Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Re: [Freesurfer] FreeSurfer 5.2 TRACULA and FSL 5
by Anastasia Yendiki 06 Mar '13

06 Mar '13

Hi Sean - This works on our redhat centos 4 and centos 6. I can dig around some more, but it'll have to wait for Monday b/c I'll be out of the office the next couple of days. As for your other question, the symlink part has been moved to the -prep step, specifically to make it easier to then run bedpostx outside of trac-all if needed. a.y On Wed, 6 Mar 2013, Sean Hatton wrote: > Hi Anastasia, > > FSLVersion is there and does create the variable. I believe it is a syntax > error, is the bracket suppose to be there? I have also noticed in the bedp > section of trac-all that the "Create links named as expected by bedposts" > section is removed - is this correct? Is it called elsewhere? I am running > CentrOS 4 (64bit) on Ubuntu 12.04. > > Cheers, > > Sean > > > > > > On 7/03/13 3:29 AM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > >> >> Hi Sean - Thanks for trying out the new version! >> >> From what I've seen, the file $FSLDIR/etc/fslversion exists in FSL 5 as >> well. Does it exist in your distribution? >> >> a.y >> >> On Wed, 6 Mar 2013, Sean Hatton wrote: >> >>> Hi all, >>> >>> I have installed FreeSurfer 5.2 to take advantage of improvements in >>> TRACULA. When I run trac-all -bedp I get an error: >>> >>> .../freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected >>> >>> Looking at the programming it is faulting on line 131 where it is >>> checking the FSL version. >>> >>> fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`) >>> >>> Is this syntax correct? Is TRACULA compatible with FSL 5+? >>> >>> >>> Sean Hatton >>> Brain and Mind Research Institute >>> University of Sydney >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> 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 >> http://www.partners.org/complianceline . 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. >> > > > >

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Question re: paradigm files for event-related design
by Cesar Echavarria 06 Mar '13

06 Mar '13

Hi freesurfers, I have an event-related design experiment which outputs a file with a line corresponding to every TR. i.e. for TR = 1 the first 3 columns of the file look like: 0 0 1 1 0 1 2 0 1 3 0 1 4 0 1 5 1 1 6 1 1 7 1 1 8 1 1 9 1 1 Assuming I have 5 seconds of fixation followed by seconds of condition 1. Is this the correct way to format this file? or should it have aline for every condition onset such as: 0 0 5 5 1 5 Perhaps, it makes no difference. Please let me know if you have insight into this Thanks, Cesar

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T2pial's use of bbregister failing
by Winter, Warren 06 Mar '13

