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 -----------------------------

--------------------------------------------------------------

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

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) >

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 14:45:57.637 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 14:45:57.640 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 14:45:57.644 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 14:45:57.647 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 14:45:57.650 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 14:45:57.652 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 14:45:57.655 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 14:45:57.658 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 14:45:57.661 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 14:45:57.664 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 14:45:57.667 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 14:45:57.670 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

Daniel Cole

University of Rochester

Brain and Cognitive Sciences

dcole10@u.rochester.edu