High Throughput Computing(CHTC)
HTCondor project
Computer Sciences
University of Wisconsin, Madison

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Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Bill Taylor]

I'll start the process thursday.
On 11/11/2014 12:04 PM, Douglas N Greve wrote:
> It will be the same as the DOF of the individual contrasts (don't sum them).
>
> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
>> ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar
>>
>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve > >:
>>
>>
>>  Actually, you can still do each contrast individually. Each will
>>  produce
>>  ces and cesvar files. Take the difference between the ces files
>>  and the
>>  average of the cesvar files, then feed the result into mri_glmfit FFX
>>
>>  doug
>>
>>
>>  On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote:
>>  > Hi Doug,
>>  > I wanted to follow up on this. Would you be able to provide a
>>  > workaround for contrasting multiple taskregs against each other? Is
>>  > there something I can try in the meantime? Thanks, Caspar
>>  >
>>  >
>>  > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik
>>  > mailto:cschwie...@rockefeller.edu>
>>  >  >>:
>>  >
>>  > Hi Doug,
>>  > thanks for your reply. I would like to feed the differences
>>  into a
>>  > FFX group analysis, so I think I will need to resort to your
>>  > workaround. It would be great if you could provide that. Thanks!
>>  > Caspar
>>  >
>>  > 2014-11-10 13:45 GMT-05:00 Douglas N Greve
>>  > >  
>>  >  >>:
>>  >
>>  >
>>  > To get sig maps for  an individual, this is problematic
>>  but I
>>  > could
>>  > probably come up with a work-around. For a group
>>  analysis, you can
>>  > simply compute each taskreg separately, then subtract
>>  the two
>>  > prior to
>>  > running mri_glmfit.
>>  > doug
>>  >
>>  > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
>>  > > Hi!
>>  > > A quick follow-up:
>>  > > I have a taskreg file with 6 continuous predictors. I
>>  would
>>  > like to
>>  > > run specific contrasts, e.g., predictor 1 vs.
>>  mean(predictor
>>  > 2:6).
>>  > > From what I gather, selxavg3-sess will run automatic
>>  > contrasts on
>>  > > taskregs, but the automatic contrasts are against
>>  baseline.
>>  > This is
>>  > > not what I need at this point.
>>  > > mk-contrast-sess does not like what I am putting in
>>  because
>>  > I do not
>>  > > have a paradigm file in which condition numbers are
>>  specified.
>>  > > Is there a way to compute specific contrasts between
>>  multiple
>>  > > taskregs, and if not, is there a workaround?
>>  > > Thank you very much, Caspar
>>  > >
>>  > >
>>  > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik
>>  > > >  
>>  > >  >
>>  > >  
>>  > > >  > >
>>  > > Hi!
>>  > > I have several external regressors in my analysis
>>  that I
>>  > configure
>>  > > with -taskreg in mkanalysis-sess (something like
>>  -notask
>>  > -taskreg
>>  > > nameoffile 6).
>>  > > I was wondering how to set up mkcontrast-sess to
>>  > contrast these
>>  > > regerssors given that I do not have a paradigm
>>  file for
>>  > them.
>>  > > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?
>>  > >
>>  > > Thanks, Caspar
>>  > >
>>  > >
>>  > >
>>  > >
>>  > > ___
>>  > > 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 
>>  

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Bill Taylor]

Sorry, Though we do have freesurfer pipelines we run in Madison, I 
responded to wrong email.

