Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

PETsurfer AC/TOF
by Fu, Jason (NIH/NINDS) [F] 13 Jul '17

13 Jul '17

Hi, I am currently using PETsurfer PVC to determine glucose metabolism differences in certain structures between the brain hemispheres. I am currently using ac/tof files to coregister to the anatomy. One of the patients did not have the ac/tof files, would ac/hd files work instead? Thanks, Jason Fu

2 3

Re: [Freesurfer] Simple math with freesurfer surfaces
by Van Der Deijl, Rosanne 13 Jul '17

13 Jul '17

Dear Doug, Thanks for replying about fscalc. I read in the documentation that the two input files should typically be generated on the same subject. What I want to do is to add all the thickness .mgh files from my subjects together into one file. Is this possible with fscalc or another way? Right now I get an error about a size mismatch. Thank you again! Kind regards, Rose ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Thursday, July 13, 2017 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 23 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: UPDATE: Matlab Problem LME (Diers, Kersten /DZNE) 2. Re: mri_glmfit-sim ERROR cannot find mc-z.csd file (Douglas N Greve) 3. Re: Subject with missing fMRI data {Disarmed} (Douglas N Greve) 4. Re: Running segmentation on spatially normalized data (Douglas N Greve) 5. Re: asegstats2table error (Douglas N Greve) 6. Re: Strange Discrepancy Between Activation Location on Surface vs. Volume (Douglas N Greve) 7. Re: Qdec error in analysis (Douglas N Greve) 8. Re: petsurfer stats for multiple segmentations (Douglas N Greve) 9. Re: Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0 (Douglas N Greve) 10. Re: Subject with missing fMRI data {Disarmed} (Sadie Marvel) 11. Re: Pial surface editing (Michelle VanTieghem) 12. Differences in volume between mri_segstats and mris_anatomical_stats (Bruss, Joel E) 13. Re: dmri_pathstats error (Yuwen Hung) 14. Re: dmri_pathstats error (Yuwen Hung) 15. Re: Pial surface editing (Bruce Fischl) 16. Re: petsurfer stats for multiple segmentations (Lu Zhao) 17. Re: Subject with missing fMRI data {Disarmed} (Douglas N Greve) 18. Re: petsurfer stats for multiple segmentations (Douglas N Greve) 19. Re: Differences in volume between mri_segstats and mris_anatomical_stats (Douglas N Greve) 20. Re: mkbrainmask-sess: couldn't find register.dof6.lta (Douglas N Greve) 21. Re: Subject with missing fMRI data {Disarmed} (Sadie Marvel) 22. Re: How to edit Fsgdf4G2V about the group.effect.mtx (Douglas N Greve) 23. TAR fs files (Schumman Resonance) 24. Re: BBRegister + partial FoV fail (Douglas N Greve) 25. Re: GLM question (Douglas N Greve) 26. Re: Simple math with freesurfer surfaces (Douglas N Greve) 27. Re: TAR fs files (Douglas N Greve) 28. Re: smoothing data (Douglas N Greve) 29. Re: smoothing data (Matt Glasser) 30. Re: TAR fs files (Bruce Fischl) 31. Re: TAR fs files (Schumman Resonance) 32. Re: How to edit Fsgdf4G2V about the group.effect.mtx (haidong wang) 33. Re: How to edit Fsgdf4G2V about the group.effect.mtx (Douglas Greve) 34. Re: BBRegister + partial FoV fail (Paul Glad Mihai) 35. 3G1V.fsgd (stdp82(a)virgilio.it) 36. FS 6.0 (Del Re, Elisabetta) 37. Re: FS 6.0 (Bruce Fischl) 38. Re: [External] Re: Differences in volume between mri_segstats and mris_anatomical_stats (Bruss, Joel E) 39. Pediatric Atlas/Template (Jessica Reynolds) 40. Pediatric Atlas/Template (Jessica Reynolds) 41. Pediatric Atlas/Template (Jessica Reynolds) 42. GLM Analysis Number of vertices and Area (Aman Montazeri) ---------------------------------------------------------------------- Message: 1 Date: Wed, 12 Jul 2017 18:14:58 +0200 From: "Diers, Kersten /DZNE" <Kersten.Diers(a)dzne.de> Subject: Re: [Freesurfer] UPDATE: Matlab Problem LME To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1327935B-0065-4A56-98A8-8AF8F4DED407(a)dzne.de> Content-Type: text/plain; charset="us-ascii" Hi Clara, thanks for the additional information, this is helpful! If you are calling the scripts with [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere, lhRe, lhTh0, lhcortex, 2, 95); then 'lhcortex' will contain the analysis mask, i.e. indices for those vertices for which the analysis will be performed. 'lhcortex' should already be a subset of the vertices specified by 'lhsphere', i.e. excluding some portions of the medial wall. If you have zero-valued columns in your data matrix, one thing worth trying is to remove the corresponding indices from 'lhcortex', i.e. further restrict the analysis mask. This should be done before the initial covariance estimation, i.e. prior to calling lme_mass_fit_init or lme_mass_fit_EMinit. In addition, it is of course worthwhile to investigate the cause of the zero-columns. Best, Kersten ------------------------------ Message: 2 Date: Wed, 12 Jul 2017 12:17:45 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <a1d5416e-5e09-d7ab-e2c1-10c802dbe8be(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Is this for a volume analysis? If so, then you'll need to use the --grf option instead of using the mcz simulations (those are just for surface) On 07/08/2017 01:03 PM, Aly Negreira wrote: > Hi Doug! > > Thank you for the reply! Re-ran w/ --debug as first option. Below is > the output. Not sure if this is helpful, but when I cd to > /Applications/freesurfer/average/mult-comp-cor/fsaverage > there are only directories for lh and rh, nothing for mni. > > Thanks for the help! > > Aly > > Alysons-iMac:~/analyses/EMOT_REG_FX_DISS] aneg% mri_glmfit-sim \ > --debug \ > > --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > \ > > --cache 1.3 abs \ > > --cwp 0.05\ > > --3spaces \? --debug \ > > ? --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > \ > > ? --cache 1.3 abs \ > > ? --cwp 0.05\ > > ? --3spaces \ > > ? > > set echo = 1 ; > > breaksw > > breaksw > > > end > > end > > while ( $#argv != 0 ) > > while ( 8 != 0 ) > > > set flag = $argv[1] ; shift ; > > set flag = --glmdir > > shift > > > switch ( $flag ) > > switch ( --glmdir ) > > if ( $#argv < 0 ) goto arg1err ; > > if ( 7 < 0 ) goto arg1err > > set glmdir = $argv[1] ; shift ; > > set glmdir = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > > shift > > breaksw > > breaksw > > > end > > end > > while ( $#argv != 0 ) > > while ( 6 != 0 ) > > > set flag = $argv[1] ; shift ; > > set flag = --cache > > shift > > > switch ( $flag ) > > switch ( --cache ) > > if ( $#argv < 2 ) goto arg2err ; > > if ( 5 < 2 ) goto arg2err > > set thresh = $argv[1] ; shift ; > > set thresh = 1.3 > > shift > > set simsign = $argv[1] ; shift ; > > set simsign = abs > > shift > > set UseCache = 1 ; > > set UseCache = 1 > > set DoSim = 0 ; > > set DoSim = 0 > > set thresh = `printf %2.1f $thresh` > > set thresh = `printf %2.1f $thresh` > > printf %2.1f 1.3 > > if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != > 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then > > if ( 1.3 != 1.3 && 1.3 != 2.0 && 1.3 != 2.3 && 1.3 != 3.0 && 1.3 != > 3.3 && 1.3 != 4.0 ) then > > breaksw > > breaksw > > > end > > end > > while ( $#argv != 0 ) > > while ( 3 != 0 ) > > > set flag = $argv[1] ; shift ; > > set flag = --cwp > > shift > > > switch ( $flag ) > > switch ( --cwp ) > > case "--cwpvalthresh": > > case --cwpvalthresh: > > if ( $#argv < 1 ) goto arg1err ; > > if ( 2 < 1 ) goto arg1err > > set cwpvalthresh = $argv[1] ; shift ; > > set cwpvalthresh = 0.05 > > shift > > breaksw > > breaksw > > > end > > end > > while ( $#argv != 0 ) > > while ( 1 != 0 ) > > > set flag = $argv[1] ; shift ; > > set flag = --3spaces > > shift > > > switch ( $flag ) > > switch ( --3spaces ) > > set Bonferroni = 3 ; > > set Bonferroni = 3 > > 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 ( $#glmdir == 0 ) then > > if ( 1 == 0 ) then > > if ( $DoSim ) then > > if ( 0 ) then > > > if ( $DiagCluster && $DoBackground ) then > > if ( 0 && 0 ) then > > if ( $DiagCluster && $DoPBSubmit ) then > > if ( 0 && 0 ) then > > if ( $DiagCluster && $DoSim == 0 ) then > > if ( 0 && 0 == 0 ) then > > > goto check_params_return ; > > goto check_params_return > > > if ( ! -e $glmdir ) then > > if ( ! -e > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > ) then > > > set glmfitlog = $glmdir/mri_glmfit.log > > set glmfitlog = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > > if ( ! -e $glmfitlog ) then > > if ( ! -e > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > ) then > > > set mask = `stem2fname $glmdir/mask` > > set mask = `stem2fname $glmdir/mask` > > stem2fname > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mask > > if ( $status ) then > > if ( 0 ) then > > > if ( $nulltype != perm ) then > > if ( != perm ) then > > set fwhmfile = $glmdir/fwhm.dat > > set fwhmfile = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat > > if ( ! -e $fwhmfile ) then > > if ( ! -e > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat > ) then > > > set fwhm = `cat $fwhmfile` ; > > set fwhm = `cat $fwhmfile` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat > > else > > else > > > set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'` > > set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > > awk {if($1 == "cwd") print $2} > > if ( ! -e $glmfitcwd ) then > > if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS ) then > > > set anattype = volume ; > > set anattype = volume > > set subject = ( ) ; > > set subject = ( ) > > set hemi = ( ) ; > > set hemi = ( ) > > set surf = "white" ; > > set surf = white > > set y = ( ) ; > > set y = ( ) > > set wls = ( ) ; > > set wls = ( ) > > > set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'` > > set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > > awk {if($1 == "cwd") print $2} > > > > set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'` > > set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log > > awk {if($1 == "cmdline") print $0} > > set glmfitcmd = ( $glmfitcmd0 ) ; > > set glmfitcmd = ( cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz ) > > echo $glmfitcmd > > echo cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz > > cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz > > set gd2mtx = dods > > set gd2mtx = dods > > set label = ( ) ; > > set label = ( ) > > while ( $#glmfitcmd ) > > while ( 10 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = cmdline > > shift glmfitcmd > > > switch ( $flag ) > > switch ( cmdline ) > > case "mri_glmfit" > > case mri_glmfit > > case "--osgm" > > case --osgm > > case "--prune" > > case --prune > > case "--no-prune" > > case --no-prune > > case "--pca" > > case --pca > > case "--synth" > > case --synth > > case "--allowsubjrep" > > case --allowsubjrep > > case "--illcond" > > case --illcond > > case "--debug" > > case --debug > > case "--synth" > > case --synth > > case "--cortex" > > case --cortex > > case "--kurtosis" > > case --kurtosis > > case "--nii" > > case --nii > > case "--nii.gz" > > case --nii.gz > > case "--rescale-x" > > case --rescale-x > > case "--no-rescale-x" > > case --no-rescale-x > > case "dods" > > case dods > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 9 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = mri_glmfit > > shift glmfitcmd > > > switch ( $flag ) > > switch ( mri_glmfit ) > > case "--osgm" > > case --osgm > > case "--prune" > > case --prune > > case "--no-prune" > > case --no-prune > > case "--pca" > > case --pca > > case "--synth" > > case --synth > > case "--allowsubjrep" > > case --allowsubjrep > > case "--illcond" > > case --illcond > > case "--debug" > > case --debug > > case "--synth" > > case --synth > > case "--cortex" > > case --cortex > > case "--kurtosis" > > case --kurtosis > > case "--nii" > > case --nii > > case "--nii.gz" > > case --nii.gz > > case "--rescale-x" > > case --rescale-x > > case "--no-rescale-x" > > case --no-rescale-x > > case "dods" > > case dods > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 8 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --y > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --y ) > > set y = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ; > > set y = > /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > > shift glmfitcmd > > if ( ! -e $y ) then > > if ( ! -e > /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > ) then > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 6 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --wls > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --wls ) > > set wls = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ; > > set wls = > /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > > shift glmfitcmd > > if ( ! -e $wls ) then > > if ( ! -e > /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > ) then > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 4 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --osgm > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --osgm ) > > case "--prune" > > case --prune > > case "--no-prune" > > case --no-prune > > case "--pca" > > case --pca > > case "--synth" > > case --synth > > case "--allowsubjrep" > > case --allowsubjrep > > case "--illcond" > > case --illcond > > case "--debug" > > case --debug > > case "--synth" > > case --synth > > case "--cortex" > > case --cortex > > case "--kurtosis" > > case --kurtosis > > case "--nii" > > case --nii > > case "--nii.gz" > > case --nii.gz > > case "--rescale-x" > > case --rescale-x > > case "--no-rescale-x" > > case --no-rescale-x > > case "dods" > > case dods > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 3 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --glmdir > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --glmdir ) > > case "--o" > > case --o > > case "--C" > > case --C > > case "--X" > > case --X > > case "--w" > > case --w > > case "--fwhm" > > case --fwhm > > case "--mask" > > case --mask > > case "--seed" > > case --seed > > case "--var-fwhm" > > case --var-fwhm > > case "--yffxvar" > > case --yffxvar > > case "--ffxdof" > > case --ffxdof > > case "--ffxdofdat" > > case --ffxdofdat > > shift glmfitcmd ; > > shift glmfitcmd > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 1 ) > > set flag = $glmfitcmd[1] ; shift glmfitcmd ; > > set flag = --nii.gz > > shift glmfitcmd > > > switch ( $flag ) > > switch ( --nii.gz ) > > case "--rescale-x" > > case --rescale-x > > case "--no-rescale-x" > > case --no-rescale-x > > case "dods" > > case dods > > breaksw > > breaksw > > end > > end > > while ( $#glmfitcmd ) > > while ( 0 ) > > > if ( $UseGRF && $anattype != volume ) then > > if ( 0 && volume != volume ) then > > if ( $UseGRF ) then > > if ( 0 ) then > > > if ( $#subjectOverride ) set subject = $subjectOverride > > if ( 0 ) set subject = > > > > if ( $#subject != 0 ) then > > if ( 0 != 0 ) then > > > > if ( $#tmpdir == 0 ) set tmpdir = $glmdir/tmp.mri_glmfit-sim-$$ > > if ( 0 == 0 ) set tmpdir = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128 > > set tmpdir = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128 > > mkdir -p $tmpdir > > mkdir -p > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128 > > set clist = ( $glmdir/*/C.dat ) > > set clist = ( > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//*/C.dat > ) > > if ( $status ) then > > if ( 0 ) then > > set clist2 = ( ) ; > > set clist2 = ( ) > > set conlist = ( ) ; > > set conlist = ( ) > > foreach c ( $clist ) > > foreach c ( > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat > ) > > set tmp = `dirname $c` > > set tmp = `dirname $c` > > dirname > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat > > set conname = `basename $tmp` > > set conname = `basename $tmp` > > basename > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm > > set conlist = ( $conlist $conname ) ; > > set conlist = ( osgm ) > > set confile = $tmpdir/$conname.mtx > > set confile = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx > > cp $c $confile > > cp > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx > > set clist2 = ( $clist2 --C $confile ) ; > > set clist2 = ( --C > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx > ) > > > > set sig = `stem2fname $glmdir/$conname/sig` > > set sig = `stem2fname $glmdir/$conname/sig` > > stem2fname > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/sig > > if ( $status ) then > > if ( 0 ) then > > > > if ( $DoSim ) then > > if ( 0 ) then > > end > > end > > > set StartDate = `date` > > set StartDate = `date` > > date > > > > if ( $#LF == 0 ) then > > if ( 0 == 0 ) then > > if ( $UseCache == 0 ) then > > if ( 1 == 0 ) then > > > set LF = $glmdir/cache.mri_glmfit-sim.log > > set LF = > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > endif > > endif > > rm -f $LF > > rm -f > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > endif > > endif > > echo "log file is $LF" > > echo log file is > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > log file is > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > > echo "" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo > > > echo "cd `pwd`" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo cd `pwd` > > pwd > > cd /Users/aneg/analyses/EMOT_REG_FX_DISS > > echo $0 | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo /Applications/freesurfer/bin/mri_glmfit-sim > > /Applications/freesurfer/bin/mri_glmfit-sim > > echo $inputargs | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo --debug --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --cache 1.3 abs --cwp 0.05 --3spaces > > --debug --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --cache 1.3 abs --cwp 0.05 --3spaces > > echo "" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo > > > echo $VERSION | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ > > $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ > > date | tee -a $LF > > date > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > Sat Jul 8 12:57:27 EDT 2017 > > uname -a | tee -a $LF > > uname -a > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > Darwin Alysons-iMac.local 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr > 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 > > echo $user | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo aneg > > aneg > > echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS > > setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS > > echo "FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo FREESURFER_HOME /Applications/freesurfer > > FREESURFER_HOME /Applications/freesurfer > > echo "" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo > > > echo "Original mri_glmfit command line:" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo Original mri_glmfit command line: > > Original mri_glmfit command line: > > echo $glmfitcmd0 | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz > > cmdline mri_glmfit --y > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz > --wls > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz > --osgm --glmdir > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ > --nii.gz > > echo "" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo > > > echo "DoSim = $DoSim" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DoSim = 0 > > DoSim = 0 > > echo "UseCache = $UseCache" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo UseCache = 1 > > UseCache = 1 > > echo "DoPoll = $DoPoll" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DoPoll = 0 > > DoPoll = 0 > > echo "DoPBSubmit = $DoPBSubmit" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DoPBSubmit = 0 > > DoPBSubmit = 0 > > echo "DoBackground = $DoBackground" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DoBackground = 0 > > DoBackground = 0 > > echo "DiagCluster = $DiagCluster" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo