Freesurfer January 2008

freesurfer@nmr.mgh.harvard.edu

54 participants
69 discussions

comparison of twins
by Thomas Doering 23 Jan '08

23 Jan '08

Hi, i am wondering how i can do a comparison of just two subjects (twins), calculating differences between them in cortical thickness, gm-volume .etc... I tried to find some paper with a processing pipline for this but without success... Perhaps somebody has a hint for me? Thanks, Thomas

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losing aseg edits
by Michael Harms 23 Jan '08

23 Jan '08

Hello, Kristine's earlier post got me wondering why she was "losing" any previous aseg edits if her data were re-processed under FS v4, since it was my simple understanding that all edits (e.g., control points, brainmaks, talairach, white matter, aseg) are intended to be preserved, unless you explicitly set one of the "clean" flags. Looking at the recon-all script for FS v4.0.2, I now see that any aseg edits will indeed be lost if the corpus callosum segmentation has not been previously already run (e.g., say if you are re-processing data originally processed under FS v3). Namely, if the file "aseg.auto_CCseg.mgz" does not exist, then variable 'AsegDiff' gets set to 0, which in turn results in aseg.auto_CCseg.mgz being subsequently copied to aseg.mgz, thus losing any previous edits to the aseg.mgz. Is this the intended behavior? Is there an easy way to get the CC segmentation while still preserving any previous aseg edits? cheers, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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?h.volume files
by bell0368＠umn.edu 23 Jan '08

23 Jan '08

Freesurfers, The wiki mentions one of the "known issues" with the current release is that recon-all does not create ?h.volume files. I have been using the following command to create what appear to be volume files for cortical and wm parcellations. Is the problem just that these files are not created automatically? mri_extract_label aparc+aseg.mgz (number corresponding to the desired label) (name of the output label/volume file) Chris Bell

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Re: [Freesurfer] recommended scan parameters
by Sebastian Moeller 22 Jan '08

22 Jan '08

Hi Michael, On Jan 22, 2008, at 4:18 PM, Michael Chee wrote: > Hi Sebastian and Bruce, > > I'll respond by the end of the week as I have some things to tend to > presently. Cool, thanks a lot and no hurry (no(t much) time this week either for testing/acquiring new anatomical scans myself). ahoi & thanks Sebastian > > Mike > > >> From: Sebastian Moeller <sebastian.moeller(a)lur.rwth-aachen.de> >> Date: Tue, 22 Jan 2008 15:10:15 +0100 >> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Cc: Mailing Freesurfer List <freesurfer(a)nmr.mgh.harvard.edu>, >> Andre van der >> Kouwe <andre(a)nmr.mgh.harvard.edu>, Mike Chee <mchee(a)pacific.net.sg> >> Subject: Re: [Freesurfer] recommended scan parameters >> >> Hi Bruce, >> >> thanks for your quick response. >> >> On Jan 22, 2008, at 3:06 PM, Bruce Fischl wrote: >> >>> Hi Sebastian, >>> >>> we put together some Allegra-specific postprocessing tools that >>> helped for Mike Chee (ccd). Maybe Mike can give you the benefit of >>> his experience? >> That would be marvellous. Thanks in advance. >> >> ahoi >> Sebastian >> >>> >>> cheers, >>> Bruce >>> >>> On Tue, 22 Jan 2008, Sebastian Moeller wrote: >>> >>>> Dear Experts, >>>> >>>> after ages of monkey scanning, we recently also included human >>>> subjects in our study. I would like to use freesurfer for surface >>>> reconstruction, mainly as "canvas" for the display of activation >>>> maps. >>>> While functional scans seem to be reasonable, the anatomicals >>>> taken on our Siemens Allegra (3T) with the default Siemens head >>>> coil are not well reconstructed by freesurfer (pial surface is >>>> both under- and over-inclusive, white matter in temporal pole is >>>> mis-classified as gray). Just in case it matters, test >>>> reconstructions were performed using the 64 bit centos_4 >>>> FreeSurfer 4.0.2 build on SuSUE 10.1 64 bit (and no errors in from >>>> the recon-all -autorecon1 and -autorecon2 stages). I assume that >>>> this is a driver's error on my part, as switching to the sequence >>>> parameters given on http://www.nmr.mgh.harvard.edu/~andre/ >>>> Sequences/SagMPR8Min3T.html improves the quality of the >>>> reconstruction considerably. (Even though with our sequence we can >>>> actually set the FFT scaling factor.) >>>> Now I would be happy to know whether these protocol parametrs are >>>> still the recommended set for anatomical scans on an Allegra >>>> (using only standard "off-site" Siemens sequences)? I would also >>>> be grateful for anybodies input on the matter of "optimising" the >>>> raw data for the surface reconstruction, so manual interventions >>>> can be minimised. >>>> >>>> >> >> -- >> Sebastian Moeller >> >> Tel.: 04 21 - 2 18 - 78 38 oder 96 91 >> Fax.: 04 21 - 2 18 - 90 04 >> GSM: 0 15 77 - 1 90 31 41 >> moeller(a)brain.uni-bremen.de >> >> AG Kreiter / FB 2 >> Institut fuer Hirnforschung III >> Abteilung Theoretische Neurobiologie >> Universitaet Bremen >> Biogarten >> Hochschulring 16a >> Postfach 33 04 40 >> 28359 Bremen >> >> > > -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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recommended scan parameters
by Sebastian Moeller 22 Jan '08

