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