Freesurfer October 2009

freesurfer@nmr.mgh.harvard.edu

99 participants
151 discussions

Edits in the longitudinal stream
by hakon.grydeland＠psykologi.uio.no 15 Oct '09

15 Oct '09

Hi, I have a couple of questions regarding manual edits such as deleting non-brain tissue included in the pial surface in the longitudinal stream (v4.5): 1. Where in the longitudinal stream would you recommend doing edits? On the brainmask.mgz of the base? 2. If so, would you then re-run the base as a cross-sectional (recon-all -s baseid -autorecon2-pial -autorecon3)? Thanks, Håkon

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Re: [Freesurfer] transverse gyrus and translucent brain renderings
by Nick Schmansky 15 Oct '09

15 Oct '09

forwarding to the list.... On Thu, 2009-08-06 at 20:57 +0200, Christophe Destrieux wrote: > Hi Narly > > below are a few explanations on the transverse temporal gyrus in the > a2005 parcellation > > At the superior aspect of the superior temporal gyrus: > > * the transverse temporal *sulcus* limits the planum temporale > (posteriorly) from the transverse temporal gyrus (anteriorly); it > originates at the posterior segment of the lateral sulcus, runs > anterior and lateral and joins the lateral aspect of the temporal > lobe. > > * The transverse temporal gyrus (or Heschl's gyrus) is just anterior > and parallel to the transverse temporal sulcus. Instead of a > single transverse temporal gyrus, several “transverse” temporal > gyri bordered by intermediate sulci may be present. Only the more > anterior transverse temporal gyrus is labeled in Freesurfer, the > posterior ones being included in the planum temporale since they > where shown not to correspond to primary, but to secondary > auditory cortex > > I hope that it helped > > cheers > > -- > Christophe Destrieux > Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé > 37032 Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > Narly, > > > > I'm forwarding this to Christophe Destrieux, cc'd, who I think can > > answer your question about how that region is labelled. > > > > It is not possible to do translucent viewing in tksurfer. However, it > > is possible in qdec. Just use the load surface and load annotation menu > > options. > > > > Nick > > > > > > On Thu, 2009-08-06 at 16:26 +0100, Narly A Golestani wrote: > > > >> 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. > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > > >

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a question about mri_label_volume -eTIV
by Guang Zeng 14 Oct '09

14 Oct '09

Hi, there, >From FS Wiki, eTIV - estimated Total Intracranial Volume, aka ICV, I read mri_label_volume requires specifying the transform file to use, and the scale factor: mri_label_volume -eTIV \ $sdir/transforms/talairach.xfm 1948 \ $sdir/aseg.mgz 17 53where $sdir is the path to the subject's mri directory (ie, $SUBJECTS_DIR/<subjid>/mri). The '17' and '53' are label ID's, in this case left and right hippocampus (see the subjects /stats/aseg.stats file for IDs). The output will look like: using eTIV from atlas transform of 1528 cm^3 processing label 17... 3822 voxels (3822.0 mm^3) in label 17, %0.250119 of eTIV volume (1528075) processing label 53... 4410 voxels (4410.0 mm^3) in label 53, %0.288598 of eTIV volume (1528075)>From a previous post at FS mailing list, I also read something similar, Just as an aside, once you have a talairach_with_skull.lta file (whether from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta), where the scale_factor employed is 2150. Just want to know where dose this scale factor number 1948 and 2150 come from? Thanks a lot! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/

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Any way to calculate overlap of labels to atlas regions quickly?
by Laluz, Victor 14 Oct '09

14 Oct '09

Hello, I'm interested in subdividing some of the standard atlas regions into anterior and posterior divisions. Besides creating individual labels for each of the labels, is it possible to create a generic anterior label for multiple subregions (encompassing an entire lobe at a time), then quickly calculate areas of overlap between each individual atlas region and the anterior lobe label in order to calculate anterior volumes per region? Victor Laluz

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index out of bounds
by Alessandro D. Gagliardi 14 Oct '09

14 Oct '09

Hello FreeSurfers, I'm trying to analyze some BOLD data where the subject moves through a dozen or so states over the course of an hour. None of these repeat but they are the same for all subjects. I have a .par file that specifies the duration of each segment with an integer index for each one. I don't need an HRF; a square wave is preferable. But that doesn't seem to be an option in mkanalysis-sess so I used a gamma function with an exponent of 0 and a long dispersion (~300 sec.) which seems to approximate a square wave well enough. There is no "resting state" to speak of, each state is meant to be contrasted against all the others. It's a very simple design and yet difficult to fit into an analysis. I thought I did it right (or well enough) but when I try to run it I get a series of errors that Google is of no help in elucidating: ??? Attempted to access a(1); index out of bounds because numel(a)=0. Error in ==> fast_st2fir at 121 b(1) = a(1); Error in ==> flac_desmat at 56 flacnew.ev(nthev).Xfir = fast_st2fir(st,flac.ntp,flac.TR,ev.psdwin,1); Error in ==> flac_customize at 272 flacnew = flac_desmat(flacnew); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Any help figuring this out would certainly be appreciated! Thank you, Alessandro D. Gagliardi Ph.D. Candidate Integrative Neuroscience Program Rutgers University Mind Brain Analysis adfgagliardi(a)gmail.com

