Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Help：Freesurfer reg-feat2anat error
by 王志伟 21 Jun '13

21 Jun '13

Dear Sir or Madam, I am trying to apply FreeSurfer Tools to FSL fMRI Analysis (FEAT) as your tutorial. But there were many errors and I cannot figure them out. Could you help me deal with them? Thank you so much!The log files are attached. The details are as follows: the version of Linux: rhel6.2; the version of freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 SUBJECTS_DIR: /usr/local/freesurfer/subjects working directory /usr/local/freesurfer/subjects/fbert-feat command: reg-feat2anat --feat fbert1.feat --subject bert there is no ERROR in anat2std.register.dat.fslregister.log the first ERROR in anat2exf.register.dat.fslregister.log is '' /usr/local/freesurfer/subjects/fbert-feat mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii'' the reg-feat2anat.log is as follow: Wed Jun 19 20:41:16 CST 2013 /usr/local/freesurfer/subjects/fbert-feat /usr/local/freesurfer/bin/reg-feat2anat --feat fbert1.feat --subject bert Linux T7600-3 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux example_func ras_good_flag 1 ------------------------------------------------------- Initializing exf2anat with header tkregister2_cmdl --targ /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz movable volume fbert1.feat/example_func.nii.gz reg file fbert1.feat/reg/freesurfer/anat2exf.register.dat.init LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fbert1.feat/example_func.nii.gz Tmov: -------------------- -3.438 0.000 0.000 110.000; 0.000 0.000 4.000 -70.000; 0.000 -3.438 0.000 110.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 5.400; 0.000 0.000 1.000 0.000; 0.000 -1.000 0.000 -18.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 5.400; 0.000 0.000 1.000 0.000; 0.000 -1.000 0.000 -18.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 5.400; 0.000 0.000 1.000 0.000; 0.000 -1.000 0.000 -18.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -47.2656, ref det = -1 fslregister --s bert --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --mov fbert1.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp fbert1.feat/reg/freesurfer/tmp --out fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz Log file is fbert1.feat/reg/freesurfer/anat2exf.register.dat.fslregister.log Wed Jun 19 20:41:18 CST 2013 --s bert --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --mov fbert1.feat/example_func.nii.gz --dof 6 --bins 256 --cost corratio --fslmat fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp fbert1.feat/reg/freesurfer/tmp --out fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ T7600-3 Linux T7600-3 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local/freesurfer/subjects/fbert-feat mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/bert/mri/ERROR: fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /usr/local/freesurfer/subjects/fbert-feat mri_convert fbert1.feat/example_func.nii.gz fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0 mri_convert fbert1.feat/example_func.nii.gz fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from fbert1.feat/example_func.nii.gz... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii... Mov determinant is -47.2656 Wed Jun 19 20:41:18 CST 2013 /usr/local/freesurfer/subjects/fbert-feat flirt.fsl -ref fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init fbert1.feat/reg/freesurfer/exf2anat.init.fsl.mat ** ERROR (nifti_image_read): failed to find header file for 'fbert1.feat/reg/freesurfer/tmp/refvol.fslregister' ** ERROR: nifti_image_open(fbert1.feat/reg/freesurfer/tmp/refvol.fslregister): bad header info Error: failed to open file fbert1.feat/reg/freesurfer/tmp/refvol.fslregister ERROR: Could not open image fbert1.feat/reg/freesurfer/tmp/refvol.fslregister Image Exception : #22 :: Failed to read volume fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Wed Jun 19 20:41:18 CST 2013 /usr/local/freesurfer/subjects/fbert-feat flirt.fsl -ref fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii -in fbert1.feat/reg/freesurfer/tmp/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/freesurfer/exf2anat.fsl.mat -init fbert1.feat/reg/freesurfer/tmp/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch -o fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii ** ERROR (nifti_image_read): failed to find header file for 'fbert1.feat/reg/freesurfer/tmp/refvol.fslregister' ** ERROR: nifti_image_open(fbert1.feat/reg/freesurfer/tmp/refvol.fslregister): bad header info Error: failed to open file fbert1.feat/reg/freesurfer/tmp/refvol.fslregister ERROR: Could not open image fbert1.feat/reg/freesurfer/tmp/refvol.fslregister Image Exception : #22 :: Failed to read volume fbert1.feat/reg/freesurfer/tmp/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Wed Jun 19 20:41:18 CST 2013 /usr/local/freesurfer/subjects/fbert-feat mri_convert fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz mri_convert fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii fbert1.feat/reg/freesurfer/tmp/exf-in-anat.nii.gz niiRead(): error opening file fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from fbert1.feat/reg/freesurfer/tmp/outvol.fslregister.nii... tkregister2_cmdl --s bert --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --fslreg fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ERROR: cannot open fbert1.feat/reg/freesurfer/exf2anat.fsl.mat Started at Wed Jun 19 20:41:18 CST 2013 Ended at Wed Jun 19 20:41:18 CST 2013 fslregister Done To check results, run: tkregister2 --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --surf orig bbregister --mov fbert1.feat/example_func.nii.gz --bold --6 --init-reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat ERROR: cannot find fbert1.feat/reg/freesurfer/anat2exf.register.dat fslregister --mov fbert1.feat/reg/standard.nii.gz --s bert --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --dof 12 Log file is fbert1.feat/reg/freesurfer/anat2std.register.dat.fslregister.log Wed Jun 19 20:41:18 CST 2013 --mov fbert1.feat/reg/standard.nii.gz --s bert --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --dof 12 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ T7600-3 Linux T7600-3 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local/freesurfer/subjects/fbert-feat mri_convert /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii mri_convert /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/brainmask.