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