Freesurfer August 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
143 discussions

Re: [Freesurfer] Registering aseg to base for volume overlap calc ulations
by Elizabeth Selgrade 06 Aug '09

06 Aug '09

Hi FreeSurfer Users, I'm still having no luck getting my timepoints to realign to the base space so that I can calculate volume overlap between the timepoints. Here's what I've been trying: BASEDIR=path to base/mri TPDIR=path to timepoint Convert the .lta tpNid_to_baseid.lta transform to .xfm and .dat: tkregister2 --mov $BASEDIR/norm.mgz --targ $TPDIR/mri/aseg.mgz --lta $BASEDIR/transforms/${TP}_to_base.lta --reg $TPDIR/aseg_to_base.dat --xfmout $TPDIR/aseg_to_base.xfm Apply transform using mri_convert or mri_label2vol: mri_convert -T $TPDIR/aseg_to_base.xfm --out_type nii $TPDIR/mri/aseg.mgz $TPDIR/aseg.base.nii OR mri_label2vol --seg $TPDIR/mri/aseg.mgz --temp $BASEDIR/norm.mgz --reg $TPDIR/aseg_to_base.dat --o $TPDIR/aseg.base.mgz When I do this for multiple scans, I expect them to overlap. But, when I view them as NIfTIs in fslview, they do not align. Any suggestions for what might be going on? Thank you! Liz -----Original Message----- From: Sita Kakunoori [mailto:sita@nmr.mgh.harvard.edu] Sent: Tuesday, August 04, 2009 12:33 PM To: Elizabeth Selgrade Cc: 'Martin Reuter'; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registering aseg to base for volume overlap calc ulations Hi Liz, I think you can run tkregister2 with --noedit flag to convert .lta files to .dat files. tkregister2 --mov <..> --s <..> --lta <...> --noedit --reg <test.dat> Sita. On Tue, 4 Aug 2009, Elizabeth Selgrade wrote: > Martin and FreeSurfer Users, > > A few more questions. What is the best way to apply this transform to > my aseg.mgz? I've tried using mri_label2vol, but that fails because > the transform is a .lta instead of a .dat. Then I used tkregister2 to > register my timepoint's aseg.mgz to the base's norm.mgz with the --lta > flag, thinking that this would save my .lta as a .dat. But, when I do > this (tkregister2 then mri_label2vol) for multiple timepoints and > compare the results, the scans are still not overlapping. > > So, is there a way to change .lta files into .dat files? Or is there > a different tool that I should be using to apply the transform? > > Thank you for your help! > Liz Selgrade > > > > -----Original Message----- > From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] > Sent: Monday, August 03, 2009 5:28 PM > To: Elizabeth Selgrade > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Registering aseg to base for volume overlap > calc ulations > > Liz, > > to be precise, this is true for the standard FS stream. > > The longitudinal stream is different, as in FS 4.4 the base actually > lives in two similar, but slightly different spaces, because the > template is created for T1 and recreated for the norm.mgz. The aseg is > in the space of the norm and the maps, I pointed you to, map to that space. > > We improved the base for the next FS release 4.5, where it lives only > in one space, to make things easier. > > Best, Martin > > On Mon, 2009-08-03 at 17:05 -0400, Martin Reuter wrote: >> Its in the native space of the TP (orig, nu, T1, norm, brainmask, >> aseg, brain .. all in the same space). >> >> -Martin >> >> On Mon, 2009-08-03 at 16:40 -0400, Elizabeth Selgrade wrote: >>> Hi Martin, >>> >>> Thanks for the quick response. I have a follow-up question: In what >>> space do the segmentations take place? (What space is aseg.mgz in?) >>> I'm assuming that it must be in the timepoint's native space in >>> order to use the inverse transform you pointed me to, but I had >>> always thought that they were in a normalized space. >>> >>> Thank you again! >>> Liz >>> >>> -----Original Message----- >>> From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] >>> Sent: Monday, August 03, 2009 4:35 PM >>> To: Elizabeth Selgrade >>> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >>> Subject: Re: [Freesurfer] Registering aseg to base for volume >>> overlap calculations >>> >>> Hi Liz, >>> >>> the registrations are stored in >>> baseid/mri/transforms >>> look for files baseid_to_tpNid.lta >>> and the inverse tpNid_to_baseid.lta (which is the map you are >>> looking > for). >>> These should align all your TPs to the base space. >>> >>> >>> Best, Martin >>> >>> On Mon, 2009-08-03 at 16:19 -0400, Elizabeth Selgrade wrote: >>>> Hello FreeSurfer Users, >>>> >>>> I am using the longitudinal stream to look at four >>>> timepoints/subject, and I'd like to transform all of my timepoints >>>> to the base scan's unbiased space so that I can calculate ROI >>>> volume overlap. I have been using tkregister2 to calculate the >>>> transform from my scan.base.long/mri/aseg.mgz to >>>> base/mri/rawavg.mgz and then using >>> mri_label2vol to apply the transform. >>>> When I do this for all of my scans, I expect to see that the brains >>>> are overlapping in the same space. But, I'm not getting that. Any >>>> suggestions for how to get all of these scans back in the > base space? >>>> >>>> Thank you! >>>> Liz Selgrade >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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FSGDF Format Error ?
by Erick Jorge Canales 06 Aug '09

