Freesurfer June 2007

freesurfer@nmr.mgh.harvard.edu

59 participants
82 discussions

Problems with surface topologies
by jorge luis 28 Jun '07

28 Jun '07

Hello all I have the freesurfer automatic hippocampus segmentation for some subjects. It seems that the segmentation is not bad. I have produced the binary masks (after labels generation in tksurfer)with the following command: mri_label2vol --label label/lefthipoca.label --temp mri/orig.mgz --o lefthipoca.img I have loaded the lefthipoca.img mask in matlab and used the standard matlab isosurface algorithm to triangulate the contours of the binary mask. The problem is that the resulting surface although no topological defects and no boundaries does not have spherical topology (euler number<2). Is it a consequence of imperfections in the freesurfer segmentation? How can I correct it? I have seen that with litter volumetric smoothing of the mask I get surfaces with spherical topology after the triangulation, but the structure volume is remarkable increased after the smoothing. Any tip is welcome In advance Thank you Jorge ____________________________________________________________________________________ ¡Descubre una nueva forma de obtener respuestas a tus preguntas! Entra en Yahoo! Respuestas. http://es.answers.yahoo.com/info/welcome

2 1

make_average-subject
by Lars M. Rimol 27 Jun '07

27 Jun '07

Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong? Thank you! Lars M. Rimol make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp $ Wed Jun 27 18:06:43 PDT 2007 /space/emc1/3/data/TOP/Analysis_lmr setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers output sdir is /space/emc1/3/data/TOP/Containers uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) context=user_u:system_r:unconfined_t ==================== make_average_surface ==================== input subjects: output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mri_add_xform_to_header -c auto /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz /space/emc1/3/data/TOP/Containers//space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest/mri/mni305.cor.mgz INFO: extension is mgz #@# Making rh annotation --------------------- Wed Jun 27 18:06:47 PDT 2007 mris_ca_label -ml-annot rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.curvature.buckner40.filled.desikan_killiany.gcs 7 label/rh.aparc.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.curvature.buckner40.filled.desikan_killiany.gcs reading color table from GCSA file.... average std = 35.0 0.3 using min determinant for regularization = 0.011 0 singular and 829 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 376 changed) writing colortable into annotation file... mris_ca_label -ml-annot rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest ML Label: rh.atlas2005_simple.gcs 7 label/rh.aparc.a2005s.annot Reading icosahedron /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/lib/bem/ic7.tri Reading gcsa from /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R304/average/rh.atlas2005_simple.gcs reading color table from GCSA file.... average std = 1.0 0.2 using min determinant for regularization = 0.000 0 singular and 827 ill-conditioned covariance matrices regularized Building most likely labels Filtering labels 2 filter iterations complete (2 requested, 1935 changed) writing colortable into annotation file... #@# Making average rh.orig surface --------------------- Wed Jun 27 18:07:06 PDT 2007 /space/emc1/3/data/TOP/Containers/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mris_make_average_surface -i 7 -o orig -sdir-out /space/emc1/3/data/TOP/Containers rh orig_avg sphere.reg/space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest reading vertex positions from orig... mris_make_average_surface [options] hemi outsurfname cansurfname outsubject subj1 subj2 subj3 ... Run with -help for more info -- yours, LMR

2 1

OASIS Freesurfer Data
by Daniel Marcus 27 Jun '07

27 Jun '07

Hi folks- The Freesurfer processing of the OASIS cross-sectional data set is now available for download via anonymous FTP. The whole set will also be available at the OASIS website in the coming weeks. Check out www.oasis-brains.org for more information on the OASIS project. Download instructions: -ftp to www.oasis-brains.org -login as anonymous (use email address as password) -cd to data -mget oasis_cs_freesurfer* The full set is ~150 GB. It is divided into 11 separate .tar.gz files. This data set falls under the same Data Usage Agreement as the core OASIS data (http://www.oasis-brains.org/app/template/UsageAgreement.vm) Most importantly, please make sure to properly acknowledge its origin. Again, thanks to Bruce, Jenni, and the rest of the folks at MGH for generating this very cool data set and for making it widely available. Dan Marcus dmarcus(a)wustl.edu Neuroinformatics Research Group Washington University School of Medicine http://nrg.wustl.edu

1 0

Making labels from the commandline
by Morgan Hough 27 Jun '07

27 Jun '07

I was wondering if I can make a cortical label from a volume ROI from the commandline. I would like to extract thickness values from a region defined in each subject's volume space. Thanks in advance. Cheers, -Morgan

3 10

RE: [Freesurfer] ROI of SI cortex
by Rahul Desikan 27 Jun '07

27 Jun '07

Hi Xin, I will Doug handle this one. And please email the list in your replies. Best, rahul On Mon, 30 Apr 2007, Wang, Xin wrote: > Many thanks, Rahul. I found readings in /stats/*h.aparc.stats. I am a freesurfer beginner. I have another question. I want to compare the cortical thickness between two small groups (2X2). I can not work through the steps in the tutorial on my data. The mri_glmfit commend always returns with "bad design, ill-constructed," and stops. Do you have any detail instructions of two group comparison? > Thank you again, > > Xin > > ________________________________ > > From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] > Sent: Mon 4/30/2007 4:06 PM > To: Wang, Xin > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] ROI of SI cortex > > > > Hi Xin, > > Within the *h.aparc.annot files for each subject, there should be > individual label files for *h.precentral.label and *h.postcentral.label. > If you take a look at your *h.aparc.stats, there should be a value for the > thickness and volume. You can, of course, take this *h.aparc.stats file > and upload it into matlab, spss or any other stats package and do > statistics on these values. > > Best, > > rahul > > On Mon, 30 Apr 2007, Wang, Xin wrote: > >> Dear Rahul >> The SI is primary somatosensory cortex (or postcentral gyrus) and MI is primary motor cortex (or precentral gyrus). I want to compare the thickness and volume of these two areas from left side to right side. >> Thank you, >> >> Xin >> >> ________________________________ >> >> From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] >> Sent: Mon 4/30/2007 3:52 PM >> To: Wang, Xin >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] ROI of SI cortex >> >> >> >> Hi Xin, >> >> What exactly do SI and MI cortices refer to? >> >> rahul >> >> On Mon, 30 Apr 2007, Wang, Xin wrote: >> >>> Hello, group >>> I need to compare thickness of left v.s. the right SI and MI cortices. I saw some matlab tools for comparsion of left and right hippocampus in Lundervold.pdf. I could not find similar tools in the matlab folder of Freesurfer stable release 3.0.5 that I just installed. Could anybody kindly tell me the tools I could use for my study? >>> Thank you in advance. >>> Xin Wang >>> >> >> -- >> >> >> >> >> >> >> >> >> >> > > -- > > > > > > > > > > --

3 2

(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!!!

1 0

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

27 Jun '07

1 0

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 %

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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

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Freesurfer June 2007