DiagCluster = 0 > > DiagCluster = 0 > > echo "gd2mtx = $gd2mtx" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo gd2mtx = dods > > gd2mtx = dods > > if ( $#Seed ) echo "Seed = $Seed" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > if ( 0 ) echo Seed = > > echo "fwhm = $fwhm" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo fwhm = 9.625207 > > fwhm = 9.625207 > > if ( $#fwhmOverride ) then > > if ( 0 ) then > > > if ( $UseCache ) then > > if ( 1 ) then > > set fwhm = `cat $glmdir/fwhm.dat` ; > > set fwhm = `cat $glmdir/fwhm.dat` > > cat > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat > > set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+.5 ) ) "` > > set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+.5 ) ) "` > > perl -e printf('%02d',int ( 9.625207+.5 ) ) > > set threshStr = `perl -e "print 10*$thresh"` ; > > set threshStr = `perl -e "print 10*$thresh"` > > perl -e print 10*1.3 > > set csdCache = > $CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd > > set csdCache = > /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd > > if ( ! -e $csdCache ) then > > if ( ! -e > /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd > ) then > > echo "ERROR: cannot find $csdCache" | tee -a $LF > > tee -a > GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log > > echo ERROR: cannot find > /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd > > ERROR: cannot find > /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd > > exit 1 ; > > exit 1 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 3 Date: Wed, 12 Jul 2017 12:19:17 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed} To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5f1ae473-c099-44f9-396d-cff4730d1883(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=UTF-8; format=flowed it might not be possible to use the frame mask with wls. Does it work without it? On 07/09/2017 04:46 PM, Sadie Marvel wrote: > So now that I am using --no-prune, I'm getting this error: > group wrfx error: MRInormWeights: value less than or eq to 0. > ?I found another thread in the mailing list about this error saying > that there may be values in cesvar.nii that are =0, and that pruning > normally masks out these values. But here, I am trying to use my own > masks to do so. Is it possible now that my masks and my --y input have > different sizes? If so, how can I solve this? > ------------------------------------------------------------------------ > *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas Greve > <greve(a)nmr.mgh.harvard.edu> > *Sent:* Friday, July 7, 2017 11:57 AM > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Subject with missing fMRI data {Disarmed} > > Add --no-prune > > > On 7/7/17 11:38 AM, Sadie Marvel wrote: >> >> ?When I use a script like this, >> >> mri_glmfit --y ces.nii --wls cesvar.nii --osgm --frame-mask masks.nii >> --surface fsaverage rh --glmdir my-glm2.wls --nii.gz? >> >> using the individual binary masks for all the subjects, the command >> seems to revert to using mask.nii, the single mask that was averaged >> over subjects. The output then just looks like it was using the >> single mask instead of being subject specific. Any idea why? >> >> >> >> ------------------------------------------------------------------------ >> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas Greve >> <greve(a)nmr.mgh.harvard.edu> >> *Sent:* Thursday, July 6, 2017 12:58 PM >> *To:* freesurfer(a)nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] Subject with missing fMRI data {Disarmed} >> >> yes >> >> >> On 7/6/17 12:50 PM, Sadie Marvel wrote: >>> >>> From using isxconcat-sess to concatenate all of my subjects >>> together, the command creates binary masks called masks.nii and >>> mask.nii, masks.nii being all of the binary masks for each subject. >>> Is this what I would use with --frame-mask? >>> >>> >>> Thanks, >>> >>> Sadie >>> >>> ------------------------------------------------------------------------ >>> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas Greve >>> <greve(a)nmr.mgh.harvard.edu> >>> *Sent:* Wednesday, July 5, 2017 7:28 PM >>> *To:* freesurfer(a)nmr.mgh.harvard.edu >>> *Subject:* Re: [Freesurfer] Subject with missing fMRI data >>> >>> We don't have any tools to do imputation. It is possible to have a >>> subject specific mask with the --frame-mask option to mri_glmfit. >>> The frame mask must be the same size as the input (--y) with 1s and >>> 0s to indicate whether a given voxel for a given subject should be >>> included in the model. I've not been happy with this method as it >>> can create some strange results as different voxels will now have >>> different DOFs. >>> >>> >>> On 6/29/17 8:49 AM, Sadie Marvel wrote: >>>> >>>> Hi List, >>>> >>>> >>>> I am currently doing a group analysis of 26 subjects, one of which >>>> has missing fMRI data where the signal cuts off through parts of >>>> the occipital and temporal lobes. I was wondering if freesurfer has >>>> any way of dealing with this, such as multiple imputation, or other >>>> methods of filling the missing data. Alternatively, is there a way >>>> to only use the portions of the brain that have data when doing >>>> mri_glmfit? Does freesurfer do this automatically? >>>> >>>> >>>> Thanks. >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> *MailScanner has detected a possible fraud attempt from >>>> "urldefense.proofpoint.com" claiming to be* >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> *MailScanner has detected a possible fraud attempt from >>> "urldefense.proofpoint.com" claiming to be* >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "urldefense.proofpoint.com" claiming to be* >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 4 Date: Wed, 12 Jul 2017 12:23:53 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Running segmentation on spatially normalized data To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <9c6996a8-dbd2-8c58-4f06-ae7cc2c6ae8f(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed sorry, I don't know anything about .tlrc files (or much about AFNI). If the transform is linear, then you should be able to map between the spaces with mri_vol2vol or mri_label2vol, but you will need to get the transform into a FS-compatible format. On 07/06/2017 01:50 PM, Lauren Stephanie Hopkins wrote: > > Hi all: > > > We ran FreeSurfer's recon sequence of anatomy files that had already > been aligned to the MNI template - so spatially normalized. We're > doing all of our processing in AFNI and the resulting segmentation > output files open in AFNI's orig space, not in tlrc space. So > basically we can't overlay the segmentation files on our anat+tlrc > files where they should already be aligned to each other. When we > converted the file to a .tlrc file with the AFNI command 3dcopy we > could then overlay the mask on the normalized anatomy but it was no > longer aligned. > > > So I suppose my question is - is there any way to have the > segmentation files maintain their positioning or output in .tlrc space > so they are still aligned to our anatomy files? > > Thanks for any insight. > > Lauren > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 5 Date: Wed, 12 Jul 2017 12:27:20 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] asegstats2table error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <614c9872-917a-9eb3-748e-12c1247ec242(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Not sure what the problem is, but it might be something specific to your site (looks like it cannot find the proper libraries to import). Can you run it at all. Eg, if just run the script without any arguments, do you get the same thing? What about if you run it with -h ? On 07/06/2017 03:33 AM, Elizabeth Dao wrote: > Dear experts, > > I have completed recon-all with no errors. Now I would like to use the > 'asegstats2table' command but I've received the error below. I would > appreciate any help in solving this problem. I am using FreeSurfer > v6.0.0 on a Linux CentOS machine. > > [TLA@CogmobCentOS MCI]$ asegstats2table --subjects 201.MR1 202.MR1 > 203.MR1 --meas volume --tablefile aseg_stats_all.txt > 'import site' failed; use -v for traceback > Traceback (most recent call last): > File "/home/TLA/Desktop/Liz/freesurfer6/bin/asegstats2table", line > 4, in <module> > import os > File "/usr/local/lib/python2.7/os.py", line 398, in <module> > import UserDict > File "/usr/local/lib/python2.7/UserDict.py", line 84, in <module> > _abcoll.MutableMapping.register(IterableUserDict) > File "/usr/local/lib/python2.7/abc.py", line 109, in register > if issubclass(subclass, cls): > File "/usr/local/lib/python2.7/abc.py", line 184, in __subclasscheck__ > cls._abc_negative_cache.add(subclass) > File "/usr/local/lib/python2.7/_weakrefset.py", line 84, in add > self.data.add(ref(item, self._remove)) > TypeError: cannot create weak reference to 'classobj' object > > Thank you in advance for your help! > > Liz > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 6 Date: Wed, 12 Jul 2017 12:32:02 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Strange Discrepancy Between Activation Location on Surface vs. Volume To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <7e0e01ff-08b1-636d-bdf7-aec2586ea290(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Hi Johnmark, sorry, I can't reconstruct the thread from the earlier emails. Can you resubmit with just the thread from your email and not all 29 threads from July 5? thanks doug On 07/06/2017 02:00 PM, Taylor, Johnmark wrote: > The subject name when I call tksurfer, the subject name when I call > tkmedit, and the subject name in the registration file are all exactly > the same: red_badger. One thing I noticed is that in the left > hemisphere everything seems normal (the activation is in the expected > location); things only look weird in the right hemisphere. There's no > possibility that the surface reconstruction could have been off the > mark? Though it seems implausible that it would take the IPS and > somehow warp it all the way onto the medial surface of the brain... > > Here are pictures of both the volume and surface views of the > activation in question (it's the medial patch on the surface view, the > patch with the red cursor in the volume view), in case they didn't > load before for some reason. > > ????https://ibb.co/b8HFCv > https://ibb.co/cWYcQF > > On Thu, Jul 6, 2017 at 12:00 PM, > <freesurfer-request(a)nmr.mgh.harvard.edu > <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > <mailto:freesurfer-request@nmr.mgh.harvard.edu> > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > <mailto:freesurfer-owner@nmr.mgh.harvard.edu> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: error message while using autorecon1 (Hoopes, Andrew) > 2. Re: error message while using autorecon1 (Buckless, Colleen) > 3. Re: Additional surface area (Bruce Fischl) > 4. Fwd: remove skull from gtmseg.mgz (miracle ozzoude) > 5. Re: error message while using autorecon1 (Hoopes, Andrew) > 6. Re: error message while using autorecon1 (Buckless, Colleen) > 7. Re: error message while using autorecon1 (Hoopes, Andrew) > 8. Re: recon-all on newborn (Lilla Zollei) > 9. Re: recon-all on newborn (Das S.) > 10. Re: Still confused by group analysis.. (Douglas Greve) > 11. Re: Raw Cortical thickness values (Douglas Greve) > 12. Re: Average myelination within ROI (Douglas Greve) > 13. Re: bbregister vs spmregister vs mri_coreg (Douglas Greve) > 14. Re: Recon-all: too many ('s (Douglas Greve) > 15. Re: Using multimodal slab input for hippocampus subfield > segmentation in FS6 (Douglas Greve) > 16. Re: Strange Discrepancy Between Activation Location on > Surface vs. Volume (Douglas Greve) > 17. Re: negative header after preproc-sess (Douglas Greve) > 18. Re: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> (Douglas Greve) > 19. Re: Building your own fsaverage (Douglas Greve) > 20. Re: Qdec error in analysis (Douglas Greve) > 21. Re: mri_glmfit error (mri_reshape number of elements) > (Douglas Greve) > 22. Re: Fwd: remove skull from gtmseg.mgz (Douglas Greve) > 23. Re: GLM fitting for the cortical volume (Douglas Greve) > 24. Re: Subject with missing fMRI data (Douglas Greve) > 25. Re: Question mri_glmfit fwhm smoothing (Douglas Greve) > 26. Re: viewing mri_glmfit FDR corrected results (Douglas Greve) > 27. Re: content of "subjects_dir" (Douglas Greve) > 28. Re: Qdec error in analysis (AYUSHI SHUKLA) > 29. asegstats2table error (Elizabeth Dao) > 30. Re: Fwd: remove skull from gtmseg.mgz (miracooloz(a)gmail.com > <mailto:miracooloz@gmail.com>) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 Jul 2017 17:29:23 +0000 > From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu > <mailto:AHOOPES@mgh.harvard.edu>> > Subject: Re: [Freesurfer] error message while using autorecon1 > To: "'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>'" > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > > <BLUPR04MB4662F945780124666F30CD2F9D40(a)BLUPR04MB466.namprd04.prod.outlook.com > <mailto:BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466.namprd04.prod.outlook.com>> > > Content-Type: text/plain; charset="Windows-1252" > > Hi Colleen, > If you source freesurfer, and run: > ls $FREESURFER_HOME/mni/bin > It should output a list of mni tools, including nu_correct. Is > this what you see? There's a possibility that your mni > sub-directory isn't sourced. > Andrew > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of > Buckless, Colleen <Buckless(a)kennedykrieger.org > <mailto:Buckless@kennedykrieger.org>> > Sent: Wednesday, July 05, 2017 12:18 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>' > Subject: [Freesurfer] error message while using autorecon1 > > Hi All, > I am using the newest version of freesurfer, and I keep getting > errors when I run recon-all ?autorecon1. It appears that the error > might have to do with nu_correct, and I have attached the > recon-all.log. > Any suggestions on how to fix this? > Thanks, > > Colleen Buckless > Research Assistant > Center for Neurodevelopmental and Imaging Research > Kennedy Krieger Institute > 443-923-2747 <tel:443-923-2747> > Buckless(a)kennedykrieger.org <mailto:Buckless@kennedykrieger.org> > > ________________________________ > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not > encrypted by default. You have the right to request further emails > be encrypted by notifying the sender. Your continued use of e-mail > constitutes your acknowledgment of these confidentiality and > security limitations. If you are not the intended recipient, be > advised that any unauthorized use, disclosure, copying, > distribution, or the taking of any action in reliance on the > contents of this information is strictly prohibited. If you have > received this e-mail in error, please immediately notify the > sender via telephone or return e-mail. > > > > ------------------------------ > > Message: 2 > Date: Wed, 5 Jul 2017 17:36:47 +0000 > From: "Buckless, Colleen" <Buckless(a)kennedykrieger.org > <mailto:Buckless@kennedykrieger.org>> > Subject: Re: [Freesurfer] error message while using autorecon1 > To: "'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>'" > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > <6F20C54B58C269489AA5CC858A1F58AF95125F(a)GSP-MAIL1.kki.org > <mailto:6F20C54B58C269489AA5CC858A1F58AF95125F@GSP-MAIL1.kki.org>> > Content-Type: text/plain; charset="us-ascii" > > Hi Andrew, > The output list includes nu_correct. > Thanks, > Colleen > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] On Behalf Of > Hoopes, Andrew > Sent: Wednesday, July 05, 2017 1:29 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>' > Subject: Re: [Freesurfer] error message while using autorecon1 > > Hi Colleen, > If you source freesurfer, and run: > ls $FREESURFER_HOME/mni/bin > It should output a list of mni tools, including nu_correct. Is > this what you see? There's a possibility that your mni > sub-directory isn't sourced. > Andrew > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of > Buckless, Colleen <Buckless(a)kennedykrieger.org > <mailto:Buckless@kennedykrieger.org>> > Sent: Wednesday, July 05, 2017 12:18 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>' > Subject: [Freesurfer] error message while using autorecon1 > > Hi All, > I am using the newest version of freesurfer, and I keep getting > errors when I run recon-all -autorecon1. It appears that the error > might have to do with nu_correct, and I have attached the > recon-all.log. > Any suggestions on how to fix this? > Thanks, > > Colleen Buckless > Research Assistant > Center for Neurodevelopmental and Imaging Research Kennedy Krieger > Institute > 443-923-2747 <tel:443-923-2747> > Buckless(a)kennedykrieger.org <mailto:Buckless@kennedykrieger.org> > > ________________________________ > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not > encrypted by default. You have the right to request further emails > be encrypted by notifying the sender. Your continued use of e-mail > constitutes your acknowledgment of these confidentiality and > security limitations. If you are not the intended recipient, be > advised that any unauthorized use, disclosure, copying, > distribution, or the taking of any action in reliance on the > contents of this information is strictly prohibited. If you have > received this e-mail in error, please immediately notify the > sender via telephone or return e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…> > > > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli…> > . 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. > > > > > ------------------------------ > > Message: 3 > Date: Wed, 5 Jul 2017 13:51:41 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Additional surface area > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > > <alpine.LRH.2.20.1707051351070.31440(a)gate.nmr.mgh.harvard.edu > <mailto:alpine.LRH.2.20.1707051351070.31440@gate.nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Michael > > you need to look in the volume to see what is causing it. I would > guess > some dura that is being incorrectly included, but you will be able > to tell > in the slice view > > cheers > Bruce > > > On Mon, 3 Jul > 2017, Michael Davies wrote: > > > > > Hello, when inspecting a subject i discovered an anomaly on top > of the 3D > > surface i have not previously encountered on other subjects i have > > inspected. Could you please let me know if this would be > problematic when at > > the analysing group data please? > > > > > > Kind regards, Michael > > > > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 5 Jul 2017 13:53:57 -0400 > From: miracle ozzoude <miracooloz(a)gmail.com > <mailto:miracooloz@gmail.com>> > Subject: [Freesurfer] Fwd: remove skull from gtmseg.mgz > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > > <CANfOk0h=UyBU_4ZV0E9mEaoE0NMvvx1_A-x63JxaLxj=54nuLg(a)mail.gmail.com > <mailto:54nuLg@mail.gmail.com>> > Content-Type: text/plain; charset="utf-8" > > ---------- Forwarded message ---------- > From: miracle ozzoude <miracooloz(a)gmail.com > <mailto:miracooloz@gmail.com>> > Date: Tue, Jul 4, 2017 at 10:23 AM > Subject: remove skull from gtmseg.mgz > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Hello Freesurfer, > > After running the first step of PETsurfer (https://surfer.nmr.mgh. > harvard.edu/fswiki/PetSurfer > <http://harvard.edu/fswiki/PetSurfer>). I viewed the image it > created using > freeview. When I change, the color map to Lookup Table, the image also > included the skull. How can I remove the skull from > gtmseg.mgz/prevent it > from showing? Any help will be appreciated. Thanks. Please, see > attached > image > > Best, > Paul >

