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: [EMAIL PROTECTED]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
::::::::::::::
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' ...
);
< M A T L A B >
Copyright 1984-2002 The MathWorks, Inc.
Version 6.5.0.180913a Release 13
Jun 18 2002
Using Toolbox Path Cache. Type "help toolbox_path_cache" for more info.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> >> >> >> >> >> >> Parsing Arguments
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
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