yes, you will need FSL. The GUI for mkanalysis was too difficult to maintain so it is nolonger available. doug
On 03/07/2013 03:47 AM, 古木 wrote:
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年 03月 07日 星期四 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年 03月 07日 星期四 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年 03月 07日 星期四 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年 03月 07日 星期四 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年 03月 07日 星期四 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: 没有那个 文件或目录 /usr/local/freesurfer/bin/bet.fsl: line 151: /bin/remove_ext: 没有那个 文件或目录 /usr/local/freesurfer/bin/bet.fsl: line 153: /bin/imtest: 没有那个文件 或目录 /usr/local/freesurfer/bin/bet.fsl: line 153: [: =: unary operator expected /usr/local/freesurfer/bin/bet.fsl: line 231: /bin/bet2: 没有那个文件或目录 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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