06 Mar '13

Hi all, Congrats on the new version! I've been excited to see how the use of data from T2 images could help pial surface estimation, but I'm encountering a problem with getting that to work. It seems to be failing to properly execute the bbregister command built into this part of the new recon-all script. My command was 'recon-all -s <subjid> -i <path/to/T1dcm> -T2 <path/to/T2dcm> -all -T2pial', from an x86_64 Linux platform, and using the stable release of FreeSurfer 5.2. Appended below my signature is the full log of errors that I get (which I've replicated with another subject). Any advice or insights would be much appreciated. Thanks! Warren -- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ######################################################## #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Wed Mar 6 02:52:25 EST 2013 bbregister --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --lta /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat.log Wed Mar 6 02:52:25 EST 2013 setenv SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer cd /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/bin/bbregister --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --lta /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz... TR=2800.00, TE=327.00, TI=-1.00, flip angle=120.00 i_ras = (0.0328993, -0.992771, -0.115425) j_ras = (0.0303427, 0.116427, -0.992736) k_ras = (-0.998998, -0.029158, -0.0339537) writing to /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii... fslregister --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister --dof 6 --fsvol brainmask Log file is /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fslregister.log Wed Mar 6 02:52:25 EST 2013 --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ rc-twice Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts mri_convert ERROR: could not determine file for /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/ERROR: /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/ERROR: /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii --frame 0 mri_convert /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii... TR=2800.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0328993, -0.992771, -0.115425) j_ras = (0.0303427, 0.116427, -0.992736) k_ras = (-0.998998, -0.029158, -0.0339537) keeping frame 0 writing to /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii... Mov determinant is -1.72201 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts tkregister2_cmdl --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/reg0.15619.dat --regheader --fslregout /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat0 --s 2012_T2 --noedit tkregister_tcl /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii reg file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/reg0.15619.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig.mgz 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 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.198 0.000 0.000 115.000; 0.000 0.000 1.200 -86.400; 0.000 -1.198 0.000 115.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -0.033 0.993 0.115 0.704; -0.999 -0.029 -0.034 -0.506; -0.030 -0.116 0.993 1.573; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.033 0.993 0.115 0.704; -0.999 -0.029 -0.034 -0.506; -0.030 -0.116 0.993 1.573; 0.000 0.000 0.000 1.000; Determinant 1 subject = 2012_T2 RegMat --------------------------- -0.033 0.993 0.115 0.704; -0.999 -0.029 -0.034 -0.506; -0.030 -0.116 0.993 1.573; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1.72201, ref det = -1 Wed Mar 6 02:52:29 EST 2013 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts flirt.fsl -ref /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii -in /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/fslmat0.trans.mat -schedule /chb/pices/arch/x86_64-Linux/packages/fsl419/etc/flirtsch/xyztrans.sch -init /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister ERROR: Could not open image /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Wed Mar 6 02:52:29 EST 2013 /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/scripts flirt.fsl -ref /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii -in /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat -init /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/fslmat0.trans.mat -schedule /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister ERROR: Could not open image /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) tkregister2_cmdl --s 2012_T2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --fslreg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat --noedit tkregister_tcl /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/tktools/tkregister2.tcl ERROR: cannot open /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat.fsl.mat cat: /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Wed Mar 6 02:52:25 EST 2013 Ended at Wed Mar 6 02:52:29 EST 2013 fslregister Done To check results, run: tkregister2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --surf orig mri_segreg --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --init-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat --out-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.init.dat mri_segreg --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/template.nii --init-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/bbr.pass1.dat --out-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat.param --surf white --cur-reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/tmp.bbregister.15585/bbr.pass1.dat tkregister2_cmdl --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat --noedit --ltaout /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta regio_read_register(): No such file or directory Could not open /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat tkregister_tcl /chb/pices/arch/x86_64-Linux/packages/freesurfer/stable/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz reg file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ERROR: reading /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat Cleaning up Started at Wed Mar 6 02:52:25 EST 2013 Ended at Wed Mar 6 02:52:29 EST 2013 BBR-Run-Time-Sec 4 bbregister Done To check results, run: tkregister2 --mov /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz --reg /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.dat --surf mri_convert -at /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta -rl /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/T2.mgz mri_convert -at /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta -rl /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/T2.mgz ltaReadFile(/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta): can't open file $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/orig/T2raw.mgz... TR=2800.00, TE=327.00, TI=-1.00, flip angle=120.00 i_ras = (0.0328993, -0.992771, -0.115425) j_ras = (0.0303427, 0.116427, -0.992736) k_ras = (-0.998998, -0.029158, -0.0339537) INFO: Reading transformation from file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() No such file or directory ERROR: Reading transform from file /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/2012_T2/mri/transforms/T2raw.lta Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2012_T2 exited with ERRORS at Wed Mar 6 02:52:30 EST 2013

1 0

Re: [Freesurfer] Fwd: Tracula 5.2 debugging
by Anastasia Yendiki 06 Mar '13

06 Mar '13

Hi Salil - The problem is that you've set dob0 = 1 but you haven't set b0mlist and b0plist, so it doesn't know where to find your field maps to do the B0 unwarping. a.y On Wed, 6 Mar 2013, Salil Soman wrote: > Thank you. > Please see attached. > > -S > > > > > On Wed, Mar 6, 2013 at 12:40 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Salil - Can you send your trac-all.log and dmrirc files? Thanks! > > a.y > > On Wed, 6 Mar 2013, Salil Soman wrote: > > Dear Experts, > I am setup fs 5.2 and have successfully run freesurfer processing on a SPGR dataset. However, when I attempt to > run Tracula on that > dataset, I keep getting a corRead(): can't open file /path/to/ducks/COR-.info (where to path to ducks is the > patch to where my subjects > are located), with additional subsequent errors about b0mag.nii.gz not existing. > > My data is comprised of two consecutive 30 drxn plus 5 b0 GE product acquisitions, combined into 1 dataset using > mri_concat. The data is > then sliced int 2.5mm isotropic data using mri_convert. . The bvec file is create by transposing and then > concatenating 2 bvec files > outputed by dcm2nii using a perl script (the bval file is made in a similar way using the bval files outputted > by dcm2nii). As I am > trying to run this on a cluster, it is easier for me to deal in nifti's instead of dicoms, and so I am providing > the anonymized > isotropic nii file (as created by dcm2nii) as the input along with the bvec and bval files. > > I have tried checking the bval and bvec files for extra spaces/lines (using vi), and have not found any (as I > had seen mentioned in > other posts). Any suggestions on what I may be doing incorrectly would be greatly appreciated. > > Best wishes, > > Salil Soman > > > > > 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 > http://www.partners.org/complianceline . 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. > > > >

