Dear Doug,

Thanks for your earlier reply. I have installed fsl on my machine, and have progressed a little further through the retinotopy analysis. However, I now have the following error. 

ERROR: TR mismatch between analysis and data
analysis TR = 2, data TR = 0

I used

mri_convert f.nii f.nii -tr 2000 

to try to fix the problem, but had no success (below is the output). 

Your help would be very much appreciated.

Thanks in advance

Kiley


FreeSurfer:/data1/RETINOTOPY> selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc
Surface data self lh
--------------------------------------------------------------
selxavg3-sess logfile is /media/sf_DATA1/RETINOTOPY/log/selxavg3-sess-bold-rtopy.self.lh-120326071335.log
--------------------------------------------------------------
-------------------------------------------
/media/sf_DATA1/RETINOTOPY/IFEE2211 
Mon Mar 26 07:13:35 EDT 2012
anadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------------------------------------------
------- matlab output --------------------

                            < M A T L A B (R) >
                  Copyright 1984-2012 The MathWorks, Inc.
                    R2012a (7.14.0.739) 32-bit (glnx86)
                              February 9, 2012

 
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
 
>> >> >> >> >> >> >> /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 

#@# IFEE2211 ###############################
/media/sf_DATA1/RETINOTOPY/IFEE2211
-------------------------
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
/home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m
/home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/home/virtualuser/freesurfer/matlab/MRIread.m
-------------------------
outtop = /media/sf_DATA1/RETINOTOPY
Extension format = nii.gz
FreeSurfer Virtual Machine
sudo password: freesurfer

FreeSurfer Virtual Machine
sudo password: freesurfer

nruns = 4
autostimdur = 


outanadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh


FreeSurfer Virtual Machine
sudo password: 

Found 111344/120028 (92.8) voxels in mask
Creating Design Matrix
 ... creation time =  0.007 sec
DoMCFit = 1
ntptot = 492, nX = 36, DOF = 456
Saving X matrix to /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh/Xtmp.mat
XCond = 1.20413 (normalized)
Computing contrast matrices
 

FreeSurfer Virtual Machine
sudo password: 

OLS Beta Pass 
  run 1    t= 0.0
: 

FreeSurfer Virtual Machine
sudo password: 

ERROR: TR mismatch between analysis and data
analysis TR = 2, data TR = 0


From: Kiley Seymour <kiley_seymour@yahoo.com.au>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Sunday, 25 March 2012 1:05 PM
Subject: Re: mkbrainmask-sess

Hi again,

Could this error be due to the fact that I don't have a full version
of fsl installed and configured on my ubuntu virtual machine? i.e.
does fsfast require fsl to be installed?

Thanks

K

From: Kiley Seymour <kiley_seymour@yahoo.com.au>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Friday, 23 March 2012 3:04 PM
Subject: mkbrainmask-sess

Dear Freesurfers,

I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc (  -no-preproc since I have co-registered and motion corrected my files in SPM). 

I was unable to run this command as freesurfer could not find  /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat

So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). 

Any help with this would be much appreciated.

Thanks

Kiley

 
FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY
------------------------------------------------
/media/sf_DATA1/RETINOTOPY/IFEE2211 
Fri Mar 23 09:42:26 EDT 2012
mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_7930
/media/sf_DATA1/RETINOTOPY/IFEE2211/bold
mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii 
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from template.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998558, -0.0534653, -0.00482299)
j_ras = (-0.0536701, 0.992375, 0.110955)
k_ras = (0.00114604, -0.111054, 0.993814)
writing to /tmp/mkbrainmask_7930/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/media/sf_DATA1/RETINOTOPY/IFEE2211/bold
bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1
/home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found
[: 158: =: unexpected operator
/home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found
mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold
cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii 
sysname  Linux
hostname FreeSurfer
machine  i686
user     virtualuser

input      /tmp/mkbrainmask_7930/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_7930/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0