2 1

Error with glmfit in Qdec
by DANIEL RICHARD WAYER 13 Jul '17

13 Jul '17

Hello all, I keep running into the following error when attempting to run a qdec analysis: ERROR: matrix is ill-conditioned or badly scaled, condno = 10196.8 Attempting to diagnose further SumSq: Min=2.449490 (col 1), Max=26.457514 (col 7) The scale is much different between columns 1 and 7, you may want to normalize by subtracting the mean and dividing by the standard deviation. My analysis is setup to have Gender and Delirium selected as discrete factors, and Age and RThickness selected as the nuisance factors. This corresponding LH analysis does work when using LThickness. Per an earlier suggestion in the archives, I have de-meaned the age which is what allowed me to use LThickness as a nuisance factor in the first place as it threw errors initially. I have included my .dat file to reference. Below is what the error suggested to include: * Command line: mri_glmfit.bin --y /Volumes/data/Paul/CorticalT/subjects/qdec/Untitled/y.mgh --fsgd /Volumes/data/Paul/CorticalT/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Volumes/data/Paul/CorticalT/subjects/qdec/Untitled --surf fsaverage rh --label /Volumes/data/Paul/CorticalT/subjects/fsaverage/label/rh.aparc.label --C /Volumes/data/Paul/CorticalT/subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-thickness.mat --C /Volumes/data/Paul/CorticalT/subjects/qdec/Untitled/contrasts/rh-Diff-Male-Female-Intercept-thickness.mat --C /Volumes/data/Paul/CorticalT/subjects/qdec/Untitled/contrasts/rh-Diff-1-0-Intercept-thickness.mat --C /Volumes/data/Paul/CorticalT/subjects/qdec/Untitled/contrasts/rh-X-Gender-Delirium-Intercept-thickness.mat * FSGD file: I am not using one * Design matrix: attached Any help is greatly appreciated! Best, Dan

1 0

2 post-doc positions available at University of Michigan
by Martijn Muller 13 Jul '17

