oops.. I guess that's what made it, I'm unsure though how that may have
happened..
anyway, to speed it all up I just made a new .fsf file through the
interface and so far it seems to be working correctly.
cheers
martin
Steve Smith wrote:
> Hi - it appears that your design.fsf that you attached is
> incomplete....it ends in the middle of a line?
> Cheers.
>
>
> On 16 Apr 2007, at 19:52, Martin M Monti wrote:
>
>> Hi,
>>
>> I'm piecing together a second level FEAT, but as I load it into the
>> GUI I get the following error.
>>
>> invalid command name "V"
>> invalid command name "V"
>> while executing
>> "V 1 wrt EV 4"
>> (file
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_all.fsf"
>> line 422)
>> invoked from within
>> "source ${filename}"
>> (procedure "feat5:load" line 22)
>> invoked from within
>> "feat5:load .r 1
>> /mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_all.fsf"
>>
>> ("uplevel" body line 1)
>> invoked from within
>> "uplevel #0 $cmd $args"
>>
>> Unfortunately I can't really parse it out, could I please get some
>> help making sense of this?
>>
>> cheers
>>
>> martin
>>
>> PS: I attach the script
>>
>> ----------------------------------------------
>>
>> “Well! I’ve often seen a cat without a grin,” thought Alice, “but a
>> grin without a cat! It’s the most curious thing I ever saw in my
>> life!” [Lewis Carroll, Alice in Wonderland]
>>
>> --------------------------------------------
>> Martin M. Monti
>> Princeton University
>> Department of Psychology
>> Green Hall 3-S-8
>> (609) 258-5679
>> www.webmartin.net
>> --------------------------------------------
>>
>>
>>
>>
>>
>> # FEAT version number
>> set fmri(version) 5.63
>>
>> # Analysis level
>> # 1 : First-level analysis
>> # 2 : Higher-level analysis
>> set fmri(level) 2
>>
>> # Which stages to run
>> # 0 : No first-level analysis (registration and/or group stats only)
>> # 7 : Full first-level analysis
>> # 1 : Pre-Stats
>> # 3 : Pre-Stats + Stats
>> # 2 : Stats
>> # 6 : Stats + Post-stats
>> # 4 : Post-stats
>> set fmri(analysis) 6
>>
>> # Delay before starting (hours)
>> set fmri(delay) 0
>>
>> # Use relative filenames
>> set fmri(relative_yn) 0
>>
>> # Balloon help
>> set fmri(help_yn) 1
>>
>> # Run Featwatcher
>> set fmri(featwatcher_yn) 1
>>
>> # Cleanup first-level standard-space images
>> set fmri(sscleanup_yn) 0
>>
>> # Output directory
>> set fmri(outputdir) "DB_All"
>>
>> # TR(s)
>> set fmri(tr) 3
>>
>> # Total volumes
>> set fmri(npts) 36
>>
>> # Delete volumes
>> set fmri(ndelete) 0
>>
>> # Perfusion tag/control order
>> set fmri(tagfirst) 1
>>
>> # Number of first-level analyses
>> set fmri(multiple) 36
>>
>> # Higher-level input type
>> # 1 : Inputs are lower-level FEAT directories
>> # 2 : Inputs are cope images from FEAT directories
>> set fmri(inputtype) 2
>>
>> # Carry out pre-stats processing?
>> set fmri(filtering_yn) 0
>>
>> # Brain/background threshold, %
>> set fmri(brain_thresh) 10
>>
>> # Critical z for design efficiency calculation
>> set fmri(critical_z) 5.3
>>
>> # Noise level
>> set fmri(noise) 0.66
>>
>> # Noise AR(1)
>> set fmri(noisear) 0.34
>>
>> # Post-stats-only directory copying
>> # 0 : Overwrite original post-stats results
>> # 1 : Copy original FEAT directory for new Contrasts, Thresholding,
>> Rendering
>> set fmri(newdir_yn) 0
>>
>> # Motion correction
>> # 0 : None
>> # 1 : MCFLIRT
>> set fmri(mc) 1
>>
>> # Spin-history (currently obsolete)
>> set fmri(sh_yn) 0
>>
>> # B0 fieldmap unwarping?
>> set fmri(regunwarp_yn) 0
>>
>> # EPI dwell time (ms)
>> set fmri(dwell) 0.7
>>
>> # EPI TE (ms)
>> set fmri(te) 35
>>
>> # % Signal loss threshold
>> set fmri(signallossthresh) 10
>>
>> # Unwarp direction
>> set fmri(unwarp_dir) y-
>>
>> # Slice timing correction
>> # 0 : None
>> # 1 : Regular up (0, 1, 2, 3, ...)
>> # 2 : Regular down
>> # 3 : Use slice order file
>> # 4 : Use slice timings file
>> # 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )
>> set fmri(st) 0
>>
>> # Slice timings file
>> set fmri(st_file) ""
>>
>> # BET brain extraction
>> set fmri(bet_yn) 1
>>
>> # Spatial smoothing FWHM (mm)
>> set fmri(smooth) 5
>>
>> # Intensity normalization
>> set fmri(norm_yn) 0
>>
>> # Perfusion subtraction
>> set fmri(perfsub_yn) 0
>>
>> # Highpass temporal filtering
>> set fmri(temphp_yn) 1
>>
>> # Lowpass temporal filtering
>> set fmri(templp_yn) 0
>>
>> # MELODIC ICA data exploration
>> set fmri(melodic_yn) 0
>>
>> # Carry out main stats?
>> set fmri(stats_yn) 1
>>
>> # Carry out prewhitening?
