All,
This is a repeat question for a problem I am still encountering (see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05104.html on the wiki). I am still having trouble getting the intergroupavg-sess to generate all the files that it should. Right now I can generate the 'h-offset' and 'register.dat' files and within each contrast I can get the script to create the 'minsig' and 'sig' files but I don't get a 'sig.bhdr' file so I am unable to check the results.
The command I am using is as follows...
intergroupavg-sess -analysis ${analysis} -contrast ${c} -group1 ${groupA} -group2 ${groupB} -intergroup ${groupA}_v_${groupB} -space tal
The output log file is included below.
Thanks for any help you can offer, Avram
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes@fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:::::::::::::: intergroupavg-sess.log :::::::::::::: intergroup-sess log file $Id: intergroupavg-sess,v 1.2 2005/08/30 17:05:21 greve Exp $ uid=506(aholmes) gid=500(lab) groups=500(lab),10(wheel),440(REWARD),435(REfMRI),310(ANTCON),325(CONCON),350(DEPFED),358(EMOGNG),380( FPPALL),445(REWPUN),472(ATTLRN),613(phonescreen),506(aholmes),440(REWARD),435(REfMRI),506(aholmes),325(CONCON),358(EMOGNG),310(ANTCO N),445(REWPUN),613(phonescreen),350(DEPFED),380(FPPALL) /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional /apps/freesurfer/freesurfer//fsfast/bin/intergroupavg-sess -analysis taumax30_stc_smooth6 -contrast all_v_fix -group1 LowTrauma -group2 HighTrauma -intergroup LowTrauma_v_HighTrauma -space ta l Linux daplab1.fas.harvard.edu 2.4.18-27.8.0smp #1 SMP Fri Mar 14 07:13:13 EST 2003 i686 athlon i386 GNU/Linux Tue Jun 5 11:11:57 EDT 2007 %%% --------------------------------- %% % temporary matlab script for intergroupavg-sess % /tmp/LowTrauma_v_HighTrauma3582_iga.m global QuitOnError; QuitOnError = 1; if(exist('fast_intergroupavg')==0) qoe('ERROR: matlab path incorrect');end; cd /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional; fast_intergroupavg(... '-avg1', 'LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg', ... '-std1', 'LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std', ... /exp/REfMRI/fMRI_FPPREW/functional/log> ls *inter* intergroupavg-sess.log intergroupavg-sess.log.old /exp/REfMRI/fMRI_FPPREW/functional/log> ll intergroupavg-sess.log -rw-rw-r-- 1 aholmes REfMRI 3372 Jun 5 10:59 intergroupavg-sess.log /exp/REfMRI/fMRI_FPPREW/functional/log> more intergroupavg-sess.log intergroup-sess log file $Id: intergroupavg-sess,v 1.2 2005/08/30 17:05:21 greve Exp $ uid=506(aholmes) gid=500(lab) groups=500(lab),10(wheel),440(REWARD),435(REfMRI),310(ANTCON),325(CONCON),350(DEPFED),358(EMOGNG),380( FPPALL),445(REWPUN),472(ATTLRN),613(phonescreen),506(aholmes),440(REWARD),435(REfMRI),506(aholmes),325(CONCON),358(EMOGNG),310(ANTCO N),445(REWPUN),613(phonescreen),350(DEPFED),380(FPPALL) /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional /apps/freesurfer/freesurfer//fsfast/bin/intergroupavg-sess -analysis taumax30_stc_smooth6 -contrast all_v_fix -group1 LowTrauma -group2 HighTrauma -intergroup LowTrauma_v_HighTrauma -space ta l Linux daplab1.fas.harvard.edu 2.4.18-27.8.0smp #1 SMP Fri Mar 14 07:13:13 EST 2003 i686 athlon i386 GNU/Linux Tue Jun 5 11:11:57 EDT 2007 %%% --------------------------------- %% % temporary matlab script for intergroupavg-sess % /tmp/LowTrauma_v_HighTrauma3582_iga.m global QuitOnError; QuitOnError = 1; if(exist('fast_intergroupavg')==0) qoe('ERROR: matlab path incorrect');end; cd /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional; fast_intergroupavg(... '-avg1', 'LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg', ... '-std1', 'LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std', ... '-avg2', 'HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg', ... '-std2', 'HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std', ... '-tsig', 'LowTrauma_v_HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/sig', ... '-tminsig', 'LowTrauma_v_HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/minsig', ... '-polarity', '0', ... '-polarity2', '0' ... );
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Checking Parameters SynthSeed = 0 _______________________________________________ Intergroup Averaging Parameters avg1id LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg std1id LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std dof1 4 avg2id HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg std2id HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std dof2 17 tid tsigid LowTrauma_v_HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/sig tminsigid LowTrauma_v_HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/minsig synth _______________________________________________ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 fast_intergroupavg Completed
Tue Jun 5 11:13:17 EDT 2007 intergroup-sess completed SUCCESSFULLY