Hello Freesurfers,
I think my last email failed to send so here it is again -
I'm running into problems using fs-fast for a polar only, retinotopic analysis.
The error message I get is:
*********************
Retinotopy dcole$ selxavg3-sess -analysis rtopy.self.lh -sf sessid
Surface data self lh
--------------------------------------------------------------
selxavg3-sess logfile is /rcbiUsers/dcole/Retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120209144554.log
--------------------------------------------------------------
preproc-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $
dcole
setenv FREESURFER_HOME /Volumes/RCBI/freesurfer
setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test
Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64
/rcbiUsers/dcole/Retinotopy
/Volumes/RCBI/freesurfer/fsfast/bin/preproc-sess
-s SUB01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh -nolog
Thu Feb 9 14:45:54 EST 2012
instem f
mc 1 f fmcpr
stc 0 fmcpr
sm 0
mask 1 brain
SUB01 Template -----------------------------
mktemplate-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -nolog -update
Session: /rcbiUsers/dcole/Retinotopy/SUB01 ----------------
Thu Feb 9 14:45:54 EST 2012
Detected input format at nii
SUB01 Update not needed
Run: 001 ----------------
Thu Feb 9 14:45:54 EST 2012
SUB01 001 Update not needed
Run: 002 ----------------
Thu Feb 9 14:45:54 EST 2012
SUB01 002 Update not needed
Run: 003 ----------------
Thu Feb 9 14:45:55 EST 2012
SUB01 003 Update not needed
Run: 004 ----------------
Thu Feb 9 14:45:55 EST 2012
SUB01 004 Update not needed
Run: 005 ----------------
Thu Feb 9 14:45:55 EST 2012
SUB01 005 Update not needed
Thu Feb 9 14:45:55 EST 2012
mktemplate-sess completed
SUB01 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s SUB01 -d /rcbiUsers/dcole/Retinotopy -nolog -update
------------------------------------------------
/rcbiUsers/dcole/Retinotopy/SUB01
Thu Feb 9 14:45:55 EST 2012
SUB01 Update not needed for session-level mask
SUB01 Update not needed for run 001 mask
SUB01 Update not needed for run 001 meanval
SUB01 Update not needed for run 002 mask
SUB01 Update not needed for run 002 meanval
SUB01 Update not needed for run 003 mask
SUB01 Update not needed for run 003 meanval
SUB01 Update not needed for run 004 mask
SUB01 Update not needed for run 004 meanval
SUB01 Update not needed for run 005 mask
SUB01 Update not needed for run 005 meanval
Thu Feb 9 14:45:55 EST 2012
mkbrainmask-sess done
SUB01 Registration -----------------------------
register-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 -per-run -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Thu Feb 9 14:45:55 EST 2012
setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test
cd /rcbiUsers/dcole/Retinotopy
/Volumes/RCBI/freesurfer/fsfast/bin/register-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 -per-run -nolog -update
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64
Session: /rcbiUsers/dcole/Retinotopy/SUB01 ----------------
Thu Feb 9 14:45:55 EST 2012
Run: 001 ----------------
Thu Feb 9 14:45:55 EST 2012
Update not needed
Run: 002 ----------------
Thu Feb 9 14:45:55 EST 2012
Update not needed
Run: 003 ----------------
Thu Feb 9 14:45:55 EST 2012
Update not needed
Run: 004 ----------------
Thu Feb 9 14:45:55 EST 2012
Update not needed
Run: 005 ----------------
Thu Feb 9 14:45:55 EST 2012
Update not needed
Thu Feb 9 14:45:55 EST 2012
register-sess completed
SUB01 MC -----------------------------
mc-sess -fstem f -fmcstem fmcpr -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -per-run -nolog -update
Logfile is /dev/null
-------------------------------------------
/rcbiUsers/dcole/Retinotopy/SUB01
RunList: 001 002 003 004 005
SUB01 001 Update not needed
SUB01 002 Update not needed
SUB01 003 Update not needed
SUB01 004 Update not needed
SUB01 005 Update not needed
Thu Feb 9 14:45:55 EST 2012
mc-sess completed SUCCESSFULLY
SUB01 To Surface -----------------------------
rawfunc2surf-sess -fwhm 5 -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -hemi lh -self -nolog -update
instem fmcpr
outstem fmcpr.sm5.self.hemi
------------------------------
1/1 SUB01
1/1 SUB01 001 lh ---------
Thu Feb 9 14:45:55 EST 2012
SUB01 001 Update not needed
1/1 SUB01 002 lh ---------
Thu Feb 9 14:45:55 EST 2012
SUB01 002 Update not needed
1/1 SUB01 003 lh ---------
Thu Feb 9 14:45:56 EST 2012
SUB01 003 Update not needed
1/1 SUB01 004 lh ---------
Thu Feb 9 14:45:56 EST 2012
SUB01 004 Update not needed
1/1 SUB01 005 lh ---------
Thu Feb 9 14:45:56 EST 2012
SUB01 005 Update not needed
Thu Feb 9 14:45:56 EST 2012
rawfunc2surf-sess completed
----------------------------------------
Started at Thu Feb 9 14:45:54 EST 2012
Ended at Thu Feb 9 14:45:56 EST 2012
preproc-sess done
-------------------------------------------
/rcbiUsers/dcole/Retinotopy/SUB01
Thu Feb 9 14:45:56 EST 2012
anadir = /rcbiUsers/dcole/Retinotopy/SUB01/bold/rtopy.self.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
