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30091 discussions

Bug in DOSS implementation in QDEC
by Douglas N Greve 28 Mar '13

28 Mar '13

Dear FreeSurferers, it has just come to my attention that there may be a bug in the way that QDEC computes contrasts for DOSS. If you are using QDEC in this way, please hold off until I track down the problem. Also, please let me know if you are using it in this way. thanks and sorry for the inconvenience doug -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Recon-all errors (reposting)
by Marcos Martins da Silva 28 Mar '13

28 Mar '13

Hi, freesurferers I am trying to execute the post installation tests as recommended at Freesurfer Wiki. Using a CentOS6 Virtual Machine (kernel 2.6.32-358.2.1.el6.x86_64) over Fedora 18 using VirtualBox 4.2.8. Freesurfer version is 5.2. Tkmedit, Tksurfer, qdec and freeview all work great. However, recon-all tests return errors. Thank you for your attention. _______________________________________ recon-all -s bert -autorecon1 running loop to estimate saturation parameter: A or b constain NAN or infinity values!! _______________________________________ recon-all -s bert -all talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log _______________________________________ The log indicated above shows: imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

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Re: [Freesurfer] Underestimated Pial surface - after deleting problematic voxels
by Bruce Fischl 28 Mar '13

28 Mar '13

well, something is really wrong. Did you happen to change the voxel type of brain.finalsurfs.mgz? Can you run mri_info on it and send us the results? If not, then upload the tarred and gzipped subject dir and I'll take a look. I don't think it will be hard to fix On Thu, 28 Mar 2013, preciado(a)nmr.mgh.harvard.edu wrote: > A) Log attached. > B) That was my next step but I wanted to check first to see if there was > something obvious I was missing. > > I actually ran "recon-all -autorecon-pial -subjid subject_name" twice. I > thought the first time, that it was the result of some process failing/not > completing along the way without entirely crashing freesurfer. I ran it > again in the hopes that it was some crazy fluke but the result is exactly > the same. > > -Ronny > >> eek, that's pretty bad. No idea why that would happen. Can you send us >> the recon-all.log? If you rerun with the original brain.finalsurfs.mgz >> does it restore good surfaces? >> On Thu, 28 Mar 2013, >> preciado(a)nmr.mgh.harvard.edu wrote: >> >>> Hello Freesurfers, >>> >>> I ran recon-all on a subject's structural data like so: >>> recon-all -autorecon-all -subjid subect_name >>> >>> The resulting pial surface looked pretty good except that there were a >>> few >>> voxels of dura and cerebellum that were included in the pial surface. >>> not >>> a big deal. I deleted some voxels of dura from brainmask.mgz and deleted >>> voxels of from the cerebellum by creating and saving a copy of >>> brain.finalsurfs.mgz. >>> /subject_name/mri/ >>> cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz >>> >>> >>> Then I ran recon all to regenerate the pial surface: >>> recon-all -autorecon-pial -subjid subject_name >>> >>> >>> The results from the pial surface redrawing are now totally wrong and >>> completely underestimated. The weird thing is that it looked perfectly >>> fine before and removing some problematic voxels caused this result. >>> >>> Any insights as to how/why this occurred and how to fix it? Images of >>> the >>> AFTER picture attached. >>> >>> Thanks! >>> -Ronny >> >> >> >

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Underestimated Pial surface - after deleting problematic voxels
by preciado＠nmr.mgh.harvard.edu 28 Mar '13

28 Mar '13

Hello Freesurfers, I ran recon-all on a subject's structural data like so: recon-all -autorecon-all -subjid subect_name The resulting pial surface looked pretty good except that there were a few voxels of dura and cerebellum that were included in the pial surface. not a big deal. I deleted some voxels of dura from brainmask.mgz and deleted voxels of from the cerebellum by creating and saving a copy of brain.finalsurfs.mgz. /subject_name/mri/ cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then I ran recon all to regenerate the pial surface: recon-all -autorecon-pial -subjid subject_name The results from the pial surface redrawing are now totally wrong and completely underestimated. The weird thing is that it looked perfectly fine before and removing some problematic voxels caused this result. Any insights as to how/why this occurred and how to fix it? Images of the AFTER picture attached. Thanks! -Ronny

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qdec covariates
by stdp82＠virgilio.it 28 Mar '13

28 Mar '13

Hi list,I'm performing qdec. This my file.dat1 diagnosis discrete 2 1 Pathology 2 Controls2 Thickness_lh continuous 03 Thickness_rh continuous 04 NPStest continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- Thickness_lh 2.643 0.116 Thickness_rh 2.630 0.099 NPStest 0.774 1.203Number of subjects: 31Number of factors: 4 (1 discrete, 3 continuous)Number of classes: 2Number of regressors: 8NPStest is scored from 0 to 8 and for controls it is all 0.Previously I have performed qdec without problem but I'm noting that when I use covariates that contains all 0 in a group, qdec give me an error. What's happen?Thanks, Stefano

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Admin: Please unsubscribe this email address
by Dalwani, Manish 27 Mar '13

27 Mar '13

Hello Admin, Please unsubscribe this email address. Regards, Manish

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bbregister error with hardi data
by Corinna Bauer 27 Mar '13