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Fwd: probabilistic segmentation of gray matter
by Giacomo Mandruzzato 14 Oct '09

14 Oct '09

---------- Forwarded message ---------- From: Giacomo Mandruzzato <giacomo.mandru(a)gmail.com> Date: 2009/10/14 Subject: probabilistic segmentation of gray matter To: freesurfer(a)nmr.mgh.harvard.edu Hi, I have a question about a probabilistic segmentation of gray matter with freesurfer. How can I do it? if I binarize like this: mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz I obtain only a mask 0-1. Can I obtain a probablistic map like I obtained with SPM and FSL of the gray matter? thank you in advance Giacomo Mandruzzato Student of Bioengineering Universiti of Padova

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Re: [Freesurfer] [martinos-tech] surfcluster & simulations
by Frida Polli 14 Oct '09

14 Oct '09

so doug we ran them using qdec. can you expand? On Tue, Oct 13, 2009 at 6:00 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> >> >> It depends on which program you ran and how you ran it. >> >> >> Frida Polli wrote: >> > >> > >> > hey bruce, nick, doug >> > >> > when we use qdec to generate simulations to find CWP, the cluster >> > sizes that we get are smaller area than if we make a label from the >> > cluster and use label_area to determine the size of the cluster. >> > >> > im just wondering if the CWP value that we get is therefore correct? >> > and what could be the cause of this discrepancy? >> > >> > i feel like i might have seen this before with surfcluster and fMRI >> > data but i dont totally remember. >> > >> > thnx, frida >> > >> > >> > -- >> > Frida E. Polli, PhD >> > Postdoctoral Fellow >> > Brain & Cognitive Sciences, MIT >> > 43 Vassar St., Room 46-4033 >> > Cambridge, MA 02139 >> > email: fpolli(a)mit.edu <fpolli%40mit.edu> <mailto:fpolli@mit.edu<fpolli%40mit.edu> >> > >> > tel: (617) 324 2897 >> > >> > >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <greve%40nmr.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 >> >> __._,_.___ >> Messages in this topic >> <http://groups.yahoo.com/group/martinos-tech/message/4903;_ylc=X3oDMTM0cTJmY…>( >> 2) Reply (via web post) >> <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwNzdjNWViBF9TA…>| Start >> a new topic >> <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlcmVxZ3JkBF9TA…> >> Messages<http://groups.yahoo.com/group/martinos-tech/messages;_ylc=X3oDMTJlbWU5N3Q5B…>| >> Files<http://groups.yahoo.com/group/martinos-tech/files;_ylc=X3oDMTJmb3Zxcm9rBF9T…>| >> Photos<http://groups.yahoo.com/group/martinos-tech/photos;_ylc=X3oDMTJlcDBhZGJmBF9…>| >> Links<http://groups.yahoo.com/group/martinos-tech/links;_ylc=X3oDMTJmcTEyMDBmBF9T…>| >> Database<http://groups.yahoo.com/group/martinos-tech/database;_ylc=X3oDMTJjcTZzNjI1B…>| >> Polls<http://groups.yahoo.com/group/martinos-tech/polls;_ylc=X3oDMTJmaWt0djJ1BF9T…>| >> Members<http://groups.yahoo.com/group/martinos-tech/members;_ylc=X3oDMTJlNWhkNjZvBF…>| >> Calendar<http://groups.yahoo.com/group/martinos-tech/calendar;_ylc=X3oDMTJkN2FiczhrB…> >> MARKETPLACE >> Mom Power: Discover the community of moms doing more for their families, >> for the world and for each other<http://us.ard.yahoo.com/SIG=14kt86mmb/M=493064.12016295.13271503.10835568/D…> >> [image: Yahoo! Groups]<http://groups.yahoo.com/;_ylc=X3oDMTJkdnFpZThmBF9TAzk3MzU5NzE0BGdycElkAzQ5O…> >> Change settings via the Web<http://groups.yahoo.com/group/martinos-tech/join;_ylc=X3oDMTJmaDF1bHQ2BF9TA…>(Yahoo! ID required) >> Change settings via email: Switch delivery to Daily Digest<martinos-tech-digest@yahoogroups.com?subject=Email+Delivery:+Digest>| Switch >> format to Traditional<martinos-tech-traditional@yahoogroups.com?subject=Change+Delivery+Format:+Traditional> >> Visit Your Group >> <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJkNzB0cDc4BF9TAzk3Mz…>| Yahoo! >> Groups Terms of Use <http://docs.yahoo.com/info/terms/> | Unsubscribe >> <martinos-tech-unsubscribe(a)yahoogroups.com?subject=> >> Recent Activity >> >> - 1 >> New Members<http://groups.yahoo.com/group/martinos-tech/members;_ylc=X3oDMTJmbGpncnZ1BF…> >> >> Visit Your Group >> <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlcTdwdmI3BF9TAzk3Mz…> >> Yahoo! Search >> >> Start Searching<http://us.ard.yahoo.com/SIG=14h8ql1md/M=493064.12016265.12445672.8674578/D=…> >> >> Find exactly >> >> what you want. >> Y! Messenger >> >> Want a quick chat?<http://us.ard.yahoo.com/SIG=14hrgv4uq/M=493064.12016274.12445679.8674578/D=…> >> >> Chat over IM with >> >> group members. >> Group Charity >> >> Be the Change<http://us.ard.yahoo.com/SIG=14h073ovj/M=737447.13475021.13554044.8674578/D=…> >> >> A citizen movement >> >> to change the world >> . >> >> __,_._,___ >> > > > > -- > Frida E. Polli, PhD > Postdoctoral Fellow > Brain & Cognitive Sciences, MIT > 43 Vassar St., Room 46-4033 > Cambridge, MA 02139 > email: fpolli(a)mit.edu > tel: (617) 324 2897 > > > -- Frida E. Polli, PhD Postdoctoral Fellow Brain & Cognitive Sciences, MIT 43 Vassar St., Room 46-4033 Cambridge, MA 02139 email: fpolli(a)mit.edu tel: (617) 324 2897