Bill Taylor
Center for High Throughput Computing
Computer Sciences
University of Wisconsin, Madison

On 11/11/2014 12:09 PM, Bill Taylor wrote:
> I'll start the process thursday.
> On 11/11/2014 12:04 PM, Douglas N Greve wrote:
>> It will be the same as the DOF of the individual contrasts (don't sum them).
>>
>> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
>>> ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar
>>>
>>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve >> <mailto:gr...@nmr.mgh.harvard.edu>>:
>>>
>>>
>>>   Actually, you can still do each contrast individually. Each will
>>>   produce
>>>   ces and cesvar files. Take the difference between the ces files
>>>   and the
>>>   average of the cesvar files, then feed the result into mri_glmfit FFX
>>>
>>>   doug
>>>
>>>
>>>   On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote:
>>>   > Hi Doug,
>>>   > I wanted to follow up on this. Would you be able to provide a
>>>   > workaround for contrasting multiple taskregs against each other? Is
>>>   > there something I can try in the meantime? Thanks, Caspar
>>>   >
>>>   >
>>>   > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik
>>>   > mailto:cschwie...@rockefeller.edu>
>>>   <mailto:cschwie...@rockefeller.edu
>>>   <mailto:cschwie...@rockefeller.edu>>>:
>>>   >
>>>   > Hi Doug,
>>>   > thanks for your reply. I would like to feed the differences
>>>   into a
>>>   > FFX group analysis, so I think I will need to resort to your
>>>   > workaround. It would be great if you could provide that. Thanks!
>>>   > Caspar
>>>   >
>>>   > 2014-11-10 13:45 GMT-05:00 Douglas N Greve
>>>   > >>   <mailto:gr...@nmr.mgh.harvard.edu>
>>>   <mailto:gr...@nmr.mgh.harvard.edu
>>>   <mailto:gr...@nmr.mgh.harvard.edu>>>:
>>>   >
>>>   >
>>>   > To get sig maps for  an individual, this is problematic
>>>   but I
>>>   > could
>>>   > probably come up with a work-around. For a group
>>>   analysis, you can
>>>   > simply compute each taskreg separately, then subtract
>>>   the two
>>>   > prior to
>>>   > running mri_glmfit.
>>>   > doug
>>>   >
>>>   > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
>>>   > > Hi!
>>>   > > A quick follow-up:
>>>   > > I have a taskreg file with 6 continuous predictors. I
>>>   would
>>>   > like to
>>>   > > run specific contrasts, e.g., predictor 1 vs.
>>>   mean(predictor
>>>   > 2:6).
>>>   > > From what I gather, selxavg3-sess will run automatic
>>>   > contrasts on
>>>   > > taskregs, but the automatic contrasts are against
>>>   baseline.
>>>   > This is
>>>   > > not what I need at this point.
>>>   > > mk-contrast-sess does not like what I am putting in
>>>   because
>>>   > I do not
>>>   > > have a paradigm file in which condition numbers are
>>>   specified.
>>>   > > Is there a way to compute specific contrasts between
>>>   multiple
>>>   > > taskregs, and if not, is there a workaround?
>>>   > > Thank you very much, Caspar
>>>   > >
>>>   > >
>>>   > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik
>>>   > > >>   <mailto:cschwie...@rockefeller.edu>
>>>   > <mailto:cschwie...@rockefeller.edu
>>>   <mailto:cschwie...@rockefeller.edu>>
>>>   > <mailto:cschwie...@rockefeller.edu
>>>   <mailto:cschwie...@rockefeller.edu>

[Freesurfer] Code changes to use Compiled Matlab?

[Bill Taylor]

Mathworks loves their parallel toolbox. We love using Condor.

I won't go into the reasons.

http://www.cs.wisc.edu/condor/

We have negotiated an unlimited license of for Matlab and I have freesurfer
recon-all broken into the three phases. This gives us currently 1700 
dedicated cores
where we can process brain scans for groups on the Madison, WI campus.
We are contractually prevented from running anything but compiled Matlab
on any cluster on the UW-Madison campus.

I have had to modify "mris_computer_lgi" to call compiled matlab entry 
points
after setting up a Matlab runtime within the Freesurfer 5.1.0 staged 
executable.

What I ran into was a type mismatch from the way I now call the matlab
functionality.

Is there a known solution for this or do I have to change the matlab 
entry points
to do initial type changing?

