Freesurfer August 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
143 discussions

tksurfer display
by corinna bauer 11 Aug '09

11 Aug '09

When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help. surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...

3 7

mri_normalize problem
by Guang Zeng 10 Aug '09

10 Aug '09

Hi, there, I have a question about the mri_normalize command, I do not want to use conform, so my command line is mri_normalize -g 1 -noconform nu.mgz T1.mgz I got an error message as: using max gradient = 1.000 performing kinder gentler normalization... not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... talairach transform -1.241 0.006 0.133 1.851; 0.087 0.889 0.292 1.071; 0.125 -0.275 0.973 -6.721; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRIsplineNormalize(): npeaks = 3 Starting OpenSpline(): npoints = 3 MRInormGentlyFindControlPoints: unsupported src format 3 MRI3dGentleNormalize failure! mri_ctrl=NULL Does this mean that I must load a control data? Is there a way that I can use the mri_normalzie command without conform and control data? Thanks a lot! Guang _________________________________________________________________ Get free photo software from Windows Live http://www.windowslive.com/online/photos?ocid=PID23393::T:WLMTAGL:ON:WL:en-…

3 3

N-Back Test for E-prime?
by Dave Brohawn 10 Aug '09

10 Aug '09

Hello Freesurfers, Josh Roffman and I are going to begin a study in the near future that utilizes both the SIRP task and the N-Back test. I am curious if anyone has a working N-Back paradigm that can be run through E-prime? We don't possess one currently, and if we can avoid creating one from scratch, that would be nice. Please let me know, and thanks, Dave Brohawn

2 1

Lesion Quantification
by Jose Soares 09 Aug '09

09 Aug '09

Hello all, I would like to know if there is a way to measure the number of brain lesions on Freesurfer? If no, what can I use? Thanks for the help, Miguel. ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

2 2

mri_convert question
by Guang Zeng 07 Aug '09

07 Aug '09

Hi, there, I am new to FreeSurfer, just got a question about the mri_convert command. I have a 169x256x256 binary volume, the format is .nii. I called the mri_convert command to convert it to .mgz format. I open the .mgz volume using tkmedit, and then open the .nii volume using fsl view, I got to a problem, I input the same volume index in tkmedit and fsl view, I got the two different views. I think that is because mri_convert will automatically convert the input volume to a 256x256x256 volume, am I right? If I am right, how can I convert the 256x256x256 volume to the original size when I call mri_convert again to convert the .mgz back to .nii. Thanks a lot! Guang _________________________________________________________________ Windows Live™: Keep your life in sync. http://windowslive.com/explore?ocid=PID23384::T:WLMTAGL:ON:WL:en-US:NF_BR_s…

2 2

ascii file
by Feng-Xian Yan 07 Aug '09

07 Aug '09

Hi, I had asked two problems before; one is what is coordinates when I type mris_convert -c lh.thickness lh.white lh.thickness.asc, and another is if the asc file doesn't use Tal coordinate, what commands do I type to obtain the thickness asc with Tal coordinate?, and then you responded me with “the coordinates are native RAS. You can use mri_surf2surf to convert the surface to tal coords with the talairach.xfm.” So, first, I change the native RAS cooridinate to Tal coordinate with “mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh --sval-tal-xyz orig --tval-xyz” srcsubject = noise0.5_0 srcval = thickness srctype = trgsubject = noise0.5_0 trgval = noise0.5_0_tal.xfm trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg Loading source data Reading surface file /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig Applying MNI305 talairach transform 0.966 0.002 -0.004 0.426; 0.018 0.989 0.041 -19.382; -0.006 0.032 0.962 17.438; 0.000 0.000 0.000 1.000; INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data Then, I obtain the thickness asc file with Tal coordinate using this command “mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc” But, this has an error: MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm What’s wrong? Would you tell me how to resolve? Thank you in advance! Feng-Xian

3 5

PostDoc Position at UCL Institute of Neurology - London (UK)
by Dr. Claudia Wheeler-Kingshott 07 Aug '09

