Freesurfer June 2007

freesurfer@nmr.mgh.harvard.edu

59 participants
82 discussions

Re: 回复:RE: [Freesurfer] (no subject)
by Jenni Pacheco 13 Jun '07

13 Jun '07

Hi, The instructions for this are on the wiki page you indicated previously, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis When you run mris_preproc you specify thickness as the measure you are looking at. We have a new group analysis tool, with a GUI interface, that is now available. Tutorials on that are available here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis The new tool, Qdec, performs the same analyses - but it is hopefully more user friendly. Jenni On Wed, 13 Jun 2007 duhanjian(a)sohu.com wrote: > Which command to specify the thickness, can you tell me how to use? Thank you very much!

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mri_motion_correct.fsl
by Catherine Hartley 12 Jun '07

12 Jun '07

Hi, I'm trying to run mri_motion_correct.fsl to generate the rawavg.mgz file, and it's failing somewhere before the process completes. I can't seem to figure out from reading the log file just what is going wrong. Any insight would be much appreciated! Thanks ------ mri_motion_correct.fsl log file $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ /Applications/freesurfer/bin//mri_motion_correct.fsl /Volumes/phelpslab/Cate/extinction/AS083182 Darwin saks.psych.nyu.edu 8.9.1 Darwin Kernel Version 8.9.1: Thu Feb 22 20:55:00 PST 2007; root:xnu-792.18.15~1/RELEASE_I386 i386 i386 Mon Jun 11 18:33:21 EDT 2007 /Applications/freesurfer/bin//mri_convert /Applications/freesurfer/fsl/bin/flirt ----------------------------------------- Converting mri/orig/002.mgz Mon Jun 11 18:33:23 EDT 2007 /Volumes/phelpslab/Cate/extinction/AS083182 mri_convert mri/orig/002.mgz /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /cor-1.img -odt float mri_convert mri/orig/002.mgz /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /cor-1.img -odt float reading from mri/orig/002.mgz... TR=2500.00, TE=4.38, TI=900.00, flip angle=8.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, 0, 0) changing data type from 4 to 3 (noscale = 0)... writing to /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /cor-1.img... Analyze Output Matrix -0.000 -0.000 -1.000 80.325; -1.000 -0.000 0.000 129.500; 0.000 -1.000 0.000 128.777; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting mri/orig/003.mgz Mon Jun 11 18:33:26 EDT 2007 /Volumes/phelpslab/Cate/extinction/AS083182 mri_convert mri/orig/003.mgz /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /cor-2.img -odt float mri_convert mri/orig/003.mgz /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /cor-2.img -odt float reading from mri/orig/003.mgz... TR=2500.00, TE=4.38, TI=900.00, flip angle=8.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, 0, 0) changing data type from 4 to 3 (noscale = 0)... writing to /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /cor-2.img... Analyze Output Matrix -0.000 -0.000 -1.000 89.000; -1.000 -0.000 0.000 126.608; 0.000 -1.000 0.000 129.500; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /cor-2.img Mon Jun 11 18:33:28 EDT 2007 /Volumes/phelpslab/Cate/extinction/AS083182 fsl_rigid_register -maxangle 90 -r /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /cor-1.img -i /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /cor-2.img -o /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 /resampled.img -tmpdir /Volumes/phelpslab/Cate/extinction/AS083182/tmp-mri_motion_correct.fsl-12111 -cleanup USAGE: fsl_rigid_register Required Arguments: -r refvol : reference/target volume -i inputvol : input/moveable volume -o outputvol : input resampled to reference Optional Arguments -fslmat fsmatfile : spec explicitly -regmat regmatfile : get reg matrix as register.dat file -xfmmat xfmmatfile : get reg matrix as MNI xfm file -ltamat ltamatfile : get reg matrix as MGH lta file -noinitgeom : do not initialize matrix based on geometry -initxfm xfmfile : use this as an initial matrix -applyxfm xfmfile : do not reg, just apply xfm to input -maxangle maxangle : only search over +/- maxangle degrees -interp method : <trilinear>, nearestneighbour, sinc -dof dof : use dof instead of 6 -bins bins : number of bins to use (default 256) -cost cost : objective function (default corratio) valid costs are mutualinfo corratio normcorr normmi leastsq -tmp tmpdir (default is ). Implies -nocleanup -tmpdir tmpdir : same as -tmp -nocleanup : do not delete temporary files -cleanup : delete temporary files (default) -version : print version and exit -help : print help and exit This is a front-end for the FSL (www.fmrib.ox.ac.uk/fsl/index.html) flirt program. Computes the registration matrix that transforms inputvol to refvol and resamples inputvol to outputvol using that matrix. The matrix is stored in outputvol.fslmat. The registration is constrained to be rigid (ie, 6 dof). The input and ref volumes are automatically converted to analyze, and the output volume is automatically converted from analyze to the output format. Note: if using COR as output, the COR directory must exist prior to running this script. The FLIRT/FSL registration matrix will be stored in outvol.fslmat (unless -fslmat). By default, an init FSL registration matrix is computed from the geometry information in the header ref and input headers. This is a good idea because the anlyze format does not keep the direction cosine info around. -fslmat fslmatfile Store the FSL registration matrix in fslmatfile instead of outvol.fslmat -regmat regmatfile Convert the FSL matrix to register.dat format and save in regmatfile. You will have to edit the subject name. -ltamat ltamatfile Convert the FSL matrix to an MGH lta file. -noinitgeom Do not compute init registration matrix from geometry. -initxfm fslmatfile Use matrix in fslmatfile as the initial registation matrix. If no initialization is specified, the identity is assumed. Forces -noinitgeom. -maxangle maxangle Search only +/- maxangle degrees around the initial starting point. Default is 90. -applyxfm When the -applyxfm flag is is used, the input is resampled to the output using the FSL mat file supplied as the argument to the -applyxfm. The ref volume is still needed in order to get the proper geometry for the output file. Forces -noinitgeom. -dof dof Non-rigid registration can be performed by changing the dof from 6. BUGS: If using COR as output, the COR directory must exist prior to running this script.

