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Dear Mary,

You've only run Pre-stats + Stats.
It is only in the Post-stats that it uses the contrasts.
So if you want COPE results and thing like that, then you must run Post-stats.

All the best,
Mark



On 17 Apr 2013, at 15:38, Mary Elizabeth Sutherland <[log in to unmask]>
 wrote:

Hello Steve,

It's not the post-stats that I'm looking for, but rather the stats output to use in my higher level analyses. When I run what I sent, I don't get a complete stats output, so when I go to run a higher-level analysis and select my input as lower level feat directories, I get the error that there are no stats images / cope files in my lower-level analysis. As I understand it, this isn't yet at the post-stats phase...?

Thanks for the help!

~ mary e.

On Apr 17, 2013, at 10:56 AM, Stephen Smith wrote:

The reason you don't have any post-stats outputs is because you have turned post-stats off.
Steve.


On 17 Apr 2013, at 07:29, Mary Elizabeth Sutherland <[log in to unmask]> wrote:

Dear Mark,

Thank you for looking through the log file. I am running at least one contrast (see attached file) and so am a bit confused to why the stats folder ends up incomplete. I tried another version of the analysis (including a different EV, one I am not actually interested in) and it ran, which leads me to believe that it isn't my computer / version of FSL.

Let me know if you have any ideas!

Thank you again...

~ mary e.
<design.fsf>
<design.png>

On Apr 17, 2013, at 7:56 AM, Mark Jenkinson wrote:

Dear Mary,

This all looks fine to me.
Are you running a full analysis with at least one contrast?

If you cannot see the problem it would help us if you sent the design.fsf file.

All the best,
    Mark


Mary Elizabeth Sutherland <[log in to unmask]> wrote:

Dear Mark,

Thank you! I have copied and pasted the logfile into this email. Let me know if you need any additional information!

~ mary e.

Progress Report / Log

Started at Fri Apr 12 19:58:26 ART 2013

Feat main script

/bin/cp /tmp/feat_FtJgqd.fsf design.fsf

/usr/local/fsl/bin/feat_model design 

mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;ln -s /usr/local/fsl/doc/images .files/images

/usr/local/fsl/bin/fsl_sub -T 10 -l logs -N feat0_init   /usr/local/fsl/bin/feat /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/design.fsf -D /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat -I 1 -init
26585

/usr/local/fsl/bin/fsl_sub -T 60 -l logs -N feat1b_reg -j 26585  /usr/local/fsl/bin/feat /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/design.fsf -D /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat -I 1 -reg
26657

/usr/local/fsl/bin/fsl_sub -T 12 -l logs -N feat2_pre -j 26657,26585  /usr/local/fsl/bin/feat /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/design.fsf -D /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat -I 1 -prestats
29608

/usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat3_film -j 29608  /usr/local/fsl/bin/feat /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/design.fsf -D /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat -I 1 -film
30211

/usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 29608,30211,26657  /usr/local/fsl/bin/feat /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/design.fsf -D /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat -stop

/usr/local/fsl/bin/mainfeatreg -d /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat -l /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/logs/feat5_reg -R /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/report_unwarp.html -r /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/report_reg.html  -i /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/example_func.nii.gz  -n 10 -h /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_anat_brain -w  BBR -x 90 -s /Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm_brain -y 12 -z 90 -a /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/fieldmap -b /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/mag1_brain -e 30.0 -f 10 -g 0.58 -p y- -w BBR
Option -d ( output directory ) selected with  argument "/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat"
Option -l ( logfile )input with argument "/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/logs/feat5_reg"
Option -R ( html unwarping report ) selected with  argument "/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/report_unwarp.html"
Option -r ( html registration report ) selected with  argument "/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/report_reg.html"
Option -i ( main input ) input with argument "/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/example_func.nii.gz"
Option -n ( use nonlinear reg ) input with argument "10"
Option -h ( high-res structural image ) selected with  argument "/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_anat_brain"
Option -w ( highres dof ) selected with  argument "BBR"
Option -x ( highres search ) selected with  argument "90"
Option -s ( standard image ) selected with  argument "/Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm_brain"
Option -y ( standard dof ) selected with  argument "12"
Option -z ( standard search ) selected with  argument "90"
Option -a ( fieldmap image ) selected with  argument "/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/fieldmap"
Option -b ( field ) selected with  argument "/Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/mag1_brain"
Option -e ( echo time ) selected with  argument "30.0"
Option -f ( signal loss Threshold ) selected with  argument "10"
Option -g ( echo spacing ) selected with  argument "0.58"
Option -p ( phase encoding direction ) selected with  argument "y-"
Option -w ( highres dof ) selected with  argument "BBR"
whirlgif Rev 3.04 (c) 1997-1999 by Hans Dinsen-Hansen
                  (c) 1995-1996 by Kevin Kadow
                  (c) 1990-1993 by Mark Podlipec
Processed 2 files.

