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

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