27 Mar '13

Hello all, I am attempting to run bbregister on 4D HARDI data that has already been motion, eddy, and epi-distortion corrected in fsl. I run the command: bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat and get a number of errors that seem to begin in the mri_convert section as seen below. Any insight? Cheers, Corinna FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15356/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15356/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask Log file is ./tmp.bbregister.15356/reg.init.dat.fslregister.log Mon Mar 25 12:22:23 EDT 2013 --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ lotfi Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR: ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /usr/local/freesurfer/subjects/symmetry/lindsay mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.15356/template.nii ./tmp.bbregister.15356/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 ./tmp.bbregister.15356/template.nii... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) keeping frame 0 writing to ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii... Mov determinant is -6.125 /usr/local/freesurfer/subjects/symmetry/lindsay tkregister2_cmdl --mov ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.15356/fslregister/reg0.15393.dat --regheader --fslregout ./tmp.bbregister.15356/reg.init.dat.fsl.mat0 --s lindsay --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.15356/fslregister/reg0.15393.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 /usr/local/freesurfer/subjects/symmetry/lindsay/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 ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.750 0.000 0.000 112.000; 0.000 0.000 2.000 -60.000; 0.000 -1.750 0.000 112.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; Determinant 1 subject = lindsay RegMat --------------------------- 0.991 0.026 -0.130 2.508; 0.130 0.003 0.992 -30.941; 0.026 -1.000 -0.000 1.279; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -6.125, ref det = -1 Mon Mar 25 12:22:34 EDT 2013 /usr/local/freesurfer/subjects/symmetry/lindsay flirt.fsl -ref ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.15356/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.15356/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.15356/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.15356/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.15356/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Mon Mar 25 12:22:34 EDT 2013 /usr/local/freesurfer/subjects/symmetry/lindsay flirt.fsl -ref ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.15356/reg.init.dat.fsl.mat -init ./tmp.bbregister.15356/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for './tmp.bbregister.15356/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister): bad header info ERROR: failed to open file ./tmp.bbregister.15356/fslregister/refvol.fslregister ERROR: Could not open image ./tmp.bbregister.15356/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) tkregister2_cmdl --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --fslreg ./tmp.bbregister.15356/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ERROR: cannot open ./tmp.bbregister.15356/reg.init.dat.fsl.mat cat: ./tmp.bbregister.15356/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Mon Mar 25 12:22:23 EDT 2013 Ended at Mon Mar 25 12:22:34 EDT 2013 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.15356/template.nii --reg ./tmp.bbregister.15356/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.15356/template.nii --init-reg ./tmp.bbregister.15356/reg.init.dat --out-reg ./tmp.bbregister.15356/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 ./tmp.bbregister.15356/reg.init.dat mri_segreg --mov ./tmp.bbregister.15356/template.nii --init-reg ./tmp.bbregister.15356/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.15356/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 ./tmp.bbregister.15356/bbr.pass1.dat Cleaning up Started at Mon Mar 25 12:22:16 EDT 2013 Ended at Mon Mar 25 12:22:34 EDT 2013 BBR-Run-Time-Sec 18 bbregister Done To check results, run: tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz --reg register.dat --surf

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view retinotopy results in version 5
by Y.V. Jiang 27 Mar '13

27 Mar '13

Hi, I was able to view retinotopic mapping results using rtview in version 5. However, the display was on the inflated surface. Is there a way to view the results on the flattened occipital map, similar to version 4's surf-sess -flat? Thanks! -Yuhong

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surf2vol
by Daniel Lumsden 27 Mar '13

27 Mar '13

Bruce Many thanks - that's given me a lot more guidance. Following the help, i've put together the command below: mri_surf2vol --hemi lh --template <path to>/orig.mgz --outvol <path to where I want the file>/leftfrontallobe.nii.gz --surfval <path to>/left_frontal_lobe.gii --fillribbon --volregidentity mov07 Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've generated from the label files to run in probtrakx. This command runs, but produces and empty nifti file. I've changed the output to .mgz with similar effect. I've substituted the rawavg.mgz file for the orig.mgz file, and tried both .nii.gz and .mgz versions of both files and still get an empty output file. The subject is in my $SUBJECTS_DIR. Is there a way to check the .gii files? I generated them using label2surf, having used mris_convert to convert the lh.white and rh.white files from the surf folder for my subject to lh.white.asc and rh.white.asc. Thank you again for your help. Dan > Date: Mon, 25 Mar 2013 14:59:28 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: doclumsden(a)hotmail.com > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] surf2vol > > Hi Dan > > try using mri_surf2vol instead (it has a much bigger help, thanks to > Doug0 > Bruce > On Mon, 25 Mar 2013, Daniel Lumsden wrote: > > > Dear All > > > > Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical > > parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the > > parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate > > the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm > > struggling to apply the surf2vol command. > > > > From the terminal window I can see that the commands required are: > > > > surf2vol <surf> <refvol> <outvol> <convention> > > > > I presume that <surf> is the .gii file I'm trying to visualise, and <outvol> is to specify the name of the output volume the > > command will generate, but what should I be using as the <refvol>? I would be very grateful for any guidance. Please accept my > > apologies if I've missed a very obvious online explanation for this and thank you in advance. > > > > Dan Lumsden > > Clinical Research Fellow > > > > > > > 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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Re: [Freesurfer] Xhemi stat questions
by Gabriel Gonzalez Escamilla 27 Mar '13

27 Mar '13

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