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_seym...@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
