The FSL library or the path to FSL is missing.
regards,
Pedro Paulo Oliveira Jr.
-- mens. original -- Assunto: [Freesurfer] recon-all Flirt Error De: "Anil Roy" aroy85@gmail.com Data: 26/11/2007 22:38
Hello All,
I wanted to test the Freesurfer installation by running recon-all but I received an error saying flirt no found. Can someone point me to the cause of this problem, is it a missing library or some other issue?
I have posted the output from running recon-all on bert below.
Thanks,
Anil.
[root@wonglinux1 freesurfer]# recon-all -s bert -autorecon1 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-rw- 1 root root 657949 Aug 18 23:25 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux flirt: Command not found. INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /space/freesurfer/build/pub-releases/freesurfer #-------------------------------------------- #@# MotionCor Mon Nov 26 16:17:47 CST 2007 Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz #----------------------------------------------- /usr/local/freesurfer/subjects/bert
mri_motion_correct.fsl -o /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz -wild /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
tmpdir is /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz Mon Nov 26 16:18:28 CST 2007 /usr/local/freesurfer/subjects/bert mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 1.img -odt float $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) changing data type from 0 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 1.img... Analyze Output Matrix -1.000 0.000 -0.000 134.400; -0.000 0.000 1.000 -111.000; -0.000 -1.000 -0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz Mon Nov 26 16:18:33 CST 2007 /usr/local/freesurfer/subjects/bert mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 2.img -odt float $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) changing data type from 0 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 2.img... Analyze Output Matrix -1.000 0.000 -0.000 134.400; -0.000 0.000 1.000 -111.000; -0.000 -1.000 -0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Mon Nov 26 16:18:40 CST 2007 /usr/local/freesurfer/subjects/bert mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 3.img -odt float $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) changing data type from 0 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 3.img... Analyze Output Matrix -1.000 0.000 -0.000 134.400; -0.000 0.000 1.000 -111.000; -0.000 -1.000 -0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 2.img Mon Nov 26 16:18:45 CST 2007 /usr/local/freesurfer/subjects/bert fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 1.img -i
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