We are working on a work flow to not only process the brains but also do
FSL and matlab post processing at the same time and/or take preprocessed
subjects  and do either FSL or Matlab processing.

I automate researchers on campus and don't actually program Matlab
though I can work my way through this. As a computer Scientist I don't
really want to be changing the code base in an unmanaged way.

*Change 
in call
#
# make_outer_surface.m
#
# create the outer surface from the filled volume
set MLF = /tmp/mos"_$$_".m
set arg1 = ${tmpdir}/${input}.filled.mgz
set arg2 = ${closespheresize}
set arg3 =  ${tmpdir}/${input}-outer
rm -f ${arg3}
# bt commented out for converting to compiled
echo "Calling compiled matlab make_outer_surface"
echo "make_outer_surface('${arg1}',${arg2},'${arg3}')"
make_outer_surface ${arg1} ${arg2} ${arg3}
#echo "make_outer_surface('${arg1}',${arg2},'${arg3}'); exit" > $MLF
#echo "="
#echo "`cat $MLF`"
#echo "="
#if ($RunIt) then
   #cat $MLF | ${MATLAB} -display iconic -nojvm -nosplash
#endif


* 
ERROR BELOW

Calling compiled matlab make_outer_surface
reading filled volume...
closing volume...
??? Error using ==> iptcheckinput
Function STREL expected its second input, R,
to be one of these types:

   double

Instead its type was char.

Error in ==> strel>ParseInputs at 1308



Error in ==> strel>strel.strel at 143



Error in ==> make_outer_surface at 41



^G
Images:strel:invalidType




*

-- 
Bill Taylor 608-263-2656 (cell 608-219-4430)
Center for High Throughput Computing(CHTC)
Condor project
Computer Sciences
University of Wisconsin, Madison

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[Freesurfer] -localGI using compiled matlab - solved

[Bill Taylor]

We here at the University of Wisconsin, Madison
are constrained to run only compiled Matlab
on our clusters. We have a number of groups
that use freesurfer on I have just completed
creating some workflows to do longitudinal,
-localGI and a basic processing using autorecon1,2
and three.

These run in our center on execute nodes
not requiring a license since they use
the compiled version and a runtime.

For the -localGI:

Besides the basics of running a compiled
matlab in terms of setting up the environment
right, I had to change

mris_compute_lgi

and some input mappings in some of the freesurfer
matlab toolbox. My changes had all the args coming
into matlab as strings and I had to find the trouble
ones(10 or so) and convert them to the proper
expected type .

This allows thousands of jobs to be analyzed
at once on our cluster.

Anyone willing to take charge of these changes back
at Harvard. It would be great to have this variation
available to others.

-- 
Bill Taylor 608-263-2656 (cell 608-219-4430)
Center for High Throughput Computing(CHTC)
Condor project
Computer Sciences
University of Wisconsin, Madison

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[Freesurfer] Tracula time estimates

[Bill Taylor]

I looked at the wiki and the FAQ but still need an answer.

In my work to get more of Freesurfer available to researchers
using our cluster, I am concerned about the 48+ hours for a run
on one subject. Our 1700 slots which can run these jobs
only promise a 24 hour time slice before evictions. Is it likely
that all three steps will fit within a 24 hour time frame.

What are the outside limits for:
Pre-processing
FSL's bedpostX
Reconstructing white-matter (WM) pathways

If they run over, is it possible to due the
part which runs over in pieces?

Thanks in advance! There are currently  3 groups
on campus interested in our automation involving
thousands of scans.

-- 
Bill Taylor 608-263-2656 (cell 608-219-4430)
Center for High Throughput Computing(CHTC)
Condor project
Computer Sciences
University of Wisconsin, Madison

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[Freesurfer] Having Matlab portion run as compiled matlab

[Bill Taylor]

So I peaked in archive and did not get a hit.

The situation is that the University of Wisconsin
Madison site license prohibits us running Matlab
in a cluster unless it is compiled.

