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-sesslogfile 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 FSLMATHSfslmaths.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 cmdlinemri_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