13 Jul '17

*Job Summary* Two postdoctoral research fellow positions are available immediately at the *Functional Neuroimaging, Cognitive, and Mobility Laboratory*, Department of Radiology, University of Michigan, Ann Arbor, MI, USA. Our laboratory specializes in clinical, mobility, cognition, and multimodal imaging studies of neurological disorders, in particular Parkinson disease. The laboratory is directed by Drs. Nicolaas Bohnen, MD, PhD and Martijn Muller, PhD. *Responsibilities* The applicant will perform multimodal imaging analyses of structural- and functional MRI and PET datasets to address clinical research questions in patients with Parkinson disease or other conditions. The post-doctoral candidate will also assist with the development of an integrated clinical database with incorporated imaging analysis pipeline processing routines. Applicants must have completed a graduate degree (PhD) with relevant experience in multimodal imaging. The applicant must have experience in radiology/radiological sciences, signal processing, functional MRI and diffusion tensor imaging, and the use of neuroimaging software packages such as SPM, Freesurfer, Matlab, FSL, or other relevant software applications. Experience in network-based methods, such as graph theory, would be highly desirable. Fluency in English conversation and team work skills to work in a multidisciplinary environment will be important assets. Additional roles include leadership and active participation in project management activities including the administration of research projects, as well as some teaching sessions and supervision of postgraduate students. This position will require initiative and the ability to work without close supervision. *Additional Information* Compensation of this limited term position will be commensurate with experience and includes health benefits. *How to Apply* Send a brief letter of interest that describes how current skills fit with the required skills for this position, current curriculum vitae, names and contact information of three references to: Dr. Martijn Muller at mtmuller at umich.edu. *Background Screening* Michigan Medicine conducts background screening and pre-employment drug testing on job candidates upon acceptance of a contingent job offer and may use a third party administrator to conduct background screenings. Background screenings are performed in compliance with the Fair Credit Report Act. *U-M EEO/AA Statement* The University of Michigan is an equal opportunity/affirmative action employer.

1 0

Pediatric Atlas/Template
by Jessica Reynolds 13 Jul '17

13 Jul '17

I am wondering whether there are still plans to implement a pediatric atlas/template? I’m working with children aged 3-6 years. Thanks in advance, Jess.

1 1

Differences in volume between mri_segstats and mris_anatomical_stats
by Bruss, Joel E 13 Jul '17

13 Jul '17

I have a group of subjects, scans at time1 and time2 that have been run through the longitudinal stream. I have a group of ROIs in MNI space that I've been able to push up to fsaverage following the VolumeRoiCorticalThickness tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness Further, I've used mri_surf2surf to push the mgh file to each subject. I'm using mri_segstats to pull out mean thickness and a few other variables. If I load the mgh into tksurfer and create a label by hand (~99% the same), I can use mris_anatomical_stats which will also output surface area. I can also use the label with mri_segstats (--slabel) to calculate the thickness, etc. and those values match the ones from mris_anatomical_stats. Based on the input (mgh or label), I get either voxels or vertices. While not exactly the same and possibly due to creating the label by hand, the numbers are very close. However, the volume reported (GrayVol for mris_anatomical_stats, Volume_mm3 for mri_segstats) are really different between the two methods. In checking a few subjects, the volume reported for mris_anatomical_stats is usually 2-3 times larger than mri_segstats. Why is this? Which volume is correct? Is there a way to make one program calculate a volume more in line with the other? Less important, is there a way to force mri_segstats to output surface area? Thank you for taking the time to read this -Joel ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

2 2

BBRegister + partial FoV fail
by Paul Glad Mihai 13 Jul '17

13 Jul '17

Dear List, I've been quite frustrated with the BBRegister results when trying to register a partial field of view EPI mean functional image to a T1 scan. I've tried different init arguments (fsl, spm, header) and none really work. I've found that the initial registration is causing the problem, since the T1 and mean EPi are in reasonable alignment, but not perfect. As soon as it passes the initial alignment it's totally off and obviously fails in the BBR step. I have no full head EPI, unfortunately. I have a full head scout which seems to be a T1 image with really poor contrast. If I try to register this to the T1 through BBRegister it works. But if I use it as an intermediate file it still fails. What can I do? How does the intermediate file come into play? Will it get registered to the T1 initially and then the resulting matrix is used further? I also tried to feed the resulting registration matrix as init-reg but that didn't work either. Is there a way to skip the initial registration? Can I mask the T1 image with the FoV of the functional scan if they are initially in reasonable alignment? Would that work? Would that mean that I have to re-run ReconAll with the masked T1? Would love to hear back from someone. Regards, Glad -- Paul Glad Mihai, PhD Independent Research Group "Neural Mechanisms of Human Communication" Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A, 04103 Leipzig, Germany Phone: +49 (0) 341-9940-2478 E-mail: mihai(a)cbs.mpg.de

3 5

How to edit Fsgdf4G2V about the group.effect.mtx
by haidong wang 12 Jul '17

12 Jul '17

Hello FS expert, I have four groups and two covariables. The groups are MCI_P,MCI_S,MCI_R,NC and the covariables are age and education. I want to test the thickness differences of the groups regressing out age and education.My group.effect.mtx is as following with the feedback of error. 1 -1 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 1 0 0 -1 0 0 0 0 0 0 0 0 Thanks! I am looking forward for your prompt reply. Yours, Haidong

3 3

TAR fs files
by Schumman Resonance 12 Jul '17

12 Jul '17

Hi freesurfers, I'm compressing FS files for storage, and while runnig TAR I got this message for all the files in the directory I'm compressing: "tar: data/sbj001_post_anat.nii.gz/mri/transforms/talairach.m3z.inv.y.mgz: file changed as we read it" Any thoughts on whether this message is making any changes on those tailrace files so that when I decompress the file I do not get the original information in those files. Thanks for your help/advice, Kev

3 3

smoothing data
by Tamara Tavares 12 Jul '17

12 Jul '17

Hi All, I was hoping someone can help me with two naive questions I have: I have read on the Freesufer wiki that you should smooth surface data before analyzing. Should I smooth the data only after I have ran recon-all and have made edits? Also, should volumetric data be smoothed or is this limited to surface data? Thank you in advance for your help. Best, Tamara

3 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer