I have two sets of identical blocks within each fMRI run, so conditions
{1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this
numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following
output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
...
ntptot = 687, nX = 136, DOF = 551
Saving X matrix to
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat
XCond = 2926.01 (normalized)
However, if I want to treat the two sets of blocks separately, i.e.,
{1,2,3,4,5,6,7,8,9,10}
so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then
fast_selxavg3.m gives:
ntptot = 687, nX = 146, DOF = 541
Saving X matrix to
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat
XCond = 4.33238e+08 (normalized)
ERROR: design is ill-conditioned
1) why does nX increase by 10 in the 2nd case?
2) why is fast_selxavg3.m unhappy and XCond so large? Can it not handle 10
separate blocks?
The entire log file in the 2nd case is attached.selxavg3-sess log file
/usr/local/freesurfer/dev/fsfast/bin/selxavg3-sess
-s subj008_10block -analysis improv.10blocks.sm05.lh
$Id: selxavg3-sess,v 1.60 2011/12/09 20:03:03 greve Exp $
uid=8240(preciado) gid=8240(preciado) groups=8240(preciado),160(fsdev),1071(birn),1107(fddev),1576(tbi)
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Wed Oct 23 11:37:06 EDT 2013
preproc-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -a improv.10blocks.sm05.lh -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.50 2013/01/22 22:08:44 greve Exp $
preciado
setenv FREESURFER_HOME /usr/local/freesurfer/dev
setenv SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
/usr/local/freesurfer/dev/fsfast/bin/preproc-sess
-s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -a improv.10blocks.sm05.lh -nolog
Wed Oct 23 11:37:06 EDT 2013
instem f
mc 1 f fmcpr
stc 1 fmcpr fmcpr.siemens
sm 0
mask 1 brain
subj008_10block Template -----------------------------
mktemplate-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -nolog -update
Session: /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block ----------------
Wed Oct 23 11:37:06 EDT 2013
Detected input format at nii
subj008_10block Update not needed
Run: 014 ----------------
Wed Oct 23 11:37:06 EDT 2013
subj008_10block 014 Update not needed
Run: 016 ----------------
Wed Oct 23 11:37:06 EDT 2013
subj008_10block 016 Update not needed
Run: 018 ----------------
Wed Oct 23 11:37:07 EDT 2013
subj008_10block 018 Update not needed
Wed Oct 23 11:37:07 EDT 2013
mktemplate-sess completed
subj008_10block Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -nolog -update
------------------------------------------------
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
Wed Oct 23 11:37:07 EDT 2013
subj008_10block Update not needed for session-level mask
subj008_10block Update not needed for run 014 mask
subj008_10block Update not needed for run 014 meanval
subj008_10block Update not needed for run 016 mask
subj008_10block Update not needed for run 016 meanval
subj008_10block Update not needed for run 018 mask
subj008_10block Update not needed for run 018 meanval
Wed Oct 23 11:37:07 EDT 2013
mkbrainmask-sess done
subj008_10block Registration -----------------------------
register-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -dof 6 -per-run -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Wed Oct 23 11:37:07 EDT 2013
setenv SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
cd /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
/usr/local/freesurfer/dev/fsfast/bin/register-sess -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -dof 6 -per-run -nolog -update
freesurfer-Linux-centos6_x86_64-dev-20131015
Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Session: /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block ----------------
Wed Oct 23 11:37:07 EDT 2013
Run: 014 ----------------
Wed Oct 23 11:37:07 EDT 2013
Update not needed
Run: 016 ----------------
Wed Oct 23 11:37:07 EDT 2013
Update not needed
Run: 018 ----------------
Wed Oct 23 11:37:07 EDT 2013
Update not needed
Wed Oct 23 11:37:07 EDT 2013
register-sess completed
subj008_10block MC -----------------------------
mc-sess -fstem f -fmcstem fmcpr -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -per-run -nolog -update
Logfile is /dev/null
-------------------------------------------
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
RunList: 014 016 018
subj008_10block 014 Update not needed
subj008_10block 016 Update not needed
subj008_10block 018 Update not needed
Wed Oct 23 11:37:08 EDT 2013
mc-sess completed SUCCESSFULLY
subj008_10block STC -----------------------------
stc-sess -i fmcpr -o fmcpr.siemens -so siemens -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -nolog -update
Wed Oct 23 11:37:08 EDT 2013
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
/usr/local/freesurfer/dev/fsfast/bin/stc-sess
-i fmcpr -o fmcpr.siemens -so siemens -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -nolog -update
$Id: stc-sess,v 1.10 2011/02/24 20:19:03 greve Exp $
quito
subj008_10block -----------------
Wed Oct 23 11:37:08 EDT 2013
-rw-rw-r-- 1 preciado birn 378504676 Oct 21 12:18 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/014/fmcpr.siemens.nii.gz
-rw-rw-r-- 1 preciado birn 375600041 Oct 21 12:06 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/014/fmcpr.nii.gz
Update not needed
-rw-rw-r-- 1 preciado birn 378296149 Oct 21 12:21 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/016/fmcpr.siemens.nii.gz
-rw-rw-r-- 1 preciado birn 375392852 Oct 21 12:11 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/016/fmcpr.nii.gz
Update not needed
-rw-rw-r-- 1 preciado birn 378453391 Oct 21 12:25 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/018/fmcpr.siemens.nii.gz
-rw-rw-r-- 1 preciado birn 375495436 Oct 21 12:15 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/018/fmcpr.nii.gz
Update not needed
Started at Wed Oct 23 11:37:08 EDT 2013
Ended at Wed Oct 23 11:37:08 EDT 2013
stc-sess Done
subj008_10block To Surface -----------------------------
rawfunc2surf-sess -fwhm 5 -s subj008_10block -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -hemi lh -trgsubject fsaverage -stc siemens -nolog -update -per-run
instem fmcpr.siemens
outstem fmcpr.siemens.sm5.fsaverage.hemi
------------------------------
1/1 subj008_10block
1/1 subj008_10block 014 lh ---------
Wed Oct 23 11:37:08 EDT 2013
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/014/masks/brain.fsaverage.lh.nii.gz does not need updating
subj008_10block 014 Update not needed
1/1 subj008_10block 016 lh ---------
Wed Oct 23 11:37:08 EDT 2013
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/016/masks/brain.fsaverage.lh.nii.gz does not need updating
subj008_10block 016 Update not needed
1/1 subj008_10block 018 lh ---------
Wed Oct 23 11:37:08 EDT 2013
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/018/masks/brain.fsaverage.lh.nii.gz does not need updating
subj008_10block 018 Update not needed
Wed Oct 23 11:37:08 EDT 2013
rawfunc2surf-sess completed
----------------------------------------
Started at Wed Oct 23 11:37:06 EDT 2013
Ended at Wed Oct 23 11:37:08 EDT 2013
preproc-sess done
-------------------------------------------
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
Wed Oct 23 11:37:08 EDT 2013
anadir = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh
------------------------------------------
% Wed Oct 23 11:37:08 EDT 2013
% /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
% improv.10blocks.sm05.lh
%--------------------------------
sxa3pwd = '/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast'
sxa3cmd = '/usr/local/freesurfer/dev/fsfast/bin/selxavg3-sess -s subj008_10block -analysis improv.10blocks.sm05.lh'
which fast_selxavg3
okfile = '/tmp/selxavg3-sess-9851.ok';
if(fast_fileexists(okfile)) delete(okfile); end
monly = 0;
perrun = 0;
jkrun = 0;
DoGLMFit = 1;
DoContrasts = 1;
ConList = splitstring('arrange1-embellish1 arrange1-improv1.1 embellish1-improv1.1 arrange1-improv1.2 embellish1-improv1.2 arrange1-improv1.3 embellish1-improv1.3 improv1.1-improv1.2 improv1.1-improv1.3 improv1.2-improv1.3 arrange2-embellish2 arrange2-improv2.1 embellish2-improv2.1 arrange2-improv2.2 embellish2-improv2.2 arrange2-improv2.3 embellish2-improv2.3 improv2.1-improv2.2 improv2.1-improv2.3 improv2.2-improv2.3 arrange-improv1 embellish-improv1 arrange-improv2 embellish-improv2 arrange-improv3 embellish-improv3 improv1-improv2 improv1-improv3 improv2-improv3 arrange-embellish');
DoSynth = 0;
SynthNoiseAmp = 1;
SynthNoiseAR1 = .3;
SynthSignalAmp = 0;
SynthSeed = -1;
sess = '/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block';
analysis = 'improv.10blocks.sm05.lh';
flacname = '';
outtop = '';
DoFWHM = 0;
MatlabSaveRes = 0;
SaveResUnwhitened = 0;
fast_selxavg3;
if(~fast_fileexists(okfile) && ~monly); quit; end
quit;
------------------------------------------
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R) >
Copyright 1984-2012 The MathWorks, Inc.
R2012a (7.14.0.739) 64-bit (glnxa64)
February 9, 2012
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> >> >> >> >> >> >>
sxa3pwd =
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
>>
sxa3cmd =
/usr/local/freesurfer/dev/fsfast/bin/selxavg3-sess -s subj008_10block -analysis improv.10blocks.sm05.lh
>> /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
#@# subj008_10block ###############################
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block
-------------------------
$Id: fast_selxavg3.m,v 1.108 2013/10/03 19:23:56 greve Exp $
/usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/dev/fsfast/toolbox/fast_ldanaflac.m
/usr/local/freesurfer/dev/matlab/MRIread.m
-------------------------
outtop = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
Extension format = nii.gz
1 arrange-embellish.mat
2 arrange-improv1.mat
3 arrange-improv2.mat
4 arrange-improv3.mat
5 arrange1-embellish1.mat
6 arrange1-improv1.1.mat
7 arrange1-improv1.2.mat
8 arrange1-improv1.3.mat
9 arrange2-embellish2.mat
10 arrange2-improv2.1.mat
11 arrange2-improv2.2.mat
12 arrange2-improv2.3.mat
13 embellish-improv1.mat
14 embellish-improv2.mat
15 embellish-improv3.mat
16 embellish1-improv1.1.mat
17 embellish1-improv1.2.mat
18 embellish1-improv1.3.mat
19 embellish2-improv2.1.mat
20 embellish2-improv2.2.mat
21 embellish2-improv2.3.mat
22 improv1-improv2.mat
23 improv1-improv3.mat
24 improv1.1-improv1.2.mat
25 improv1.1-improv1.3.mat
26 improv1.2-improv1.3.mat
27 improv2-improv3.mat
28 improv2.1-improv2.2.mat
29 improv2.1-improv2.3.mat
30 improv2.2-improv2.3.mat
Excluding 37 points
nruns = 3
autostimdur =
outanadir = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh
Excluding 37 points
Excluding 40 points
Excluding 37 points
Found 149919/163842 (91.5) voxels in mask
Creating Design Matrix
... creation time = 0.011 sec
DoMCFit = 1
ntptot = 687, nX = 146, DOF = 541
Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat
XCond = 4.33238e+08 (normalized)
ERROR: design is ill-conditioned
>> ------------------------------------------_______________________________________________
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