22 Jan '08

Dear Experts, after ages of monkey scanning, we recently also included human subjects in our study. I would like to use freesurfer for surface reconstruction, mainly as "canvas" for the display of activation maps. While functional scans seem to be reasonable, the anatomicals taken on our Siemens Allegra (3T) with the default Siemens head coil are not well reconstructed by freesurfer (pial surface is both under- and over-inclusive, white matter in temporal pole is mis-classified as gray). Just in case it matters, test reconstructions were performed using the 64 bit centos_4 FreeSurfer 4.0.2 build on SuSUE 10.1 64 bit (and no errors in from the recon-all -autorecon1 and -autorecon2 stages). I assume that this is a driver's error on my part, as switching to the sequence parameters given on http:// www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min3T.html improves the quality of the reconstruction considerably. (Even though with our sequence we can actually set the FFT scaling factor.) Now I would be happy to know whether these protocol parametrs are still the recommended set for anatomical scans on an Allegra (using only standard "off-site" Siemens sequences)? I would also be grateful for anybodies input on the matter of "optimising" the raw data for the surface reconstruction, so manual interventions can be minimised. -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Re: [Freesurfer] Phillips 3T
by Roberto Roiz Ssantiáñez 21 Jan '08

21 Jan '08

Hi When I bring the images up with tkmedit everything is messed up. When I open the coronal view it brings up the axial view, when I open the axial view it brings up the sagital view and when I open the sagital view it brings up the coronal view. As I mentioned before this happens when I acquired the sequence in the sagital plane. When the sequence is acquired in the axial plane everything runs ok Regards Roberto Roiz > if you bring them up in tkmedit does it show them properly? That is, when > it says "coronal" etc... is it really? > > And please post these to the list so other people can answer :) > > Bruce > On Sat, 19 > Jan 2008, Roberto Roiz > Ssantiáñez wrote: > >> Hi Bruce, >> I'm using >> freesurfer-Linux-rh9-stable-pub-v4.0.2-full.tar.gz run on Ubuntu. >> The error I get when runnig a sequence acquired on the sagital plane is >> is: >> >> Sat Jan 19 11:38:02 CET 2008 >> talairach_avi done >> #-------------------------------------------- >> #@# Talairach Failure Detection Sat Jan 19 11:38:02 CET 2008 >> /usr/local/freesurfer/subjects/pilot2_sag/mri >> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm >> >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) >> Linux roberto-desktop 2.6.22-14-generic #1 SMP Tue Dec 18 08:02:57 UTC >> 2007 i686 GNU/Linux >> >> recon-all exited with ERRORS at Sat Jan 19 11:38:02 CET 2008 >> >> >> >> However when the same sequence is acquired on the axial plane the >> recon-all runs perfectly. >> I have converted both sequences using MRICRO. I attached an image of >> both >> the sagital and the axial sequences. >> >> Regards >> Roberto Roiz >> >> >> >>> Hi Roberto, >>> >>> what version of FS are you using? Usually this isn't a problem for us. >>> You can drop an example on our filedrop if you want and we'll take a >>> look. >>> >>> cheers, >>> Bruce >>> On Wed, 2 Jan 2008, Ron KILLIANY wrote: >>> >>>> Dear Roberto, >>>> >>>> I'm glad to hear that the sequence ran well. I'm going to include >>>> Bruce >>>> Fischl on this e-mail to see if he can help you with the orientation >>>> problem you seem to be having. To my knowledge we haven't experienced >>>> that problem. >>>> >>>> I hope you had a happy new year celebration! >>>> >>>> --ron >>>> >>> >>