2012-02-09 14:45:56.773 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.775 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.776 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.777 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.778 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.779 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.780 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.781 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.783 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.796 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.797 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.798 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.812 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.813 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:56.815 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
< M A T L A B (R) >
Copyright 1984-2010 The MathWorks, Inc.
Version 7.10.0.499 (R2010a) 64-bit (maci64)
February 5, 2010
2012-02-09 14:45:57.634 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.636 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.636 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.637 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.638 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.639 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.639 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.640 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.641 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.642 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.643 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.643 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.644 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.645 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.646 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.646 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.647 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.648 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.649 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.649 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.650 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.651 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.651 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.652 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.653 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.654 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.654 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.655 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.656 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.657 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.657 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.658 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.659 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.660 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.660 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.661 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.662 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.663 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.663 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.664 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.665 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.666 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.666 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.667 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.668 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.669 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.669 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2012-02-09 14:45:57.670 MATLAB[17738:7103] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> >> >> >> /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
#@# SUB01 ###############################
/rcbiUsers/dcole/Retinotopy/SUB01
-------------------------
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
/Volumes/RCBI/freesurfer/fsfast/toolbox/fast_selxavg3.m
/Volumes/RCBI/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/Volumes/RCBI/freesurfer/matlab/MRIread.m
-------------------------
outtop = /rcbiUsers/dcole/Retinotopy
Extension format = nii.gz
nruns = 5
autostimdur =
outanadir = /rcbiUsers/dcole/Retinotopy/SUB01/bold/rtopy.self.lh
Found 15746/149363 (10.5) voxels in mask
Creating Design Matrix
... creation time = 0.011 sec
DoMCFit = 1
ntptot = 1305, nX = 39, DOF = 1266
Saving X matrix to /rcbiUsers/dcole/Retinotopy/SUB01/bold/rtopy.self.lh/Xtmp.mat
??? Error using ==> svd
Input to SVD must not contain NaN or Inf.
Error in ==> cond at 40
s = svd(A);
Error in ==> fast_selxavg3 at 254
XCond = cond(XtX);
ERROR: fast_selxavg3() failed\n
*********************
I think the problem is with the "??? Error using ==> svd... " error, not the matlab errors. I've found that many people were reporting this matlab error but it's presumably more of an annoyance than a technical issue.
I'm following the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. I'm pretty sure I have my directories set up properly and I've used Mricron's dcm2nii tool on my raw functionals/structurals. I've also already successfully preprocessed my data and made the rtopy.par files (preproc-sess & mkanalysis-sess).
I haven't been able to find a response that fixed the problem and was hoping for some suggestions.
Thanks so much,
Daniel