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using freeview
by Ahmed, F, Me <fahmed＠sun.ac.za> 14 Oct '09

14 Oct '09

Hello, I had problems with the "sliver" problem with Tkmedit and tried all of the possible solutions to try and correct it, to no avail. My last resort was using freeview. I tried the example commands Nick wrote on the wiki site for this problem: cd <subjid> freeview --volume mri/T1.mgz \ --surface surf/lh.white \ --surface surf/rh.white \ --surface surf/lh.pial:annot=aparc.annot \ --surface surf/rh.pial:annot=aparc.annot And I got the following output, I just wanted to know if what I'm seeing is correct. And if this is what freeview looks like? Thank you

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fwd: Re: Re: problem display tksurfer in vmware
by Pedro Paulo de Magalhaes Oliveira Jr 14 Oct '09

14 Oct '09

-----Msg original----- De: Giacomo Mandruzzato Enviado: 14/10/2009 06:22:24 Assunto: Re: Re: [Freesurfer] problem display tksurfer in vmware Hi, I have a question about a probabilistic segmentation of gray matter with freesurfer. How can I do it? if I binarize like this: mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz I obtain only a mask 0-1. Can I obtain a probablistic map like I obtained with SPM and FSL of the gray matter? thank you in advance Giacomo 2009/9/28 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > Have you installed the VirtualBox that comes from the FreeSurfer Wiki? > VirtualBox 3.x? > > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.2 www.Netfilter.com.br > --- Novo Netfilter Small Business > > > > 2009/9/28 Giacomo Mandruzzato <giacomo.mandru(a)gmail.com> > > Hi, >> now I have installed Virtual Box with freesurfer, but I have same problem >> with tksurfer and a library problem with qdec (it can't find libtiff.so.3 >> file, and in the folder I see only libtiff.so.3 file!) >> Giacomo >> >> 2009/9/26 Giacomo Mandruzzato <giacomo.mandru(a)gmail.com> >> >> thankyou for your help and your rapid answer. >>> >>> I use bash and i set doublebufferflag=1 but the problem persists! >>> >>> >>> 2009/9/26 Pedro Paulo de Magalhaes Oliveira Jr <ppj(a)netfilter.com.br> >>> >>>> In csh use setenv doublebufferflag 1 >>>> >>>> In bash export doublebufferflag=1 >>>> >>>> >>>> -- >>>> Enviado do meu celular Nokia E71 >>>> -----Msg original----- >>>> De: Giacomo Mandruzzato >>>> Enviado: 26/09/2009 09:33:26 >>>> Para: ppj(a)netfilter.com.br >>>> Assunto: Re: [Freesurfer] problem display tksurfer in vmware >>>> >>>> Yes, I know but I have problem with VirtualBox in the first boot that I >>>> do! >>>> Can I use freesurfer (and so tksurfer) with vmware? Or Is there any >>>> solution >>>> for my problem? >>>> thank you >>>> >>>> 2009/9/26 Pedro Paulo de Magalhaes Oliveira Jr <ppj(a)netfilter.com.br> >>>> >>>> > Use the official FreeSurfer distribution for Virtualbox >>>> > >>>> > -- >>>> > Enviado do meu celular Nokia E71 >>>> > -----Msg original----- >>>> > De: Giacomo Mandruzzato >>>> > Enviado: 26/09/2009 08:22:55 >>>> > Para: freesurfer(a)nmr.mgh.harvard.edu >>>> > Assunto: [Freesurfer] problem display tksurfer in vmware >>>> > >>>> > Hi, >>>> > I'm Giacomo Mandruzzato, a student of Bioengineering at Padova (DIE) >>>> and >>>> > I'm >>>> > working on my Thesis with Freesurfer (last version). I am using a >>>> virtual >>>> > machine Vmware 2.5.3 with Cent0S 5.1 running FSL virtual disk in >>>> Windows >>>> > Vista Home premium, >>>> > I installed freesurfer and tkmedit e qdec run correctly but when run >>>> > tksurfer (i.e. tksurfer bert rh pial, like website suggests) display >>>> an >>>> > error : >>>> > >>>> > >>>> > > [root@localhost ~]# tksurfer bert rh pial >>>> > > surfer: current subjects dir: /usr/local/freesurfer/subjects >>>> > > surfer: not in "scripts" dir ==> using cwd for session root >>>> > > surfer: session root data dir ($session) set to: >>>> > > >>>> > > surfer: /root >>>> > > surfer: all rgb files written to /root >>>> > > surfer: Reading header info from /usr/local/freesurfer/ >>>> > subjects/bert/mri/T1.mgz >>>> > > surfer: vertices=131860, faces=263716 >>>> > > >>>> > > >>>> > > WARNING: No colortable found! >>>> > > >>>> > > >>>> > > >>>> > > surfer: single buffered window >>>> > > surfer: tkoInitWindow(bert) >>>> > > surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl >>>> > > Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl >>>> > > Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl >>>> > > >>>> > > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl >>>> > > Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl >>>> > > Successfully parsed tksurfer.tcl >>>> > > reading white matter vertex locations... >>>> > > % >>>> > > >>>> > > >>>> > >>>> > Tksurfer open and I can see only a little piece of brain. >>>> > I have update the video card's driver and I tried to use another vm, >>>> like >>>> > VirtualBox but I left the idea because I found some problem with boot >>>> of >>>> > it. >>>> > I have found a similar problem in internet, but without solution: >>>> > >>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07389.html(I<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07389.html%28I> >>>> > am not using a Nvidia video card). >>>> > >>>> > >>>> > characteristic of my notebook: >>>> > Olidata , Intel core duo T2450 @ 2 x 2.00 Ghz, >>>> > Ram 2 GB, Windows Vista Home Premium 32bit SP2 updated. >>>> > Video card: Mobile Intel 945 Express Chipset Family >>>> > >>>> > I apologize for bad English and little knowledge of Unix OS. >>>> > Please, if somebody can help I am grateful. >>>> > >>>> > Best Regards, >>>> > >>>> > Giacomo Mandruzzato >>>> > giacomo.mandru(a)gmail.com >>>> > >>>> > >>>> >>>> >>> >> >

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Matrix is singluar to working precision
by Maximilien Chaumon 13 Oct '09

13 Oct '09

Hi Freesurfers, I'm trying to selxavg3 my data. My design includes 6 conditions including a 0 rest condition. 3 contrasts have been defined using mkcontrast. The analysis too using mkanalysis. I use this command line : [/homes/11/chaumon/data] (nmr-std-env) selxavg3-sess -analysis "Analyse_Simple_Confidence" -s S003 -overwrite Which returns what's in the log file attached. and ends with Creating Design Matrix Warning: Matrix is singular to working precision. > In fast_selxavg3 at 212 Warning: Matrix is singular to working precision. > In fast_selxavg3 at 212 Warning: Matrix is singular to working precision. > In fast_selxavg3 at 212 Warning: Matrix is singular to working precision. > In fast_selxavg3 at 212 Warning: Matrix is singular to working precision. > In fast_selxavg3 at 212 Warning: Matrix is singular to working precision. > In fast_selxavg3 at 212 Warning: Matrix is singular to working precision. > In fast_selxavg3 at 212 Warning: Matrix is singular to working precision. > In fast_selxavg3 at 212 Warning: Matrix is singular to working precision. > In fast_selxavg3 at 212 ntptot = 693, nX = 15, DOF = 678 Saving X matrix to /autofs/space/bomba_016/users/chaumon/S003/bold/Analyse_Simple_Confidence/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 248 XCond = cond(XtX); >> 09-Oct-2009 18:03:13 Salut ! ------------------------------------------ ERROR: fast_selxavg3() failed\n I'm puzzled. I've been checking and rechecking my design. The problem does not come from the contrasts because I get the same error if I remove them... Any help will be greatly appreciated. Thanks, Max

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Freesurfer October 2009