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) writing to fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii... -------------------------------------- /usr/local/freesurfer/subjects/fbert-feat mri_convert fbert1.feat/reg/standard.nii.gz fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii --frame 0 mri_convert fbert1.feat/reg/standard.nii.gz fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from fbert1.feat/reg/standard.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii... Mov determinant is -8 /usr/local/freesurfer/subjects/fbert-feat tkregister2_cmdl --mov fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii --reg fbert1.feat/reg/tmp.fslregister.17828/reg0.17828.dat --regheader --fslregout fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat0 --s bert --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii reg file fbert1.feat/reg/tmp.fslregister.17828/reg0.17828.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/bert/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii Tmov: -------------------- -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 6.400; 0.000 0.000 1.000 -19.000; 0.000 -1.000 0.000 -35.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 6.400; 0.000 0.000 1.000 -19.000; 0.000 -1.000 0.000 -35.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = bert RegMat --------------------------- 1.000 0.000 0.000 6.400; 0.000 0.000 1.000 -19.000; 0.000 -1.000 0.000 -35.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1 Wed Jun 19 20:41:20 CST 2013 /usr/local/freesurfer/subjects/fbert-feat flirt.fsl -ref fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii -in fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii -bins 256 -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/tmp.fslregister.17828/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat0 Wed Jun 19 20:41:27 CST 2013 /usr/local/freesurfer/subjects/fbert-feat flirt.fsl -ref fbert1.feat/reg/tmp.fslregister.17828/refvol.fslregister.nii -in fbert1.feat/reg/tmp.fslregister.17828/movvol.fslregister.nii -bins 256 -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat -init fbert1.feat/reg/tmp.fslregister.17828/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s bert --mov fbert1.feat/reg/standard.nii.gz --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --fslreg fbert1.feat/reg/freesurfer/anat2std.register.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.905 0.003 0.033 43.546; 0.039 -0.091 -0.903 197.762; 0.008 1.050 -0.080 4.971; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume fbert1.feat/reg/standard.nii.gz reg file fbert1.feat/reg/freesurfer/anat2std.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/subjects/bert/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fbert1.feat/reg/standard.nii.gz Tmov: -------------------- -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8, ref det = -1 ---- Input registration matrix (computed) -------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; Determinant 1.15433 subject = bert RegMat --------------------------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; Cleaning up Started at Wed Jun 19 20:41:18 CST 2013 Ended at Wed Jun 19 20:41:48 CST 2013 fslregister Done To check results, run: tkregister2 --mov fbert1.feat/reg/standard.nii.gz --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --surf orig mri_matrix_multiply -im fbert1.feat/reg/freesurfer/anat2exf.register.dat -iim fbert1.feat/reg/freesurfer/anat2std.register.dat -om fbert1.feat/reg/freesurfer/exf2std.register.dat tkregister2_cmdl --targ fbert1.feat/reg/standard.nii.gz --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/exf2std.register.dat --fslregout fbert1.feat/reg/freesurfer/example_func2standard.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume fbert1.feat/reg/standard.nii.gz movable volume fbert1.feat/example_func.nii.gz reg file fbert1.feat/reg/freesurfer/exf2std.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ERROR: reading fbert1.feat/reg/freesurfer/exf2std.register.dat mri_matrix_multiply -im fbert1.feat/reg/freesurfer/anat2std.register.dat -iim fbert1.feat/reg/freesurfer/anat2exf.register.dat -om fbert1.feat/reg/freesurfer/std2exf.register.dat ------------------------------------------------------- tkregister2_cmdl --s bert --targ /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz --mov fbert1.feat/reg/standard.nii.gz --reg fbert1.feat/reg/freesurfer/anat2std.register.dat --fslregout fbert1.feat/reg/freesurfer/std2anat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz movable volume fbert1.feat/reg/standard.nii.gz reg file fbert1.feat/reg/freesurfer/anat2std.register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable fbert1.feat/reg/standard.nii.gz Tmov: -------------------- -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; Determinant 1.15433 subject = bert RegMat --------------------------- 1.103 -0.001 0.040 0.610; -0.048 -0.095 1.097 -22.130; -0.005 -0.945 -0.084 -12.686; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8, ref det = -1 To visually check your results, run: tkregister2 --s bert --mov fbert1.feat/example_func.nii.gz --reg fbert1.feat/reg/freesurfer/anat2exf.register.dat --fslreg fbert1.feat/reg/freesurfer/exf2anat.fsl.mat --surf orig --tag Wed Jun 19 20:41:50 CST 2013 reg-feat2anat done -- Zhiwei Wang（王志伟）, Graduate Student Laboratory of Brain Imaging Institute of Neuroscience Chinese Academy of Sciences 320 Yue-Yang Road， ION Building 313 Shanghai 200031,China