Initialisation
/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/20121106_08201300060001t2starepi2Dstandard12ch1441213s006a001 prefiltered_func_data -odt float
Total original volumes = 38

/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 19 1

Prestats
/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile reg/unwarp/EF_D_example_func -rmsrel -rmsabs

/bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc

/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png 

/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png 

/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png 

/usr/local/fsl/bin/applywarp -i reg/unwarp/FM_UD_fmap_mag_brain_mask -r example_func --abs --premat=reg/unwarp/FM_UD_fmap_mag_brain2str.mat --postmat=reg/highres2example_func.mat -o reg/unwarp/EF_UD_fmap_mag_brain_mask

/usr/local/fsl/bin/fslsplit prefiltered_func_data grot

/usr/local/fsl/bin/applywarp -i grot0000 -o grot0000 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0000 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0001 -o grot0001 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0001 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0002 -o grot0002 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0002 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0003 -o grot0003 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0003 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0004 -o grot0004 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0004 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0005 -o grot0005 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0005 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0006 -o grot0006 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0006 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0007 -o grot0007 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0007 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0008 -o grot0008 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0008 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0009 -o grot0009 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0009 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0010 -o grot0010 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0010 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0011 -o grot0011 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0011 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0012 -o grot0012 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0012 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0013 -o grot0013 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0013 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0014 -o grot0014 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0014 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0015 -o grot0015 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0015 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0016 -o grot0016 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0016 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0017 -o grot0017 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0017 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0018 -o grot0018 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0018 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0019 -o grot0019 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0019 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0020 -o grot0020 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0020 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0021 -o grot0021 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0021 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0022 -o grot0022 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0022 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0023 -o grot0023 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0023 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0024 -o grot0024 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0024 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0025 -o grot0025 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0025 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0026 -o grot0026 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0026 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0027 -o grot0027 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0027 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0028 -o grot0028 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0028 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0029 -o grot0029 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0029 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0030 -o grot0030 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0030 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0031 -o grot0031 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0031 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0032 -o grot0032 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0032 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0033 -o grot0033 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0033 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0034 -o grot0034 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0034 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0035 -o grot0035 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0035 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0036 -o grot0036 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0036 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/applywarp -i grot0037 -o grot0037 --premat=mc/prefiltered_func_data_mcf.mat/MAT_0037 -w reg/example_func2highres_warp.nii.gz -r example_func --abs --postmat=reg/highres2example_func.mat

/usr/local/fsl/bin/fslmerge -t prefiltered_func_data_unwarp grot0000   grot0001   grot0002   grot0003   grot0004   grot0005   grot0006   grot0007   grot0008   grot0009   grot0010   grot0011   grot0012   grot0013   grot0014   grot0015   grot0016   grot0017   grot0018   grot0019   grot0020   grot0021   grot0022   grot0023   grot0024   grot0025   grot0026   grot0027   grot0028   grot0029   grot0030   grot0031   grot0032   grot0033   grot0034   grot0035   grot0036   grot0037

/bin/rm -f grot*

/usr/local/fsl/bin/slicetimer -i prefiltered_func_data_unwarp --out=prefiltered_func_data_st -r 11.5000000000 --odd

/usr/local/fsl/bin/fslmaths prefiltered_func_data_st -Tmean mean_func

/usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv mask_mask mask

/usr/local/fsl/bin/fslmaths prefiltered_func_data_st -mas mask prefiltered_func_data_bet

/usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 1794.082764 

/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 179.4082764 -Tmin -bin mask -odt char

/usr/local/fsl/bin/fslstats prefiltered_func_data_st -k mask -p 50
1169.191895 

/usr/local/fsl/bin/fslmaths mask -dilF mask

/usr/local/fsl/bin/fslmaths prefiltered_func_data_st -mas mask prefiltered_func_data_thresh

/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/usr/local/fsl/bin/susan prefiltered_func_data_thresh 876.89392125 3.39702760085 3 1 1 mean_func 876.89392125 prefiltered_func_data_smooth

/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth

/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 8.55291594371 prefiltered_func_data_intnorm

/usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 5.21739130435 -1 prefiltered_func_data_tempfilt

/usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data

/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func

/bin/rm -rf prefiltered_func_data*

Stats
mkdir -p custom_timing_files ; /bin/cp /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/EventFiles/SameTempo/Subject1_run1_DiffCorrect.txt custom_timing_files/ev1.txt

mkdir -p custom_timing_files ; /bin/cp /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/EventFiles/SameTempo/Subject1_run1_SameCorrect.txt custom_timing_files/ev2.txt

paste -d  ' '  /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/logfiles/Subject01fonc1incorrect.dat > confoundevs.txt

/usr/local/fsl/bin/feat_model design confoundevs.txt

/usr/local/fsl/bin/film_gls -rn stats -sa -ms 5   filtered_func_data design.mat 1000.0
Log directory is: stats
paradigm.getDesignMatrix().Nrows()=38
paradigm.getDesignMatrix().Ncols()=3
sizeTS=38
numTS=54842
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
mode = 10074.2
sig = 1820
Spatially smoothing auto corr estimates
.....
Completed
Tukey M = 6
Tukey estimates... Completed
Completed
Prewhitening and Computing PEs...
Percentage done:
1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
Saving results... 
Completed

/usr/local/fsl/bin/smoothest -d 35   -m mask -r stats/res4d > stats/smoothness

Registration
/bin/mkdir -p /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_run1_trial_types+.feat/reg


/usr/local/fsl/bin/fslmaths ../example_func EF_D_example_func


/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/fieldmap FM_UD_fmap


/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/mag1_brain FM_UD_fmap_mag


/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/mag1_brain FM_UD_fmap_mag_brain


/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/mag1  FM_UD_fmap_mag


/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -V | awk '{ print $1 }'
38663

/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -v | awk '{ print $1 }'
122880
0.31464

/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -bin FM_UD_fmap_mag_brain_mask -odt short


/usr/local/fsl/bin/fslmaths FM_UD_fmap -abs -bin -mas FM_UD_fmap_mag_brain_mask -mul -1 -add 1 -bin FM_UD_fmap_mag_brain_mask_inv


/usr/local/fsl/bin/cluster -i FM_UD_fmap_mag_brain_mask_inv -t 0.5 --no_table -o FM_UD_fmap_mag_brain_mask_idx


/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain_mask_idx -R | awk '{ print $2 }'
79.000000

/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask_idx -thr 79.000000 -bin -mul -1 -add 1 -bin -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap_mag_brain_mask


/usr/local/fsl/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
-6.238736

/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -6.238736 -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap


/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -P 98
1651.000000

/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -thr 825.5 -bin FM_UD_fmap_mag_brain_mask50


/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero FM_UD_fmap_mag_brain_mask_ero


/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask_ero -add FM_UD_fmap_mag_brain_mask50 -thr 0.5 -bin FM_UD_fmap_mag_brain_mask


/usr/local/fsl/bin/fslmaths FM_UD_fmap -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap


/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap_mag_brain


/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero FM_UD_fmap_mag_brain_mask_ero


/usr/local/fsl/bin/fugue --loadfmap=FM_UD_fmap --savefmap=FM_UD_fmap_tmp_fmapfilt --mask=FM_UD_fmap_mag_brain_mask --despike --despikethreshold=2.1


/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub FM_UD_fmap_tmp_fmapfilt -mas FM_UD_fmap_mag_brain_mask_ero -add FM_UD_fmap_tmp_fmapfilt FM_UD_fmap


/bin/rm -f FM_UD_fmap_tmp_fmapfilt* FM_UD_fmap_mag_brain_mask_ero* FM_UD_fmap_mag_brain_mask50* FM_UD_fmap_mag_brain_i*


/usr/local/fsl/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
1.871621

/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub 1.871621 -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap


/usr/local/fsl/bin/fslstats FM_UD_fmap -R | awk '{ print $1 }'
-1267.710815

/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -1267.710815 -add 10 -mas FM_UD_fmap_mag_brain_mask grot


/usr/local/fsl/bin/fslstats grot -l 1 -p 0.1 -p 95
603.927368 1470.487793

/usr/local/fsl/bin/overlay 0 0 FM_UD_fmap_mag -a grot 603.927368 1470.487793 fmap+mag


/usr/local/fsl/bin/slicer fmap+mag -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png fmap+mag.png; rm sl?.png


/usr/local/fsl/bin/sigloss -i FM_UD_fmap --te=0.03 -m FM_UD_fmap_mag_brain_mask -s FM_UD_fmap_sigloss


/usr/local/fsl/bin/fslmaths FM_UD_fmap_sigloss -mul FM_UD_fmap_mag_brain FM_UD_fmap_mag_brain_siglossed -odt float


/usr/local/fsl/bin/fslmaths FM_UD_fmap_sigloss -thr 0.9 FM_UD_fmap_sigloss -odt float


/usr/local/fsl/bin/overlay 1 0 FM_UD_fmap_mag_brain -a FM_UD_fmap_sigloss 0 1 FM_UD_sigloss+mag


/usr/local/fsl/bin/slicer FM_UD_sigloss+mag -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png FM_UD_sigloss+mag.png; rm sl?.png


/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_anat_brain highres


/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/fmri_data_FSL/mricron_converted_nifti_data/Subject01/Subject01_anat  highres_head


/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm_brain standard


/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm standard_head


/usr/local/fsl/bin/fslmaths /Volumes/LEIPZIGDATA/Applications/fsl/data/standard/MNI152_T1_1mm_brain_mask_dil standard_mask

did not find file: example_func2highres.mat. Generating transform.

/usr/local/fsl/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres --fmap=unwarp/FM_UD_fmap --fmapmag=unwarp/FM_UD_fmap_mag --fmapmagbrain=unwarp/FM_UD_fmap_mag_brain --echospacing=0.00058 --pedir=y-
Running FAST segmentation FLIRT pre-alignment Registering fieldmap to structural Running BBR with fieldmap 0.343783 0.998858 0.042228 -0.022346 0.000000 -0.041668 0.998820 0.024966 0.000000 0.023374 -0.024006 0.999438 0.000000 -0.347484 0.804341 2.909863 1.000000 Making warp fields and applying registration to EPI series

mv example_func2highres_fieldmap2str.mat unwarp/FM_UD_fmap_mag_brain2str.mat


mv example_func2highres_fieldmaprads2epi.mat unwarp/FM_UD_fmap2epi.mat


/usr/local/fsl/bin/immv example_func2highres_fieldmaprads2epi_shift unwarp/FM_UD_fmap2epi_shift


/usr/local/fsl/bin/immv example_func2highres_fieldmap2str unwarp/FM_UD_fmap_mag_brain2str


/usr/local/fsl/bin/fslstats FM_UD_fmap2epi_shift -R -P 1 -P 99
-6.134327 7.225882 -1.369861 2.736245

/usr/local/fsl/bin/flirt -ref ../example_func -in FM_UD_fmap_mag_brain -applyxfm -init FM_UD_fmap2epi.mat -out EF_UD_fmap_mag_brain


/usr/local/fsl/bin/fslmaths FM_UD_fmap2epi_shift -mul -1 grot


/usr/local/fsl/bin/overlay 1 0 EF_UD_fmap_mag_brain -a FM_UD_fmap2epi_shift 0.0001 2.736245 grot 0.0001 1.36986 EF_UD_shift+mag


/usr/local/fsl/bin/slicer EF_UD_shift+mag -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png EF_UD_shift+mag.png; rm sl?.png


/bin/cp /usr/local/fsl/etc/luts/ramp.gif .ramp.gif


/bin/cp /usr/local/fsl/etc/luts/ramp2.gif .ramp2.gif


overlay 0 0 FM_UD_fmap_mag_brain2str -a ../example_func2highres_fast_wmedge 0.001 5 fieldmap2edges


/usr/local/fsl/bin/slicer fieldmap2edges -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png fieldmap2edges.png; rm sl?.png


/usr/local/fsl/bin/slicer FM_UD_fmap_mag_brain2str ../highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png FM_UD_fmap_mag_brain2str1.png ; /usr/local/fsl/bin/slicer ../highres FM_UD_fmap_mag_brain2str -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png FM_UD_fmap_mag_brain2str2.png ; /usr/local/fsl/bin/pngappend FM_UD_fmap_mag_brain2str1.png - FM_UD_fmap_mag_brain2str2.png FM_UD_fmap_mag_brain2str.png; /bin/rm -f sl?.png FM_UD_fmap_mag_brain2str2.png