I am assisting a Neurology lab with having a Condor
workflow which this time round will do both Matlab
and FSL post processing.

To compile the Matlab one needs to compile the
entry points. But to run it, we'd have to change how it is called.

Anyone have pointers for me?

Bill Taylor
Center for High Throughput Computing
Condor Project
Computer Sciences
University of Wisconsin, Madison
608-219-4430

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Re: [Freesurfer] Having Matlab portion run as compiled matlab

[Bill Taylor]

This is the proposed workflow and some latter parts
are done with Matlab.

I assist is masses of Matlab jobs using compiled Matlab
and run thousands of jobs both in on center, on our campus
and out in to other resources in the GRID.

My problem is not how to run a compiled Matlab job, but
how to interface the Matlab portion perhaps invisibly
and perhaps not to running with compiled matlab code.

I know and will never be a freesurfer person. I am only
trying to automate more of it. Is there perhaps a single
script which matches up to calls to Matlab entry points?

processed in parallel for two subjects three time points example;
recon-all -autorecon1 -subjid 1001a
recon-all -autorecon1 -subjid 1001b
recon-all -autorecon1 -subjid 1001c
recon-all -autorecon1 -subjid 1002a
recon-all -autorecon1 -subjid 1002b
recon-all -autorecon1 -subjid 1002c

.
.
.
After completion of -autorecon1

recon-all -autorecon2 -subjid 1001a
recon-all -autorecon2 -subjid 1001b
recon-all -autorecon2 -subjid 1001c
recon-all -autorecon2 -subjid 1002a
recon-all -autorecon2 -subjid 1002b
recon-all -autorecon2 -subjid 1002c
.
.
.
After completion of -autorecon2

recon-all -autorecon3 -subjid 1001a
recon-all -autorecon3 -subjid 1001b
recon-all -autorecon3 -subjid 1001c
recon-all -autorecon3 -subjid 1002a
recon-all -autorecon3 -subjid 1002b
recon-all -autorecon3 -subjid 1002c
.
.


After completion of -autorecon3
 OPTIONAL COMPUTATION OF LGI WHICH REQUIRES MATLAB ~3 hours
 recon-all -s 1001a -localGI
 recon-all -s 1001b -localGI
 recon-all -s 1001c -localGI
 recon-all -s 1002a -localGI
 recon-all -s 1002b -localGI
 recon-all -s 1002c -localGI
recon-all -base 1001base3 -tp 1001a -tp 1001b -tp 1001c -all
recon-all -base 1002base3 -tp 1002a -tp 1002b -tp 1002c -all
.
.
.
After completion of -base runs
recon-all -long 1001a 1001base3 -all
recon-all -long 1001b 1001base3 -all
recon-all -long 1001c 1001base3 -all
recon-all -long 1002a 1002base3 -all
recon-all -long 1002b 1002base3 -all
recon-all -long 1001c 1002base3 -all


On 7/19/2011 2:03 PM, Bruce Fischl wrote:
> Hi Bill,
> what portions are you talking about? recon-all shouldn't use any matlab.
>
> cheers
> Bruce
> On
> Tue, 19 Jul 2011, Bill Taylor wrote:
>
>> So I peaked in archive and did not get a hit.
>>
>> The situation is that the University of Wisconsin
>> Madison site license prohibits us running Matlab
>> in a cluster unless it is compiled.
>>
>> I am assisting a Neurology lab with having a Condor
>> workflow which this time round will do both Matlab
>> and FSL post processing.
>>
>> To compile the Matlab one needs to compile the
>> entry points. But to run it, we'd have to change how it is called.
>>
>> Anyone have pointers for me?
>>
>> Bill Taylor
>> Center for High Throughput Computing
>> Condor Project
>> Computer Sciences
>> University of Wisconsin, Madison
>> 608-219-4430
>>
>> ___
>> 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
>
>
> 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.
>

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