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aparc2aseg error
by Derin Cobia 12 Jun '07

12 Jun '07

I'm getting the following error on several of my subjects during the aparc2aseg stage: _________________________ #@# AParc-to-ASeg Sat Jun 9 12:19:58 EDT 2007 /disk/eli/freesurfer/conte_flash/5111 mri_aparc2aseg --s 5111 --ribbon SUBJECTS_DIR /disk/eli/freesurfer/conte_flash subject 5111 outvol /disk/eli/freesurfer/conte_flash/5111/mri/aparc+aseg.mgz useribbon 1 baseoffset 0 Reading lh white surface /disk/eli/freesurfer/conte_flash/5111/surf/lh.white Building hash of lh white Reading lh pial surface /disk/eli/freesurfer/conte_flash/5111/surf/lh.pial Building hash of lh pial ERROR: lh white and pial have a different number of vertices (190233,189041) Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jun 9 12:20:07 EDT 2007 _______________________________ Do I need to reprocess from a certain stage on, or redo the whole thing? What would have caused this (it didn't happen with some other subjects during the same process batch). I couldn't find any info on this in the archive or wiki, I'm running 3.0.4. Thanks, Derin

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changing subject's name
by Woo Suk, Tae 12 Jun '07

12 Jun '07

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } After recon-all -s tfe10 (subject name) -all, I changed a subject's name (tfe10) to 001.when I performed group analysis (mris_make_average_surface), I had the error massage.How can I correct it?---------------------------------------------------------------------------------------------------------------#@# processing subject 1/42 001... Reading /usr/local/freesurfer/subjects/001/surf/rh.sphere.reg Talairach transform /usr/local/freesurfer/subjects/tfe10/mri/transforms/talairach.xfm does not exist ...Loading tal xfm file /usr/local/freesurfer/subjects/001/mri/transforms/talairach.xfm Read /usr/local/freesurfer/subjects/001/mri/T1.mgz Surface area: 872.5 cm^2 Applying linear transform Talairach transform /usr/local/freesurfer/subjects/tfe10/mri/transforms/talairach.xfm does not exist ...Loading tal xfm file /usr/local/freesurfer/subjects/001/mri/transforms/talairach.xfm--------------------------------------------------------------------------------------------------------------------Woo Suk, Tae

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Manually editing brainmask.mgz
by Jared Conley 11 Jun '07

11 Jun '07

FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command <tkmedit subjid brainmask.mgz> and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas? Thanks, Jared

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reg -feat2anat error reg -feat2anat error
by Furlong, Carolyn 11 Jun '07

