Hi Doug

I tried to make that file executable (as root I typed chmod a+x make_average_volume) but it did not work. The file I found under the URL you send me is a text file and it is not compiled. Please can you give me any hint to make the new version of make_average_volume executable.
Is there a compiled version that is already executable?

Thanks a lot in advance
Best regards
Juergen


On 4.1.2008 23:06 Uhr, "Doug Greve" <greve@nmr.mgh.harvard.edu> wrote:

You may have to make it executable

Juergen Haenggi wrote:

Hi Doug

Thanks for the new version, but the following error occurred:

Cleaning up
-----------------------
rm -r ./tmp.mris_preproc.9682
Fri Jan  4 21:36:04 CET 2008
mris_preproc done
---------------------------------------------------



Fri Jan  4 21:36:04 CET 2008
make_average_surface done

make_average_volume --subjects SNPs_Vp01 SNPs_Vp02 SNPs_Vp03 SNPs_Vp04
SNPs_Vp05 SNPs_Vp06 SNPs_Vp07 SNPs_Vp08 SNPs_Vp09 SNPs_Vp10 SNPs_Vp11
SNPs_Vp12 SNPs_Vp13 SNPs_Vp14 SNPs_Vp15 SNPs_Vp16 SNPs_Vp17 SNPs_Vp18
SNPs_Vp19 SNPs_Vp20 SNPs_Vp21 SNPs_Vp22 SNPs_Vp23 SNPs_Vp24 SNPs_Vp25
SNPs_Vp26 SNPs_Vp27 SNPs_Vp28 SNPs_Vp29 SNPs_Vp30 SNPs_Vp31 SNPs_Vp32
SNPs_Vp33 SNPs_Vp34 SNPs_Vp35 SNPs_Vp36 SNPs_Vp37 SNPs_Vp38 SNPs_Vp39
SNPs_Vp40 SNPs_Vp41 SNPs_Vp42 SNPs_Vp43 SNPs_Vp44 SNPs_Vp45 SNPs_Vp46
SNPs_Vp47 SNPs_Vp48 SNPs_Vp49 SNPs_Vp50 SNPs_Vp51 SNPs_Vp52 SNPs_Vp53
SNPs_Vp54 SNPs_Vp55 SNPs_Vp56 SNPs_Vp57 SNPs_Vp58 SNPs_Vp59 SNPs_Vp60
SNPs_Vp61 SNPs_Vp62 SNPs_Vp63 SNPs_Vp64 SNPs_Vp65 SNPs_Vp66 SNPs_Vp67
SNPs_Vp68 SNPs_Vp69 SNPs_Vp70 SNPs_Vp71 SNPs_Vp72 SNPs_Vp73 SNPs_Vp74
SNPs_Vp75 SNPs_Vp76 SNPs_Vp77 SNPs_Vp78 SNPs_Vp79 SNPs_Vp80 SNPs_Vp81
SNPs_Vp82 SNPs_Vp83 SNPs_Vp84 SNPs_Vp85 SNPs_Vp86 SNPs_Vp87 SNPs_Vp88
SNPs_Vp89 SNPs_Vp90 SNPs_Vp91 SNPs_Vp92
'csh: Unknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
[Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects]
juergenh%


Best regards
Juergen


On 3.1.2008 21:03 Uhr, "Doug Greve" <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu>  wrote:

  
 

This is a problem when it attempts to create an "average" aseg. As a
stop-gap measure, I've created a new version that will not stop the
execution if this stage fails. You can get it from here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_vol
ume

doug

Juergen Haenggi, Psychological Institute wrote:

    
 

Dear FS experts

I tried to average the brains of 92 subjects. We used a MacPro Quad
with 5 GB RAM and about 10 GB virtual memory. When running
make_average_subject the following error occurred:

Checking 91
/Applications/freesurfer/subjects/average/tmp/make_average_vol-tmp/seg-SNPs_V
p92.mgh

nframestot = 92
Allocing output
mri_concat(13587) malloc: *** vm_allocate(size=262144) failed (error
code=3)
mri_concat(13587) malloc: *** error: can't allocate region
mri_concat(13587) malloc: *** set a breakpoint in szone_error to debug
MRIalloc(256, 256, 256): could not allocate 262144 bytes for 14117th
slice

Cannot allocate memory
[Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects]
juergenh%

Does it really mean there is too less memory or is it a similar
problem occurred in other software, i.e. memory acquisition
restriction by the Java Runtime Environment?
Is there any possibility, beside buying more RAM, to run
make_average_subject with the available 5 GB RAM?

Thanks in advance and Happy New Year
Best regards
Juergen


-------------------------------------------------
Juergen Haenggi
Ph.D. (Dr. des.)
Division of Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
-------------------------------------------------
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-----------------------------------------------------------
Juergen Haenggi
Ph.D. (Dr. des.)
Division of Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
-----------------------------------------------------------



  

-----------------------------------------------------------
Juergen Haenggi
Ph.D. (Dr. des.)
Division of Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)       
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)                     
j.haenggi@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)   
-----------------------------------------------------------

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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