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_v ol 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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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) -----------------------------------------------------------