11 Jun '07

Hi Doug we tried adding the binaries Doug sent us (MRI_convert, reg2anat and tkregister2, make average subject, make average surface anfd make avergae volume), but now we get a different error:reg-feat2anat --feat ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. What should I do? Best wishes Carolyn -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 21/05/2007 17:16 To: Furlong, Carolyn Cc: Freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reg -feat2anat error Did you see my email from last week? It looks like the problem was fixed with new versions of a few programs. doug Furlong, Carolyn wrote: > > Hi Doug > > Please find attached the logfile that you requested, sorry for the > delay, I am only able to work on this one day a week. > > Best wishes > Carolyn > > > > > > Actually, I wanted the log file found in > featdir/reg/freesurfer/reg-feat2anat.log. > > doug > > Furlong, Carolyn wrote: > > > Hi > > > > > > niiRead(): unsupported timing pattern in > Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz > > > > sorry for the delay, > > > > Best wishes > > > > Carolyn > > > > can you send the log file? > > > > Furlong, Carolyn wrote: > > > >> Hi, > >> > >> When I try to register my functional data to anatomical data using > >> > >> reg-feat2anat --feat feat_directory --subject subject_name > >> > >> I get the following error message > >> > >> ERROR: could not read ///example_func.nii.gz as 24 > >> > >> What does this mean? And how can I fix this? > >> > >> Best wishes > >> Carolyn > >> > >> > >>_______________________________________________ > >>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 > > > >In order to help us help you, please follow the steps in: > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > >_______________________________________________ > >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 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >------------------------------------------------------------------------ > >Mon May 21 10:38:18 BST 2007 >/disc2/Kate/Flatmap1 >/home/progs/freesurfer/bin//reg-feat2anat >--feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore >Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 i386 GNU/Linux >mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz >mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz >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.gz... >example_func ras_good_flag >------------------------------------------------------- >Initializing exf2anat from crude std2anat >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 >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 0 >$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 >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 >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 >RegMat --------------------------- > 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; >register: file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat written >FSLOUTPUTTYPE NIFTI_GZ >tkreg2FSL: mov det = -8, ref det = -1 >mri_matrix_multiply -fsl -bin -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat -om /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat >betfunc /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet >Mon May 21 10:38:32 BST 2007 >flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii.gz -init /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 >------------------------------------------------------- >tkregister2 --s AMoore --mov /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat --fslreg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat --noedit --mgz >niiRead(): unsupported timing pattern in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz >---- FSL registration matrix -------- > 0.974 0.200 0.103 12.477; >-0.093 -0.059 0.994 75.631; > 0.205 -0.978 -0.039 180.824; > 0.000 0.000 0.000 1.000; >--------------------------------------- >INFO: no target volume specified, assuming FreeSurfer orig volume. >target volume orig >movable volume /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz >reg file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat >LoadVol 0 >$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ >Diagnostic Level -1 >ERROR: could not read /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz as 24 >ERROR: tkregister2 > > >------------------------------------------------------------------------ > >_______________________________________________ >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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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(no subject)
by duhanjian＠sohu.com 11 Jun '07

11 Jun '07

  <p>Thank you for previous help.</p><p>Now I want to compare the cortical thickness of the two groups. Mr Pacheco tells me to use the group analysis to compare. When I read the manual of the group analysis (<a href="https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis">https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis</a>), I meet some problem. When writing the FSGD file, I don't how to input another group thickness (eg, control group) in to the FSGD. If not use method, how to compare the cortical thickness between the two group?</p>

2 1

volume to use for control points
by syc2114＠columbia.edu 08 Jun '07

08 Jun '07

Hi, I recently started using Freesurfer and I have a quick question about adding control points. I want to add control points to a stretch of white matter which was excluded - can I add them to the wm.mgz volume by referring to the T1 aux or do they need to be added to the brainmask volume only?

3 2

Where can I find global and local thickness / volume measures for individual subjects?
by Burmicz, Ryszarda 08 Jun '07

08 Jun '07

Hi! I am new to Freesurfer; I have run reconstruction steps with recon-all. I can find no reference to thickness values calculated as part of this process, apart from visualising them in Freesurfer - is there a specific file from which I can extract this information without running the GUI? I am comparing data from a single subject across different scanning protocols in order to look at variation in thickness. So ultimately I would like to produce tabulated data of global and local thicknesses. Many thanks for your help, Rysia

2 1

FRD in ROI
by Marie Schaer 07 Jun '07

07 Jun '07

Hello everybody, Following the question of Jorge Luis yesterday, I was wondering if the option "marked only" in "Set threshold using FDR" could be an option to get FDR corrected results on parcells of the cortical surface? However, when I load ROI and click on "marked only", the terminal window shows: "surfer: Error calculating threshold with FDR". Any hint would be very appreciated, many thanks, Marie Schaer

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Freesurfer June 2007