1 0

Entorhinal cortex thickness
by stdp82＠virgilio.it 06 Mar '13

06 Mar '13

Hi list, I have read the article on EC (Neuroimage). But, I do not understand how I should obtain the EC thickness outcomes /statistical maps from my analysis. I have some question, please. I have already performed recon-all and cortical thickness analysis. For entorhinal cortex thickness analysis, should I run again mris_prep, surf2surf and glmfit for EC files only? If yes, which are the files that should I use? Which are their names and where these files are locate? An additional question on other matter, please. If I'd like perfomed a ROI based cortical thickness (for example on occipital lobe), can I use a mask that is builded by recon-all? How can I extract it for example from aseg (do you advise it)?About the occipital lobe, I do not understand from tutorial if already exist a particular modality to calculate the cortical thickness specifically in that region. Thank you very much for your patience and kindness, Stefano

1 0

corRead() error with Tracula / FS 5.2
by Salil Soman 06 Mar '13

06 Mar '13

Dear Experts, I am setup fs 5.2 and have successfully run freesurfer processing on a SPGR dataset. However, when I attempt to run Tracula on that dataset, I keep getting a corRead(): can't open file /path/to/ducks/COR-.info (where to path to ducks is the patch to where my subjects are located), with additional subsequent errors about b0mag.nii.gz not existing. My data is comprised of two consecutive 30 drxn plus 5 b0 GE product acquisitions, combined into 1 dataset using mri_concat. The data is then sliced int 2.5mm isotropic data using mri_convert. . The bvec file is create by transposing and then concatenating 2 bvec files outputed by dcm2nii using a perl script (the bval file is made in a similar way using the bval files outputted by dcm2nii). As I am trying to run this on a cluster, it is easier for me to deal in nifti's instead of dicoms, and so I am providing the anonymized isotropic nii file (as created by dcm2nii) as the input along with the bvec and bval files. I have tried checking the bval and bvec files for extra spaces/lines (using vi), and have not found any (as I had seen mentioned in other posts). Any suggestions on what I may be doing incorrectly would be greatly appreciated. Best wishes, Salil Soman

2 1

Can I skip some folders to install freesurfer
by Dian Jiao 06 Mar '13

06 Mar '13

Hi, I was trying to install Freesurfer on a HPC cluster. It seems to be a pretty large distribution, ~4.3 GB after unpacking. I wonder if all the subfolders are needed for running freesurfer or is there any folders could be skipped. Thanks in advance. DJ

2 3

Error
by Varghese Chikku 06 Mar '13

06 Mar '13

All, Any idea how can I sort this error, Loading data table /Users/chikkuvarghese/subject/qdec/qdec.table.dat... Number of columns: 4 fsid column: 1 Number of factors: 3 Number of subjects: 1 ERROR: QdecDataTable::Load: problem parsing file /Users/chikkuvarghese/subject/qdec/qdec.table.dat This line did not appear to end with a newline: truetest2.long.e Female 70 Righthippocampus 4006 Error loading the data table. Many Thanks chikku

2 1

FreeSurfer 5.2 TRACULA and FSL 5
by Sean Hatton 06 Mar '13

06 Mar '13

Hi all, I have installed FreeSurfer 5.2 to take advantage of improvements in TRACULA. When I run trac-all -bedp I get an error: .../freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected Looking at the programming it is faulting on line 131 where it is checking the FSL version. fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`) Is this syntax correct? Is TRACULA compatible with FSL 5+? Sean Hatton Brain and Mind Research Institute University of Sydney

2 1

Extract cortex surface with Freesurfer
by Valtina Pouegue 06 Mar '13

06 Mar '13

Hi, I'm a new user of Freesurfer. 1) I would like to extract only the cortex cerebrum . So I think I don't need the complete subcortical segmentation ( 20-40 hours). Do you know a way to segment only cortex or only ( cortex+ pial ( left/rigt hemispher)?2) I already try the complete subcortical segmentation ( about 12 hours, with the recon-all command). Do you know a way to extract only the cortex surface from the software? I would like to get the 3D surface mesh for analysis on Matlab. Could you help me, Thanks. VP.

2 1

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Freesurfer March 2013