/bin/rm FM_UD_fmap_mag_brain2str1.png


/usr/local/fsl/bin/flirt -ref ../highres -in ../example_func -out example_func_distorted2highres -applyxfm -init ../example_func2highres.mat -interp trilinear


/usr/local/fsl/bin/slicer example_func_distorted2highres ../highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func_distorted2highres1.png ; /usr/local/fsl/bin/slicer ../highres example_func_distorted2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func_distorted2highres2.png ; /usr/local/fsl/bin/pngappend example_func_distorted2highres1.png - example_func_distorted2highres2.png example_func_distorted2highres.png; /bin/rm -f sl?.png example_func_distorted2highres2.png


/bin/rm example_func_distorted2highres1.png


/usr/local/fsl/bin/slicer ../example_func2highres ../highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png ../example_func2highres1.png ; /usr/local/fsl/bin/slicer ../highres ../example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png ../example_func2highres2.png ; /usr/local/fsl/bin/pngappend ../example_func2highres1.png - ../example_func2highres2.png ../example_func2highres.png; /bin/rm -f sl?.png ../example_func2highres2.png


/bin/rm ../example_func2highres1.png


/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat ../example_func2highres.mat 


/usr/local/fsl/bin/applywarp -i ../example_func2highres -r ../example_func --premat=highres2example_func.mat -o example_func_undistorted


/usr/local/fsl/bin/overlay  0 0 example_func_distorted2highres -a ../example_func2highres_fast_wmedge 0.001 10 grot


/usr/local/fsl/bin/slicer grot   -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png EF_D_edges.gif


/usr/local/fsl/bin/overlay  0 0 ../example_func2highres -a ../example_func2highres_fast_wmedge 0.001 10 grot


/usr/local/fsl/bin/slicer grot    -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png EF_U_edges.gif


/usr/local/fsl/bin/whirlgif -o EF_UD_movie.gif -time 50 -loop 0 EF_D_edges.gif EF_U_edges.gif; /bin/rm -f sla* slb* slc* sld* sle* slf* slg* slh* sli* slj* slk* sll* grot*


/usr/local/fsl/bin/imcp example_func_undistorted ../example_func


/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat


/usr/local/fsl/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres1.png ; /usr/local/fsl/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres2.png ; /usr/local/fsl/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png example_func2highres2.png


/bin/rm example_func2highres1.png

did not find file: highres2standard.mat. Generating transform.

/usr/local/fsl/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear 


/usr/local/fsl/bin/fnirt --iout=highres2standard_head --in=highres_head --aff=highres2standard.mat --cout=highres2standard_warp --iout=highres2standard --jout=highres2highres_jac --config=T1_2_MNI152_2mm --ref=standard_head --refmask=standard_mask --warpres=10,10,10


/usr/local/fsl/bin/applywarp -i highres -r standard -o highres2standard -w highres2standard_warp


/usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat


/usr/local/fsl/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard1.png ; /usr/local/fsl/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard2.png ; /usr/local/fsl/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png highres2standard2.png


/bin/rm highres2standard1.png


/usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat


/usr/local/fsl/bin/convertwarp --ref=standard --premat=example_func2highres.mat --warp1=highres2standard_warp --out=example_func2standard_warp


/usr/local/fsl/bin/applywarp --ref=standard --in=example_func --out=example_func2standard --warp=example_func2standard_warp


/usr/local/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat


/usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard1.png ; /usr/local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard2.png ; /usr/local/fsl/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png example_func2standard2.png


/usr/local/fsl/bin/imcp ../example_func ../example_func_distorted


/usr/local/fsl/bin/imcp example_func ../example_func

On Apr 16, 2013, at 1:35 PM, Mark Jenkinson wrote:

Dear Mary,

It is hard to know exactly what went wrong from just this info. Can you send the whole contents of your log file?

All the best,
    Mark


Mary Elizabeth Sutherland <[log in to unmask]> wrote:


Dear Jake,

The log file seems to show that the initialisation, prestats, stats, and registration run (the last lines are in the registration: /usr/local/fsl/bin/imcp ../example_func ../example_func_distorted
/usr/local/fsl/bin/imcp example_func ../example_func
However, in the stats directory in the output I only have
Corrections.nii.gz
dof
logfile
pe1.nii.gz
pe2.nii.gz
res4d.nii.gz
sigmasquareds.nii.gz
smoothness
threshac1.nii.gz

Thank you so much for your help!

~ mary




---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)  2176
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
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