Freesurfer

freesurfer@nmr.mgh.harvard.edu

30076 discussions

(no subject)
by duhanjian＠sohu.com 27 Jun '07

27 Jun '07

hi ,I have solved the the probelm.Now, I have some new question, just as belows:1  In the GUI interface, I can't type the letters ,I don't know why?2 when I choose the volume in the Morphometric-----Measure, the Qdec runs error. how to solve it ? the screenshot on the attachment.3 In the terminal command window, I type the make_average_subject command,It runs errors , show as :limit:decriptors:can't remove limite(operation not permition), how to deal with this bug?Thank you very much!!!

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anat2exf.register.dat missing
by Furlong, Carolyn 27 Jun '07

27 Jun '07

Hi We have run the command reg-feat2anat --debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore which generates several files with matricies in them but the file anat2exf.register.dat is missing. The output is below... tkregister2 popped up, the original surface green outline is not visible and there is a shift (3cm) with respect to the anatomical, I was wondering if the command ran successfully? Any comments and suggestions would be appreciated. Best wishes Carolyn >reg-feat2anat --debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore set echo = 1 ; set debug = 1 ; set debug = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 ) set flag = $argv[1] ; shift ; set flag = --feat shift switch ( $flag ) switch ( --feat ) if ( $#argv == 0 ) goto arg1err ; if ( 3 == 0 ) goto arg1err set FeatDir = $argv[1] ; shift ; set FeatDir = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat shift breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = --subject shift switch ( $flag ) switch ( --subject ) if ( $#argv == 0 ) goto arg1err ; if ( 1 == 0 ) goto arg1err set subject = $argv[1] ; shift ; set subject = AMoore shift breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#FeatDir == 0 ) then if ( 1 == 0 ) then if ( ! -e $FeatDir ) then if ( ! -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat ) then if ( ! $manual ) then if ( ! 0 ) then if ( $#subject == 0 ) then if ( 1 == 0 ) then else else if ( $?SUBJECTS_DIR == 0 ) then if ( 1 == 0 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /disc2/Kate/Flatmap1 ) then if ( ! -e $SUBJECTS_DIR/$subject ) then if ( ! -e /disc2/Kate/Flatmap1/AMoore ) then if ( $manxfm != "func2anat" && $manxfm != "std2anat" && $manxfm != "func2std" ) then if ( func2anat != func2anat && func2anat != std2anat && func2anat != func2std ) then goto check_params_return ; goto check_params_return if ( $?DEV == 0 ) set DEV = "" ; if ( 0 == 0 ) set DEV = set DEV = set TKR = tkregister2 set TKR = tkregister2 if ( $usedev ) set TKR = $DEV/$TKR/$TKR if ( 0 ) set TKR = /tkregister2/tkregister2 set MM = mri_matrix_multiply set MM = mri_matrix_multiply if ( $usedev ) set MM = $DEV/$MM/$MM if ( 0 ) set MM = /mri_matrix_multiply/mri_matrix_multiply echo FeatDir is $FeatDir echo FeatDir is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat FeatDir is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat mkdir -p $FeatDir/reg/freesurfer/tmp mkdir -p /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp set exf2std_fslmat = $FeatDir/reg/example_func2standard.mat set exf2std_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat if ( ! -e $exf2std_fslmat ) then if ( ! -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat ) then set exfbase = $FeatDir/example_func set exfbase = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func if ( -e $exfbase.nii.gz ) then if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz ) then if ( -e $exfbase.nii ) then if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii ) then setenv FSLOUTPUTTYPE NIFTI setenv FSLOUTPUTTYPE NIFTI set fslext = nii ; set fslext = nii endif endif if ( -e $exfbase.img ) then if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.img ) then if ( $#fslext == 0 ) then if ( 1 == 0 ) then set tempvol = $FeatDir/example_func.$fslext set tempvol = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii echo "template volume is $tempvol" echo template volume is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii template volume is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii set anat2exf_regdat = $FeatDir/reg/freesurfer/anat2exf.register.dat set anat2exf_regdat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat set anat2std_regdat = $FeatDir/reg/freesurfer/anat2std.register.dat set anat2std_regdat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat set std2anat_fslmat = $FeatDir/reg/freesurfer/std2anat.fsl.mat set std2anat_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat set exf2anat_init_fslmat = $FeatDir/reg/freesurfer/exf2anat.init.fsl.mat set exf2anat_init_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat set exf2anat_fslmat = $FeatDir/reg/freesurfer/exf2anat.fsl.mat set exf2anat_fslmat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat set std2exf_regdat = $FeatDir/reg/freesurfer/std2exf.register.dat set std2exf_regdat = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2exf.register.dat set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz set refvolcor = /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz if ( ! -e $refvolcor ) then if ( ! -e /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz ) then if ( $manual && $manxfm == func2anat ) then if ( 0 && func2anat == func2anat ) then if ( $manual && $manxfm == std2anat ) then if ( 0 && func2anat == std2anat ) then if ( $manual && $manxfm == func2std ) then if ( 0 && func2anat == func2std ) then set LF = $FeatDir/reg/freesurfer/reg-feat2anat.log set LF = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log if ( -e $LF ) mv $LF $LF.bak if ( -e /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log ) mv /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log.bak mv /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log.bak echo log file is $LF echo log file is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log log file is /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log date | tee -a $LF date tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log Mon Jun 18 13:55:40 BST 2007 pwd | tee -a $LF pwd tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log /disc2/Kate/Flatmap1 echo $0 | tee -a $LF echo /home/progs/freesurfer/bin//reg-feat2anat tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log /home/progs/freesurfer/bin//reg-feat2anat echo $cmdargs | tee -a $LF echo --debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log --debug --feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore uname -a | tee -a $LF uname -a tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 i386 GNU/Linux set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz set refvolcor = /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz if ( ! -e $refvolcor ) then if ( ! -e /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz ) then set refvol = $FeatDir/reg/freesurfer/tmp/anat.$fslext set refvol = /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii set cmd = ( mri_convert $refvolcor $refvol ) set cmd = ( mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii ) echo $cmd | tee -a $LF echo mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii $cmd | & tee -a $LF mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.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 /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii... if ( $status ) then if ( 0 ) then if ( $fslext == img ) then if ( nii == img ) then mri_info --o /tmp/reg-feat2anat.rasgood.$$ --ras_good $FeatDir/example_func.$fslext > & /dev/null mri_info --o /tmp/reg-feat2anat.rasgood.11254 --ras_good /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` ; set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` cat /tmp/reg-feat2anat.rasgood.11254 endif endif echo "example_func ras_good_flag $exf_ras_good" | tee -a $LF echo example_func ras_good_flag tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log example_func ras_good_flag if ( $exf_ras_good ) then if ( ) then echo "-------------------------------------------------------" | tee -a $LF echo ------------------------------------------------------- tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log ------------------------------------------------------- echo "Initializing exf2anat from crude std2anat" | tee -a $LF echo Initializing exf2anat from crude std2anat tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log Initializing exf2anat from crude std2anat set cmd = ( $TKR --targ $refvolcor --mov $FSLDIR/etc/standard/avg152T1_brain.img --reg $anat2std_regdat --fslregout $std2anat_fslmat --regheader ) set cmd = ( tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader ) if ( ! $debug ) set cmd = ( $cmd --noedit ) if ( ! 1 ) set cmd = ( tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader --noedit ) echo $cmd | tee -a $LF echo tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader $cmd | tee -a $LF tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader tee -a /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/reg-feat2anat.log ----------------------------------------------------------------- INFO: could not find /home/progs/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/progs/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- ----------------------------------------------------------------- INFO: could not find /home/progs/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/progs/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- target volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img reg file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat LoadVol 1 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz INFO: changing target type to float 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 /home/progs/fsl/etc/standard/avg152T1_brain.img INFO: changing move type to float 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 ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 30.861; 0.000 -1.000 0.000 -52.627; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 30.861; 0.000 -1.000 0.000 -52.627; 0.000 0.000 0.000 1.000; subject = subject-unknown Zoom Factor = 2 FOV = 256 Opening window subject-unknown Setting scale tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro} tkregister2: interface: /home/progs/freesurfer/lib/tcl/tkregister2.tcl %

2 3

group analysis using mri_glmfit
by T. Song 26 Jun '07

26 Jun '07

Hi Bruce and Nick: I am trying to do group analysis using mri_glmfit. It seems that I have no problem to run mri_glmfit and get the glmdir and all the files. When I load sig.mgh with average surface in tksurfer, I can configure the overlay. When I try to load group descriptor file, a window pop up with the title I defined in the fsgd file. Now, if I click a point in the tksurfer window, tksurfer will crash. I examine the command line, it seems that after the group descriptor file is loaded, tksurfer can not get the vertex number. I tried this on 32 bit machine and 64 bit machine, same result? Would you please give me some suggestion? Thanks! Tao

