Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

mris_preproc really averages?
by Jeff Sadino 04 May '09

04 May '09

Hello, I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two average pictures were slightly different. I thought that mris_preproc just simply averages all the subjects into common space. I noticed that its vector in matlab keeps the thickness value for all vertex's for all 56 subjects. I want to have the matlab capability for some custom processing I am doing, but the discrepancy leads me to think that mris_preproc is not a simple average. Can anyone elucidate this for me? Thank you! Matlab script. Only place I would suspect a wrong assumption is when I throw out the rest of the subjects at curv4=curv3(1,:,:,1) %Select your input thickness file path='/mnt/users/Jeff/fs/lc/HIV/pass2pics/416/diff/nc.rh.ave.mgh'; %Read the thickness file curv=MRIread(path); %Select the volume attribute curv2=curv.vol; %Create a duplicate thickness array for manipulation curv3=curv2; %Get the number of concatanated subjects tmp=size(curv2); m=tmp(4) clear 'tmp' %Sum each vertex for all your subjects for im=2:m for in=1:7 curv3(1,:,in,1)=curv3(1,:,in,1)+curv2(1,:,in,im); end end %Select just the first frame curv4=curv3(1,:,:,1); %Compute the average thickness curv.vol=curv4/m; %Write to thickness file MRIwrite(curv,'nc.rh.ave1.tmp.mgh'); _________________________________________________________________ Rediscover Hotmail®: Get quick friend updates right in your inbox. http://windowslive.com/RediscoverHotmail?ocid=TXT_TAGLM_WL_HM_Rediscover_Up…

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Analysis without and with a covariate
by Jürgen Hänggi 04 May '09

04 May '09

Dear FS experts I have done an analysis without a covariate. Now, I want to do the same analysis but including mean cortical thickness as a covariate. I am wondering whether I have to run all steps again incl. mris_preproc or whether it is sufficient to only run mri_glmfit with the new FSGD file that includes the covariate. 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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recon-all w/ custom aseg atlas.
by Jamie Hanson 04 May '09

04 May '09

Hi Freesurfer folks- So I have been trying to create a custom aseg atlas (which I did, thanks much to Bruce and Nick!)... Now I want to run recon-all w/ that new custom aseg atlas (on additional subjects not included in .gca / atlas creation)... I checked the web and the listserv archive, but might have missed it... Is there an easy way to simple specify this new aseg atlas to run w/ recon-all? Or do I just need to run each command for autorecon1 and autorecon2 and just replace the default .gca file when I run mri_em_register, mri_watershed, mri_ca_normalize, mri_ca_register, mri_remove_neck, and mri_ca_label? Thanks much! jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

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letters of support
by Bruce Fischl 04 May '09

04 May '09

Hi All, we are planning on putting in a grant for software development to include automated tractography into FreeSurfer. The end result we envision will be a procedure much like recon-all, but applied to diffusion data that will automatically generate models of a set of tracts such as fornix, CST, cingulum, optic radiation, etc.... One of the critical factors in reviewing these grants is the extent to which the proposed project will impact a large user community, so it would be a big help to us if anyone who might be interested in using such a tool were to send us a letter (on official letterhead) stating this. Ideally this would also include an estimate of the # of subjects you would study in the next 5 years, and a reference to any funding source that would be used for the study if the tools were developed and distributed. The grant needs to be completed in the next 10 days or so, so sooner is better than later for us :). thanks Bruce

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display registered sphere in surface?
by Zhong Jidan 04 May '09

04 May '09

Hi, I have a question about the sphere registration. The registration of surface is spherical registation, so the outpput of the surface is also a sphere. When we have the inflated and smoothwm, we can convert the surface into sphere using mris_sphere, but reversely, how to convert the deformed sphere in the form of white surface or pial surface? Also, if I want to use the surface between the white and pial surface to do registration, do I need to make the sphere myself? Thanks, -- Regards, Jidan

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04 May '09

Research position (PhD) in Cognitive and Developmental Neuroscience at the Dpt. of Child and Adolescent Psychiatry, RWTH University of Aachen/JARA-Brain Translational Brain Medicine The successful applicant will be conducting in research projects with a particular focus on the development of normal and disturbed cognitive and emotional processes using methods related to structural and functional magnetic resonance imaging, neuropsychological and neurochemical techniques. The position will be a 3-year position (Verg. Gr 0,5 TVL13) with the possibility of renewal after positive evaluation. A considerable amount of work will take place at the Jülich Research Centre, one of the world's leading research facilities. The position is funded by the Excellence Initiative of the German federal and state governments. In 2007, the RWTH Aachen earned the connotation of being an elite university in Germany. Profile of applicant: - University Diploma/Degree in Psychology, Medicine, Biology, Physics, Bioinformatics or other related fields of natural sciences. - Experience with MRI/fMRI - Current driver`s license. Candidates holding a Master's/University diploma/degree in the natural sciences or related disciplines and an excellent academic record may apply by 1 June 2009 or also independent of deadlines. Interested applicants should send their materials online (preferred) and also via post to: Prof. Dr. med. F.D. Zepf, Juniorprofessor for Translational Neuroscience in Psychiatry and Neurology Dpt. of Child and Adolescent Psychiatry and Psychotherapy RWTH University of Aachen Neuenhofer Weg 21 52076 Aachen Germany Phone: +49-(0)241-8085504 Fax: +49-(0)241-8082544 Email: fzepf(a)ukaachen.de