07 Aug '09

*Postdoctoral Research Associate - MRI Physicist *University College London, London, England, UK *UCL Institute of Neurology Department of Neuroinflammation Postdoctoral Research Associate - MRI Physicist* An MRI Postdoctoral Physicist is sought for the NMR Research Unit in the Department of Neuroinflammation at UCL Institute of Neurology, London. Over the past 20 years, the Unit has been developing new MR methods, carrying out research into Multiple Sclerosis, using a 1.5 T whole body scanner (General Electric). Recently the Multiple Sclerosis Society of Great Britain and Northern Ireland has awarded Prof. David Miller et al. a grant for funding a state of the art high field 3T Philips scanner, which will be installed in the second half of 2009. The appointee will contribute to the development and optimisation of sequences for innovative new research into multiple sclerosis, with particular focus on high resolution grey matter imaging of the brain, using a variety of MR techniques. S/he will also have the opportunity to take part in developing innovative quantitative methods, such as diffusion, perfusion, magnetisation transfer, relaxometry, chemical shift imaging and sodium imaging. MR physics support will also be required for existing longitudinal studies and newly implemented techniques. There will be active collaboration with clinical researchers and physicists in the Unit and across the Institute Applicants should have a PhD or equivalent in MR physics or biomedical engineering, a strong background in MR sequence development, and preferably experience of using a 3T scanner in a research environment and of developing one of the above mentioned quantitative methods. The post is available immediately and is funded for three years by the MS Society. Starting salary on UCL Grade 7 in the range £31,620 - £35,239 pa inclusive of London Allowance, superannuable. You are encouraged to apply for this post through UCL's online recruitment <https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=b3duZXI9NTA0MTE3OCZvd25l…> However, if you prefer, the job description and person specification can be downloaded from: http://www.ion.ucl.ac.uk/about/vacancies.htm For further information only (not applications) please contact Samantha Robinson, Personnel Officer, Institute of Neurology, 23 Queen Square, London WC1N 3BG (tel: 020 7676 2191; fax: 020 7278 5069; email: personnel(a)ion.ucl.ac.uk <mailto:personnel@ion.ucl.ac.uk>). Closing date for applications: 7 September 2009. Further information can be obtained from Dr. Claudia Wheeler-Kingshott (email: c.wheeler-kingshott(a)ion.ucl.ac.uk <mailto:c.wheeler-kingshott@ion.ucl.ac.uk>) or Prof. Xavier Golay (x.golay(a)ion.ucl.ac.uk <mailto:x.golay@ion.ucl.ac.uk>) and from the Unit website ( http://www.nmrgroup.ion.ucl.ac.uk/ ) /UCL Taking Action for Equality/

1 0

Fwd: Re: correction for behavioral varialbles in qdec
by Rosa Steimke 07 Aug '09

07 Aug '09

-------- Original-Nachricht -------- Datum: Tue, 04 Aug 2009 19:33:18 +0200 Von: "Rosa Steimke" <rosasteimke(a)gmx.de> An: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec thanks, but which input file do i have to use? where can i find this sig.mgh file from the qdec analysis? rosa -------- Original-Nachricht -------- > Datum: Tue, 04 Aug 2009 12:46:49 -0400 > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > An: Rosa Steimke <rosasteimke(a)gmx.de> > CC: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec > You can run mri_surfcluster on the sig.mgh for this kind of thing. > > doug > > Rosa Steimke wrote: > > Thanks Bruce!! > > now i wonder whether it is possible to get a table of all the > significant blobbs that i found in qdec that gives the size and average p value or > some other way to find this out? > > rosa > > -------- Original-Nachricht -------- > > > >> Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT) > >> Von: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> An: Rosa Steimke <rosasteimke(a)gmx.de> > >> CC: freesurfer(a)nmr.mgh.harvard.edu > >> Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec > >> > > > > > >> Hi Rosa, > >> > >> you have to select them. > >> > >> cheers, > >> Bruce > >> > >> On Tue, 4 Aug 2009, Rosa Steimke wrote: > >> > >> > >>> HI, > >>> i have a question regarding qdec. If i load a designfile with 4 > >>> > >> variables, but than i only select 1 for analysis, does qdec then > correct for the > >> other variables that i did not select? or do i have to select them? > >> > >>> thanks in advance!! > >>> rosa > >>> > >>> > >> _______________________________________________ > >> 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 -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01 -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

3 5

transverse gyrus and translucent brain renderings
by Narly A Golestani 06 Aug '09

06 Aug '09

Hello, I would like to know more about the automatic labelling of the transverse temporal gyrus is done. I looked at the below article but don't see any details about this structure. https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf I would for example like to know how the boundaries of this structure are defined/determined. Also, when using tksurfer to view labels ('import annotation'), is it possible to make the 3D brain surface (and labels) translucent so that one can more carefully view where this (medial-spanning) gyrus was identified? thanks in advance, Narly.

2 1

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

06 Aug '09

Martin, This works perfectly! Thanks, Liz -----Original Message----- From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] Sent: Thursday, August 06, 2009 1:31 PM To: Elizabeth Selgrade Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Registering aseg to base for volume overlap calc ulations Hi Liz, try this: mri_convert -T $BASEDIR/transforms/${TP}_to_base.lta -rl $BASEDIR/norm.mgz -rt nearest --out_type nii $TPDIR/mri/aseg.mgz $TPDIR/aseg.base.nii (that should work, if not split it into two steps: transform and then convert into nii). The -rl (reslice like) is important, if you want the voxel images to align, otherwise the images are aligned in RAS space (and some viewers cannot deal with that, if they only show the voxel data). Also the -rt (resample type) should be nearest when mapping asegs (because otherwise the values get interpolated). Cheers, Martin On Thu, 2009-08-06 at 09:41 -0400, Elizabeth Selgrade wrote: > 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 > > > > > > > >

1 0

← Newer
1
...
9
10
11
12
13
14
15
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2009