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post-doc position in cognitive and clinical neuroscience
by walhovd＠nmr.mgh.harvard.edu 20 Jan '08

20 Jan '08

Hi all There is a vacant post-doctoral research fellow position in cognitive and clinical neuroscience at the Department of Psychology, University of Oslo, Norway. If interested, please see the attached announcement. Best wishes, Kristine B Walhovd Professor University of Oslo Center for the Study of Human Cognition Department of Psychology PB 1094 Blindern 0317 Oslo Norway phone (+47) 22845130 e-mail: k.b.walhovd(a)psykologi.uio.no

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RE: [Freesurfer] FreeSurfer on SUN Linux machines
by Pedro Paulo Oliveira Jr 18 Jan '08

18 Jan '08

Solaris is another OS distinct from Linux. Freesurfer 4.0 won't run Pedro Paulo on E61 -- mens. original -- Assunto: RE: [Freesurfer] FreeSurfer on SUN Linux machines De: "Iman Aganj" <Iman(a)umn.edu> Data: 18/01/2008 19:28 Dear Nick, I think it is Solaris. Tcsh is installed, and I am not quite sure about the processor. Thanks, Iman -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2008 9:49 PM To: Iman Aganj Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer on SUN Linux machines Iman, What OS is installed on the system? What processor does it use? Do all the freesurfer commands give that error? Is tcsh installed? Nick > Hello everybody, > > > > I am trying to install FreeSurfer on SUN Linux machines, and I am not sure > which platform to choose. I have already tried CentOS 4, but when I try > for > example "tkmedit bert orig.mgz", I get the Invalid argument error. I will > appreciate any help. > > > > Thanks a lot. > > > > Best, > > Iman > > > > _______________________________________________ > 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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FreeSurfer on SUN Linux machines
by Iman Aganj 18 Jan '08

18 Jan '08

Hello everybody, I am trying to install FreeSurfer on SUN Linux machines, and I am not sure which platform to choose. I have already tried CentOS 4, but when I try for example "tkmedit bert orig.mgz", I get the Invalid argument error. I will appreciate any help. Thanks a lot. Best, Iman

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Creating one's own average sphere/template
by Graham Wideman 18 Jan '08

18 Jan '08

Folks: I'm trying to get a complete picture of what's entailed in creating our own atlas, including our own average reference sphere, so if there's a doc on this specific subject I'd love to see it. Absent that, below are questions to fill in some gaps: 1. Normal spherical reg: mris_register's command-line params don't include all files it must read, so I'm looking for a list of all the files that it reads under the usual circumstances (ie: registration to ref sphere; registration to opposite hemi), and how it decides *which* files to read. (Amongst other discrepancies, when recon-all runs, mris_register doesn't seem to read ?h.curv, whereas various postings suggest that it does.) 2. Normal labeling with mris_ca_label: Presumably this only works if subjects are registered to the same average sphere mesh as was used to create the chosen GCS file, right? Yet mris_ca_label doesn't need to read that actual ?h.sphere.reg file because equivalent position-on-sphere info is contained in the GCS file... right? 3. Creating one's own average reference sphere: What progam(s) does one use to create the average ?h.sphere(.reg?) file (presumably from each subject's ?h.sphere file)? and average curvature file (ie: the tif file)? FWIW, it looks like mris_make_template is somehow involved here, but it's entire documentation consists of just "This program will add a template into an average surface" (what does that mean?), and the source code looks like it only produces the tif file containing average sulc and curv data. (From which I conclude the here, "template" refers to just that file.) 4. What, if any, is the relationship between .../freesurfer/average and .../freesurfer/subjects/fsaverage Thanks, Graham

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Freesurfer January 2008