06 Aug '09

Hi FreeSurfer, I am trying to run Glm for a group comparison analysis I ran the mris_prepoc and mri_surf2surf and it completed without error. However, when I run mri_glmfit it gives me the following error: gdfReadHeader: reading comp_groups.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = Cont_FreeSurf_BMAMDCONTROL20 Found 1 variables, expected. 0 FSGDF Format Error: file = comp_groups.fsgd, tag=Input The "comp_groups.fsgd" file was constructed in line with the FreeSurfer rules... For instance, GroupDescriptorFile 1 Title Lista_Controles_y_Pacientes Class Home_Control Class Home_SC Class Dona_Control Class Dona_SC Variable Age Input Cont_FreeSurf_BMAMDCONTROL20 Home_Control 27 Input Cont_FreeSurf_BMAMGCONTROL27 Dona_Control 38 Input Cont_FreeSurf_BMAMMCONTROL43 Home_SC 46 Input Cont_FreeSurf_BMAMMCONTROL5 Dona_SC 28 ... Is there any problem with this format? The data corresponding to each subject is locate inside the $SUBJECTS_DIR directory (i.e., $SUBJECTS_DIR/Cont_FreeSurf_BMAMDCONTROL20) Regards, Erick

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tksurfer display
by Jerome Sallet 06 Aug '09

06 Aug '09

Help, Sorry to bother you, but I am looking for my tksurfer hero! I just installed freesurfer on my laptop (centos5 virtual machine, 4Go RAM, NIVDIA quadro 110M, intel duo T2300(a)1.66GHz) Everything goes well until I tried tksurfer. Only the anterior part of bert's brain is displayed.(medit is ok; refreshing the tksurfer view doesn't change the display). Is there a way to fix my problem or is my graphic card not performant enough ? Thanks a lot for your help Cheers, J -- __________________________________________________ Jerome SALLET Decision and Action Laboratory Department of Experimental Psychology, University of Oxford South Parks Road, OX1 3UD,UK Tel (office): (0044) 1865 271 315 Tel (elsewhere) : (0044) 7 530 060 839 http://psyweb.psy.ox.ac.uk/rushworth/default.htm

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failed skill strip
by Dana W. Moore 05 Aug '09

05 Aug '09

Hi, I have tried to run recon-all on an image and received the following error: "White matter intensity 0 is lower than CSF intensity 19. Please examine input images. Will terminate... MRIstripSkull failed. The T1 images look fine, and I have run several similar brains with no problem. This is the first time this has happened. I am using version 4.4.0. Any thoughts on what the problem is? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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modifying dicom headers
by Jared Price 05 Aug '09

05 Aug '09

Hi all, I am looking for a powerful, robust tool for modifying dicom headers that can be called from the command-line and scripted. For example, I may need to alter the subject ID with which a dicom study was uploaded. We are managing a multi-site study and the various sites do not always uplaoded the images with the correct study-wide ID. Anyone know of a good one?

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contrast matrix question
by Victoria Williams 05 Aug '09

05 Aug '09

Hello, I apologize if this is a very simple question, but how would you set up a contrast matrix to look at the interaction of 2 variables on a measure? For example, my fsgd file contains: class=1 variables=2 Input Subjid class var1 var2 When I tried using a contrast of 0_1_1 the significance map looks very similar to the glm run only containing var1 (contrast_0_1). I thought 0_1_1 was correct, but now I'm not so sure and would like to double check. What I am interested in is how the interaction of var1 and var2 is correlated with the brain measure per voxel. Is this possible with mri_glmfit? I've checked the tutorials and scoured the internet as not to ask any silly questions, but I'm having trouble finding anything helpful. Thanks in advance! Tori

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Measuring the Volume of a 3D Mask
by Nasim Maleki 05 Aug '09

05 Aug '09

Dear all, I have 3D masks defined in MNI space using FSL. I would like to transform these masks to each subjects anatomical space in FreeSurfer and measure the volumes corresponding to these masks. Should I just count the number of voxels in each mask after transformation to the structural space and report the #voxels x (1x1x1mm3) as the corresponding volume to that mask? Thanks for your help, Nasim

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Cluster size threshold for the sig.mgh file
by Jürgen Hänggi 05 Aug '09

05 Aug '09

Dear FS experts We would like to threshold the cluster size in the sig.mgh image in order to exclude clusters that are only a few vertices in size, but I cannot find this option Is it possible to do it within FS? If yes, how to do it? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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"redraw failed: no gl window open" problem
by Guang Zeng 05 Aug '09

05 Aug '09

Hi, there, I am running the tksurfer command to view the cortical surface data as tksurfer bert lh inflated. But I met a problem. I only can view a sliver part of the brain. This sliver portion can rotate and do everything that tksurfer is supposed to do, but I can't view any more of the brain than a tiny piece. Tkmedit works fine. When I run the command, it gave me something like this: surfer: current subjects dir: /home/m047599/freesurfer-install/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/m047599/freesurfer-install/freesurfer surfer: Reading header info from /home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131369, faces=262734 Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... I searched the previous posts, it looks like somebody have the same problem. There is no NVidia and native Linux system on my computer. I run tksurfer on a virtual Linux machine using NX 3. 3. 0. 6. I ran the xdpyinfo | grep GL, it shows that I have GLX and SGI-GLX. I ran the glxgrears, it works, although very slow. So, how can I solve this problem, any suggestions are highly appreciated. Thanks a lot! Guang _________________________________________________________________ Get free photo software from Windows Live http://www.windowslive.com/online/photos?ocid=PID23393::T:WLMTAGL:ON:WL:en-…

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Re: [Freesurfer] Mapping from Freesurfer to FSL
by Douglas N Greve 04 Aug '09

04 Aug '09

You can use this matrix to do it approximately $FREESURFER_HOME/average/mni152.register.dat Joseph Barrington Keller wrote: > Hello, > I'm in the process of trying to map designated voxels from Talairach space in Freesurfer to the corresponding image in subject space in FSL's gui FDT(Probtrackx). Obviously, there will not be a direct mapping between these two coordinate spaces. How would I go about this? Thanks in advance. > > -Joe > > _______________________________________________ > 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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Freesurfer August 2009