>> set fmri(prewhiten_yn) 1
>>
>> # Add motion parameters to model
>> # 0 : No
>> # 1 : Yes, orthogonalise rest of model wrt motion
>> # 2 : Yes, orthogonalise motion wrt rest of model
>> # 3 : Yes, don't orthogonalise
>> set fmri(motionevs) 0
>>
>> # Higher-level modelling
>> # 3 : Fixed effects
>> # 0 : Mixed Effects: Simple OLS
>> # 2 : Mixed Effects: FLAME 1
>> # 1 : Mixed Effects: FLAME 1+2
>> set fmri(mixed_yn) 2
>>
>> # Number of EVs
>> set fmri(evs_orig) 1
>> set fmri(evs_real) 1
>>
>> # Number of contrasts
>> set fmri(ncon_orig) 1
>> set fmri(ncon_real) 1
>>
>> # Number of F-tests
>> set fmri(nftests_orig) 0
>> set fmri(nftests_real) 0
>>
>> # Add constant column to design matrix? (obsolete)
>> set fmri(constcol) 0
>>
>> # Carry out post-stats steps?
>> set fmri(poststats_yn) 1
>>
>> # Pre-threshold masking?
>> set fmri(threshmask) ""
>>
>> # Thresholding
>> # 0 : None
>> # 1 : Uncorrected
>> # 2 : Voxel
>> # 3 : Cluster
>> set fmri(thresh) 3
>>
>> # P threshold
>> set fmri(prob_thresh) 0.05
>>
>> # Z threshold
>> set fmri(z_thresh) 2.3
>>
>> # Z min/max for colour rendering
>> # 0 : Use actual Z min/max
>> # 1 : Use preset Z min/max
>> set fmri(zdisplay) 0
>>
>> # Z min in colour rendering
>> set fmri(zmin) 2
>>
>> # Z max in colour rendering
>> set fmri(zmax) 8
>>
>> # Colour rendering type
>> # 0 : Solid blobs
>> # 1 : Transparent blobs
>> set fmri(rendertype) 1
>>
>> # Background image for higher-level stats overlays
>> # 1 : Mean highres
>> # 2 : First highres
>> # 3 : Mean functional
>> # 4 : First functional
>> # 5 : Standard space template
>> set fmri(bgimage) 1
>>
>> # Registration?
>> set fmri(reg_yn) 0
>>
>> # Registration to initial structural
>> set fmri(reginitial_highres_yn) 0
>>
>> # Search space for registration to initial structural
>> # 0 : No search
>> # 90 : Normal search
>> # 180 : Full search
>> set fmri(reginitial_highres_search) 90
>>
>> # Degrees of Freedom for registration to initial structural
>> set fmri(reginitial_highres_dof) 12
>>
>> # Do nonlinear registration to initial structural?
>> set fmri(reginitial_highres_nonlinear_yn) 0
>>
>> # Registration to main structural
>> set fmri(reghighres_yn) 0
>>
>> # Search space for registration to main structural
>> # 0 : No search
>> # 90 : Normal search
>> # 180 : Full search
>> set fmri(reghighres_search) 90
>>
>> # Degrees of Freedom for registration to main structural
>> set fmri(reghighres_dof) 12
>>
>> # Do nonlinear registration to main structural?
>> set fmri(reghighres_nonlinear_yn) 0
>>
>> # Registration to standard image?
>> set fmri(regstandard_yn) 1
>>
>> # Standard image
>> set fmri(regstandard)
>> "/usr/csbmb/pkg/FSL/fsl/bindist/etc/standard/avg152T1_brain.hdr"
>>
>> # Search space for registration to standard space
>> # 0 : No search
>> # 90 : Normal search
>> # 180 : Full search
>> set fmri(regstandard_search) 90
>>
>> # Degrees of Freedom for registration to standard space
>> set fmri(regstandard_dof) 12
>>
>> # Do nonlinear registration to standard space?
>> set fmri(regstandard_nonlinear_yn) 0
>>
>> # High pass filter cutoff
>> set fmri(paradigm_hp) 100
>>
>> # Number of lower-level copes feeding into higher-level analysis
>> set fmri(ncopeinputs) 0
>>
>> # 4D AVW data or FEAT directory (1)
>> set feat_files(1)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope1.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (2)
>> set feat_files(2)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope2.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (3)
>> set feat_files(3)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope3.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (4)
>> set feat_files(4)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope4.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (5)
>> set feat_files(5)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope5.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (6)
>> set feat_files(6)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope6.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (7)
>> set feat_files(7)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope7.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (8)
>> set feat_files(8)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope8.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (9)
>> set feat_files(9)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope9.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (10)
>> set feat_files(10)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope1.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (11)
>> set feat_files(11)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope2.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (12)
>> set feat_files(12)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope3.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (13)
>> set feat_files(13)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope4.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (14)
>> set feat_files(14)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope5.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (15)
>> set feat_files(15)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope6.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (16)
>> set feat_files(16)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope7.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (17)
>> set feat_files(17)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope8.nii.gz"
>>
>>
>> # 4D AVW data or FEAT directory (18)
>> set feat_files(18)
>> "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope9.nii.gz"
>>
>>
>> # 4D AVW d
>
>
> ---------------------------------------------------------------------------
>
> 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)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
--
--------------------------------------------
“Well! I’ve often seen a cat without a grin,” thought Alice, “but a grin without a cat! It’s the most curious thing I ever saw in my life!” [Lewis Carroll, Alice in Wonderland]
--------------------------------------------
Martin M. Monti
Princeton University
Department of Psychology
Green Hall 3-S-8
(609) 258-5679
www.webmartin.net
--------------------------------------------
|