2 1

OptSeq nullmax
by A a 21 Jun '13

21 Jun '13

Hi all, Is there a rule that let me avoid having the error message could not force null max? -- ntp 200 --tr 2.5 --psdwin 0 20 2.5 --ev 1 3 15 -ev 2 3 15 -ev 3 3 15 --ev 4 3 15 ---ev 5 3 15--tnullmin 2 --tnullmax 4.5 .. Thanks AS

2 1

Tutorial data <Adding control points>
by ye tian 20 Jun '13

20 Jun '13

Dear FreeSurfers, It seems that the tutorial sample data <cp_before> needs correction for skull strip, too. I am just curious why it only serves a sample for control points. Thank you very much! Sincerely, Ye

1 0

recon-all -localGI results in "ERROR:: Too many arguments."
by Tudor Popescu 20 Jun '13

20 Jun '13

Dear Freesurfer & localGI experts, I want to compare local GI (gyrification index) between my two groups. Following the help <https://surfer.nmr.mgh.harvard.edu/fswiki/LGI>, I ran this command for one of my subjects: recon-all -s M01 -localGI but it resulted in the error: make_outer_surface('/media/math/all38subj/M01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/media/math/all38subj/M01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= ERROR:: Too many arguments. Someone previously<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23414.html>received this error due to a space in their path, but I don't specify any path in the above command, and my $SUBJECTS_DIR path doesn't have any spaces or any other dodgy characters. I'm running FreeSurfer v5.2 from inside Virtualbux/Ubuntu, so Matlab is not included in there, although it exists separately on my Windows partition. I could run recon through FSL, but I don't see any matlab folder there either. Could Matlab be the problem? Also, which files/folders will I need to delete after I'll have fixed the problem, before re-running the recon for all subjects? Or will it just overwrite any left-overs? Many thanks in advance for any help! Tudor

3 8

FW: recon-all error MRIthickenThinWMStrands
by Sudhin A. Shah 20 Jun '13

20 Jun '13

Hi! how can I view a .mgz file? How do I fix a skull stripping error? ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Wednesday, June 19, 2013 3:33 PM To: Sudhin A. Shah Subject: RE: [Freesurfer] recon-all error MRIthickenThinWMStrands Hi Sudhin did you look at the brain.mgz? Much of the brain is stripped so there is a skull stripping error you need to fix. Bruce On Wed, 19 Jun 2013, Sudhin A. Shah wrote: > > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Wednesday, June 19, 2013 2:58 PM > To: Sudhin A. Shah > Subject: RE: [Freesurfer] recon-all error MRIthickenThinWMStrands > > can you send me the brain.mgz? > > On Wed, 19 Jun 2013, Sudhin A. Shah wrote: > >> Hi, Here it is >> >> #@# WM Segmentation Fri Jun 14 16:06:46 EDT 2013 >> >> mri_segment brain.mgz wm.seg.mgz >> >> doing initial intensity segmentation... >> using local statistics to label ambiguous voxels... >> computing class statistics for intensity windows... >> WM (109.0): 110.8 +- 7.7 [80.0 --> 125.0] >> GM (67.0) : 64.9 +- 12.1 [30.0 --> 96.0] >> setting bottom of white matter range to 77.0 >> setting top of gray matter range to 89.1 >> doing initial intensity segmentation... >> using local statistics to label ambiguous voxels... >> using local geometry to label remaining ambiguous voxels... >> >> reclassifying voxels using Gaussian border classifier... >> >> removing voxels with positive offset direction... >> smoothing T1 volume with sigma = 0.250 >> removing 1-dimensional structures... >> 22510 sparsely connected voxels removed... >> thickening thin strands.... >> ERROR: MRIthickenThinWMStrands: invalid x,y,z! >> >> Numerical result out of range >> >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Wednesday, June 19, 2013 1:42 PM >> To: Sudhin A. Shah >> Cc: Freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] recon-all error MRIthickenThinWMStrands >> >> nope, never seen that error. Probably from mri_segment. If you send me the >> input volume I'll take a look (check the recon-all.log and see what command >> was running when that happened). Also, definitely check it before sending >> to make sure it's reasonable >> >> On Wed, 19 Jun 2013, >> Sudhin A. Shah wrote: >> >>> Hi >>> >>> ERROR: MRIthickenThinWMStrands: invalid x,y,z! >>> >>> Numerical result out of range >>> >>> >>> Any tips? >>> S >>> >>> >> >> >> 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.

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long_mris_slopes/long_qdec_table command not found
by Peter Bohn 20 Jun '13

20 Jun '13

Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter

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subj: Undefined variable.
by Knut J Bjuland 20 Jun '13

20 Jun '13

Hi Strange error in tracula 5.1. When I use a dmric file that have worked before I now get subj: Undefined variable. I may have uppgrade tcsh. Is there any fix to get tracula-preproc to use the id from dmric files Knut J

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Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
by Martin Reuter 20 Jun '13

20 Jun '13

Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn <bohn-peter(a)gmx.de> wrote: >Hi Martin, > >thanks a lot fort he quick reply! When I type freesurfer into the >window it shows me v5.0.0 as the version. Sorry for my prior mistake >concerning the version’s name. All other commands I use run perfectly >fine. > >Thanks once again! > >Best regards > >Peter > >From: mreuter(a)nmr.mgh.harvard.edu >Date: Thu, 20 Jun 2013 05:21:39 -0400 >To: bohn-peter(a)gmx.de >CC: freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not >found > >Hi Peter, >can you run any free surfer command at all? Looks to me that you did >not source free surfer. What happens if you typefreesurferinto the >terminal window? It should print the version. >Best, Martin >On Jun 20, 2013, at 5:17 AM, Peter Bohn <bohn-peter(a)gmx.de> wrote: > > >Dear Freesurfer experts, > >I was trying to run some longitudinal analysis but whenever I want to >use the commands “long_mris_slopes” or “long_qdec_table” I just get >“command not found” as an answer. When I try to look up a package that >might include the command, by typing “cnf long_mris_slopes”, >I also just get “command not found” as an answer. We are currently >using version v 1.313.2.6. > >Does anyone of you know if the two commands that I would like to run, >are included in this version? Where would I have to look for the >additional package if it exists? Or am I by any chance just typing the >commands incorrect? > >Many thanks for the help! > >Sincerely yours > >Peter_______________________________________________Freesurfer mailing >listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >---------------------------------Dr. Martin ReuterAssistant in >Neuroscience - Massachusetts General Hospital >Instructor in Neurology - Harvard Medical School >MGH / HMS / MIT > >A.A.Martinos Center for Biomedical Imaging >149 Thirteenth Street, Suite 2301 >Charlestown, MA 02129 > >Phone: +1-617-724-5652 >Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.eduWeb : >http://reuter.mit.edu > > > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)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. -- Sent from my phone, please excuse brevity.

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error in lme_mass_fit using matlab tools
by Catherine Bois 20 Jun '13

20 Jun '13

Hi, Thank you for your response. I am actually using two random effects (time and intercepts), and have fixed my design matrix to incorporate this. We are actually running R2011b Matlab, however I just realised that we do not have the Statistics toolbox. Could this be what is causing the errors? Is the Statistics toolbox freely available to download? Best Wishes, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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error --qdec long
by Catherine Bois 20 Jun '13

20 Jun '13

Dear Freesurfer experts, I am trying to prepare my data for linear mixed modeling using the matlab add ons, with this command mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh However I keep getting this error message ERROR: flag --qdec-long not recognized I am using version 5.3 and read on the release notes that qdec-long only works with unix input text files (\n newline). I thought that was the format of my textfile, and also confused as to why the wrong format of the file would make the flag unrecognized as opposed to the textfile...I was also wondering whether the -long table needs to be "shrunk" to cross-sectional format as it does in the two stage model? I have attached an excerpt of my textfile qdec, would greatly appreciate help in establishing whether it is somehow the format of the textfile that is the problem? Thank you very much for your help, Best Wishes, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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