2 1

metric distortion questions
by Morgan Hough 26 Jun '07

26 Jun '07

Hi there, I would like to ask some questions about metric distortion. 1. Following the Wisco et al (2007) paper, metric distortion is defined as Metric Distortion = k * area of a triangle on a registered sphere / area of triangle on gray/white interface surface which I believe I can compute using mris_jacobian $subject/surf/lh.sphere $subject/surf/lh.sphere.reg $subject/surf/lh.sphere.reg.jacobian The subject 's ?h.sphere.reg is formed from the registration of the inflated sphere of the subject with the Desikan et al. (2006) 40 subject template? From the wiki, I think the command is mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg so the jacobian measure is derived from the parcellation stage (stage3) of recon-all. 2. I would like to extract the k factor for each subject which is defined as k = total surface area of original gray/white interface surface / total surface area of individual sphere do I compute this from the total surface area field of mris_anatomical_stats $subject $hemi orig / mris_anatomical_stats $subject $hemi sphere or do I need to use outputs from different surfaces or extract either value differently? The sphere values look rather uniform and I wanted to check if I am using the right thing. 3. Finally, I see in the study average make_average_surface.log file: setting group surface area to be 1142.0 cm^2 (scale=1.29) and I was wondering what the scale factor represented here. Thanks in advance for your time. Cheers, -Morgan

3 4

linear opaque threshold
by Robert Levy 26 Jun '07

26 Jun '07

Hello, Does anyone know if it is possible to set the overlay threshold to "linear opaque" mode in tksurfer using TCL commands? I looked at the documentation, and I didn't see a method explicitly for that purpose, but maybe there is some way to specify that option. Thanks, Rob

2 1

problems with -clean-bm flag
by Gallo, Antonio (NIH/NINDS) [F] 25 Jun '07

25 Jun '07

Hi All, I'm trying to see how much my thickness measures are affected by my manual edits. When I tried to use the -clean-bm flag with autorecon2 I always got this message: -1): read error mri_em_register: could not open mask volume brainmask.mgz. It seems to me that this flag delete the brainmask.mgz file but doesn't generate a new copy of this file from the brainmask.auto.mgz file. Could you help me with that? Thank you in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

2 1

edit brain lesion?
by Lusineh Gharapetian 25 Jun '07

25 Jun '07

Hello, One of our subjects has a left temporal lobe lesion (which appears on the MRI). But FS does not recognize the lesion. Is there any way to edit this to create better wm and pial surfaces? Attached is an image of the brainmask.mgz view as well as an image of the wm.mgz view. Thanks for you help! -Lusineh

2 1

Cortical surface tessellation and smoothing
by Kai Li 25 Jun '07

25 Jun '07

Dear list, Is there a paper or any documentation describing how freesurfer tessellate and smooth cortical surfaces? In particular, does freesurfer use any specific variety of marching cube isosurface algorithm? Regular surface smoothing (like the Laplacian smoothing) may cause undesired surface shrinking. It looks that freesurfer does a good job on surface smothing. So I'm wondering what smoothing algorithm freesurfer employ. Thanks, Kai

2 1

(no subject)
by duhanjian＠sohu.com 25 Jun '07

25 Jun '07

hi, when I run the qdec & command, the error show as below:wangjian@linux-sner:~> qdec & [1] 10941 wangjian@linux-sner:~> qdec.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory  I do't know  how to deal with this problem. Could you tell me how to resolve this, Thank you!!!

2 1

FS-FAST: missing time frame & time labeling of FIR analyses
by raij＠nmr.mgh.harvard.edu 25 Jun '07

25 Jun '07

Hi, I have done a FIR analysis of event-related data where my time window is 16 TR:s long, consisting of 2 pre-stimulus time frames plus 14 post-stimulus time frames. I view the results with tksurfer. If I load the results from the h-lh.bhdr file, I have all 16 time frames (0-15) which is as it should be. However, if I load one of the contrast stat maps (e.g., cespct-lh.bhdr) I only have 13 time frames (0-12). I should expect 14 time frames (as the two pre-stimulus time frames are not supposed to show up). I therefore have one time frame missing, and I do not know if my time scale is off by one frame or if the last frame is missing. So, which time frame is it that the cepct-lh.bhdr is missing - the 3rd or the 16th? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

1 0

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