[Freesurfer] long_mris_slopes bug

2014-05-16 Thread Katherine Reiter 
Hi Freesurfer experts,

I'm working on analyzing longitudinal data using the longitudinal 2-stage
model. When running the data through long_mris_slopes, I was getting the
following error message: ERROR 1 : mris_calc compute sym. pct. change (spc)
problem?

I saw in previous messages that this is the result of a bug. I found the
fix under the release notes, though after downloading it and placing the
fix in the bin and makign these files executable, I keep receiving the
following error messages. Does anyone have any insight into the problem and
possible solutions?

mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh
./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh

Traceback (most recent call last):
  File "/Applications/freesurfer//bin/long_mris_slopes", line 744, in

run_cmd(cmd,'mri_convert split frames 0 did not work?')
  File "/Applications/freesurfer//bin/long_mris_slopes", line 422, in
run_cmd
retcode = subprocess.call(args)
  File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 486, in call
return Popen(*popenargs, **kwargs).wait()
  File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 672, in __init__
errread, errwrite)
  File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 1202, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error

Thank you,

Katherine Reiter, M.S.

Clinical Psychology Doctoral Student

Marquette University
Phone: (414) 288-3807
Email: katherine.rei...@marquette.edu
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Re: [Freesurfer] long_mris_slopes bug

2014-05-19 Thread Martin Reuter 

Hi Katherine,

are you sure you downloaded the right executable for your operating 
system? It seems to be not able to run the command (exec format error). 
Did you replace mri_convert?

what happens if you run the command yourself:

mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh 
./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh


Best, Martin

On 05/16/2014 04:45 PM, Katherine Reiter wrote:

Hi Freesurfer experts,

I'm working on analyzing longitudinal data using the longitudinal 
2-stage model. When running the data through long_mris_slopes, I was 
getting the following error message: ERROR 1 : mris_calc compute sym. 
pct. change (spc) problem?


I saw in previous messages that this is the result of a bug. I found 
the fix under the release notes, though after downloading it and 
placing the fix in the bin and makign these files executable, I keep 
receiving the following error messages. Does anyone have any insight 
into the problem and possible solutions?


mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh 
./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh


Traceback (most recent call last):
  File "/Applications/freesurfer//bin/long_mris_slopes", line 744, in 


run_cmd(cmd,'mri_convert split frames 0 did not work?')
  File "/Applications/freesurfer//bin/long_mris_slopes", line 422, in 
run_cmd

retcode = subprocess.call(args)
  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", 
line 486, in call

return Popen(*popenargs, **kwargs).wait()
  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", 
line 672, in __init__

errread, errwrite)
  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", 
line 1202, in _execute_child

raise child_exception
OSError: [Errno 8] Exec format error

Thank you,

Katherine Reiter, M.S.

Clinical Psychology Doctoral Student

Marquette University

Phone: (414) 288-3807
Email: katherine.rei...@marquette.edu 






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--
Martin Reuter, Ph.D.

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] long_mris_slopes bug

2014-05-28 Thread Katherine Reiter 
Hi Martin,

Thanks for your  response. When I run the command alone, the following
message appears:

 mri_convert --frame 0 ./tmp-0001_base_lh_thickness_U5R6w6/glm/beta.mgh
./tmp-0001_base_lh_thickness_U5R6w6/beta0.mgh
bash: /Applications/freesurfer//bin/mri_convert: cannot execute binary file

I've made these files executable (chmod +x ) but that does not
appear to make a difference. I'm currently operating on a 64 bit Mac osX
10.7.5. I downloaded the bug fix from
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes. Is there another
version located elsewhere that has a solution that is more appropriate to
my operating system?

Thanks for your help,

Katherine Reiter, M.S.

Clinical Psychology Doctoral Student

Marquette University
Phone: (414) 288-3807
Email: katherine.rei...@marquette.edu




On Mon, May 19, 2014 at 3:33 PM, Martin Reuter
wrote:

>  Hi Katherine,
>
> are you sure you downloaded the right executable for your operating
> system? It seems to be not able to run the command (exec format error). Did
> you replace mri_convert?
> what happens if you run the command yourself:
>
>  mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh
> ./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh
>
> Best, Martin
>
> On 05/16/2014 04:45 PM, Katherine Reiter wrote:
>
> Hi Freesurfer experts,
>
>  I'm working on analyzing longitudinal data using the longitudinal
> 2-stage model. When running the data through long_mris_slopes, I was
> getting the following error message: ERROR 1 : mris_calc compute sym. pct.
> change (spc) problem?
>
>  I saw in previous messages that this is the result of a bug. I found the
> fix under the release notes, though after downloading it and placing the
> fix in the bin and makign these files executable, I keep receiving the
> following error messages. Does anyone have any insight into the problem and
> possible solutions?
>
>  mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh
> ./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh
>
>  Traceback (most recent call last):
>File "/Applications/freesurfer//bin/long_mris_slopes", line 744, in
> 
> run_cmd(cmd,'mri_convert split frames 0 did not work?')
>   File "/Applications/freesurfer//bin/long_mris_slopes", line 422, in
> run_cmd
> retcode = subprocess.call(args)
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 486, in call
> return Popen(*popenargs, **kwargs).wait()
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 672, in __init__
> errread, errwrite)
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 1202, in _execute_child
> raise child_exception
> OSError: [Errno 8] Exec format error
>
>  Thank you,
>
>  Katherine Reiter, M.S.
>
> Clinical Psychology Doctoral Student
>
> Marquette University
>  Phone: (414) 288-3807
> Email: katherine.rei...@marquette.edu
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Martin Reuter, Ph.D.
>
> Instructor in Neurology
>   Harvard Medical School
> Assistant in Neuroscience
>   Dept. of Radiology, Massachusetts General Hospital
>   Dept. of Neurology, Massachusetts General Hospital
> Research Affiliate
>   Computer Science and Artificial Intelligence Lab,
>   Dept. of Electrical Engineering and Computer Science,
>   Massachusetts Institute of Technology
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> Web  : http://reuter.mit.edu
>
>
> ___
> 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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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
di