Hi,Doug
When I run"preproc-sess -fsd bold -fwhm 0 -surface self lhrh -sf sessid
-per-run",I met the following problems.Can you tell me why?
preproc-sess
sess01
$Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $
Linux localhost.localdomain 2.6.18-308.el5PAE #1 SMP Tue Feb 21 20:46:05 EST
2012 i686 i686 i386 GNU/Linux
2013?? 03?? 07?? ?????? 16:24:05 CST
/usr/local/freesurfer/Project
-fsd bold -fwhm 0 -surface self lhrh -sf sessid -per-run
ProjectDir /usr/local/freesurfer/Project
sess01 Template -----------------------------
mktemplate-sess -s sess01 -d /usr/local/freesurfer/Project -fsd bold -update
Session: /usr/local/freesurfer/Project/sess01 ----------------
2013?? 03?? 07?? ?????? 16:24:05 CST
Detected input format at nii
/usr/local/freesurfer/Project
mri_convert /usr/local/freesurfer/Project/sess01/bold/001/f.nii
/usr/local/freesurfer/Project/sess01/bold/template.nii.gz --frame 0
mri_convert /usr/local/freesurfer/Project/sess01/bold/001/f.nii
/usr/local/freesurfer/Project/sess01/bold/template.nii.gz --frame 0
INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /usr/local/freesurfer/Project/sess01/bold/001/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999281, -0.0191918, -0.032696)
j_ras = (-0.0194077, 0.999792, 0.00629985)
k_ras = (-0.0325683, -0.00692988, 0.999445)
keeping frame 0
writing to /usr/local/freesurfer/Project/sess01/bold/template.nii.gz...
Run: 001 ----------------
2013?? 03?? 07?? ?????? 16:24:08 CST
/usr/local/freesurfer/Project
mri_convert /usr/local/freesurfer/Project/sess01/bold/001/f.nii
/usr/local/freesurfer/Project/sess01/bold/001/template.nii.gz --mid-frame
mri_convert /usr/local/freesurfer/Project/sess01/bold/001/f.nii
/usr/local/freesurfer/Project/sess01/bold/001/template.nii.gz --mid-frame
INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /usr/local/freesurfer/Project/sess01/bold/001/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999281, -0.0191918, -0.032696)
j_ras = (-0.0194077, 0.999792, 0.00629985)
k_ras = (-0.0325683, -0.00692988, 0.999445)
keeping frame 122
writing to /usr/local/freesurfer/Project/sess01/bold/001/template.nii.gz...
2013?? 03?? 07?? ?????? 16:24:11 CST
mktemplate-sess completed
sess01 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s sess01 -d
/usr/local/freesurfer/Project -update
------------------------------------------------
/usr/local/freesurfer/Project/sess01
2013?? 03?? 07?? ?????? 16:24:11 CST
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_21890
/usr/local/freesurfer/Project/sess01/bold
mri_convert template.nii.gz /tmp/mkbrainmask_21890/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_21890/in.nii
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from template.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999281, -0.0191918, -0.032696)
j_ras = (-0.0194077, 0.999792, 0.00629985)
k_ras = (-0.0325683, -0.00692988, 0.999445)
writing to /tmp/mkbrainmask_21890/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/usr/local/freesurfer/Project/sess01/bold
bet.fsl /tmp/mkbrainmask_21890/in.nii /tmp/mkbrainmask_21890/brain -m -f 0.1
/usr/local/freesurfer/bin/bet.fsl: line 150: /bin/remove_ext: ??????????????????
/usr/local/freesurfer/bin/bet.fsl: line 151: /bin/remove_ext: ??????????????????
/usr/local/freesurfer/bin/bet.fsl: line 153: /bin/imtest: ??????????????????
/usr/local/freesurfer/bin/bet.fsl: line 153: [: =: unary operator expected
/usr/local/freesurfer/bin/bet.fsl: line 231: /bin/bet2: ??????????????????
mri_binarize --i /tmp/mkbrainmask_21890/brain_mask.nii --min .01 --o
/tmp/mkbrainmask_21890/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_21890/brain_mask.nii
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /usr/local/freesurfer/Project/sess01/bold
cmdline mri_binarize --i /tmp/mkbrainmask_21890/brain_mask.nii --min .01 --o
/tmp/mkbrainmask_21890/brain_mask.nii
sysname Linux
hostname localhost.localdomain
machine i686
user root
input /tmp/mkbrainmask_21890/brain_mask.nii
frame 0
nErode3d 0
nErode2d 0
output /tmp/mkbrainmask_21890/brain_mask.nii
Binarizing based on threshold
min 0.01
max +infinity
binval 1
binvalnot 0
If I want to run preproc-sess,do I have to install FSL?
Why I can't use the mkanalysis -gui ?
Thanks
LiuYong
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