Hi,

I'm trying to get around the problems from my previous post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07669.html

I am now trying to use mri_convert to convert from nifti to bshort using the following command: mri_convert -i rfkoch-0021-00144-000144-00.nii -it nii -o fspm2_000.bshort -ot bshort

The bshort files seem to be created but then when I run inorm-sess I get the following error. The odd thing is that when I used mri_concat on exactly the same .nii files (as mentioned in my previous post) I was able to run inorm-sess with no errors... What is the difference between these two commands?

The inorm error:

Warning: Matrix is singular to working precision.
> In fast_inorm at 196
??? Error using ==> betainc at 35
X must be in the interval [0,1].

The exact output from the command is pasted below. 
Here is 
the output of bugr:
---------------------------------------------------------------------

FREESURFER_HOME: /Applications/freesurfer

Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5


Kernel info: Darwin 8.11.1 i386

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

If anyone has any suggestions I'd be grateful to hear them!

Thanks!


 inorm-sess -sf sessid -df sessdir -rlf runlist_inormcheck -funcstem fspm2
------------------------------
------------------
------------------------------------------------
------------------------------------------------
/Volumes/donnees/Imagery/imagery_data/RF005
Thu Jun 19 17:43:17 CEST 2008
Filesystem   512-blocks      Used     Avail Capacity  Mounted on
/dev/disk0s3  808067040 465870224 342196816    58%    /Volumes/donnees
RunList 021
----------------------------------------------
/Volumes/donnees/Imagery/imagery_data/RF005/bold
inorm -i 021/fspm2 -umask 22 -TR 2.0000 -ipr 3 -bpr 2.9999998958184 -seqname PerImg
----------------------------------------------
Log file is 021/inorm.log
inorm matlab file is /tmp/inorm_21280.m
----------- Matlab file --------------
%%% ----------------- %%
% matlab file to run inorm
% This is a temporary file and may be deleted
% /tmp/inorm_21280.m
global QuitOnError;
QuitOnError = 1;
r = fast_inorm( '-i', '021/fspm2', '-umask', '22', '-TR', '2.0000', '-ipr', '3', '-bpr', '2.9999998958184', '
', 'PerImg');
quit;
 
 
-----------------------------------
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display iconic, MATLAB is starting without a display.
  You will not be able to display graphics on the screen.

                              < M A T L A B >
                  Copyright 1984-2007 The MathWorks, Inc.
                         Version 7.4.0.287 (R2007a)
                              January 29, 2007

Warning: Duplicate directory name: /Users/lreddy/matlab.
 
  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.
 
>> >> >> >> >> >> >> $Id
Parsing Arguments
Checking Parameters
invol        021/fspm2
firstslice   0
nslices      32
relthresh    0.750000
reportfile   021/fspm2.report
meanvalfile  021/fspm2.meanval
twfstem      021/fspm2.twf
TR           2.000000
First Pass: Computing global mean
 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
Second Pass: Segmenting
 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
Warning: Matrix is singular to working precision.
> In fast_inorm at 125
Warning: Matrix is singular to working precision.
> In fast_inorm at 146
Warning: Matrix is singular to working precision.
> In fast_inorm at 175
Warning: Matrix is singular to working precision.
> In fast_inorm at 196
??? Error using ==> betainc at 35
X must be in the interval [0,1].

Error in ==> tTest at 37
  p = betainc(z,dof/2,0.5);

Error in ==> fast_inorm at 223
tSigCor = tTest(s.ntp-2,tCor);

>> 2008-06-19 17:43:31.661 MATLAB[21307] Process manager already initialized -- can't fully enable headless m