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MRISunfold error
by Hsin-Hao Yu 04 May '09

04 May '09

Hi, I run "mris_flatten" and got this message: "reading patch ../subjects/shiva/surf/lh.occip.patch.3d with 6095 vertices (98.2% of total)removing ripped vertices and faces...removing ripped vertices and faces...reading original vertex positions...minimizing metric distortion induced by projection...MRISunfold: could not open log file lh.occip.patch.flat.out" It's probably a very simple matter of fixing the unix permission, but I have no idea where MRISunfold is trying to save to. I checked every directory under the subject and found nothing unusual. Does anyone know which directory *.flat.out goes to? Thanx. Hsin-Hao

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mris_flatten question
by Hsin-Hao Yu 04 May '09

04 May '09

Hello, I generated a 3D mesh mode of the marmoset cortex from nissl stained slices, and I am looking for ways to flatten it. I managed to save my mesh to the FreeSurfer format. tksurfer loaded the file and displayed it correctly. I also used "mris_inflate" to blow out the calcarine sulcus. I cut off the occipital lobe with tksurfer and saved the patch. Then I tried "mris_flatten". I got this error message: mris_flatten: could not read surface file subject/xxx/surf/lh.smoothwm I don't have a white matter surface. Is there anyway to bypass lh.smoothwm? I imagined that once I have a inflated surface, flattening should be be a self-contained problem and does not require an additional surface. Why is mris_flatten looking for .smoothwm? Thanx. Hsin-Hao

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FreeSurfer Native Format (MGH/MGZ) MacOSX Quick Look Plugin Now Available
by hui Zhang 03 May '09

03 May '09

Dear FreeSurfer users, Thanks to Nick Schmansky, the DTI-TK Quick Look Plugin now supports the FreeSurfer native volume format (MGH/MGZ). If you are not familiar with the amazing visualization possibilities made possible by the plugin, please check out the earlier post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10015.html The plugin (version 1.6.2) can be downloaded from http://www.nitrc.org/projects/dtitk Best regards, Gary Hui Zhang

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Re: [Freesurfer] selxavg3-sess failure on analysis created with -fsv3 flag
by Jesse Friedman 01 May '09

01 May '09

Ok. Since the -fsv3 flag is now available in stable, I thought that might mean that I could could run selxavg3-sess in stable. It works fine in dev. I'm assuming that commands being run subsequently for group analyses (e.g. isxconcat, mri_glmfit) *can* be run in stable. Jesse -- Jesse Friedman, B.A. Massachusetts General Hospital Martinos Center, Manoach Lab Psychiatric Neuroimaging 149 13th Street #2613 Charlestown, MA 02129 Phone: (617) 726-1908 Fax: (617) 726-4078 jessef(a)nmr.mgh.harvard.edu > > Are you using dev? Definitely won't work from stable. > > doug > > > > > On Thu, 30 Apr 2009, Jesse Friedman wrote: > >> Hi, >> >> I created an analysis using the -fsv3 flag and created a contrast: >> >> <mkanalysis-sess -analysis newEMerror_fsv3_std -TR 2 -paradigm error.par >> -designtype event-related -funcstem f0mcsm8 -tpef tpx.skip8.dat >> -nconditions 4 -timewindow 24 -prestim 4 -noautostimdur -fsv3> >> >> <mkcontrast-sess -contrast AScvfix -analysis newEMerror_fsv3_std -ncond >> 4 >> -wcond 0 1 0 0> >> >> and then ran selxavg3-sess: >> >> <selxavg3-sess -analysis newEMerror_fsv3_std -sf >> Subject_files/controlsVasd_jf.txt> >> >> which failed and gave me this error: >> >> <Computing ErrCovMtx >> ??? Undefined function or method 'fast_ecvm2wmtx' for input arguments of >> type 'double'. >> >> Error in ==> fast_selxavg3 at 492 >> [fsv3W fsv3AutoCor] = fast_ecvm2wmtx(ErrCovMtx);> >> >> Is this a bug, or is it that I shouldn't expect selxavg3 to work with an >> -fsv3 analysis in stable4? The -fsv3 flag was available in stabl4, so I >> gathered this meant I would be able to run selxavg3-sess in stable4. >> >> My bugr information is below. >> >> Thanks, >> Jesse >> >> FREESURFER_HOME: /usr/local/freesurfer/stable4 >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.3.0-20090430 >> >> RedHat release: CentOS release 4.7 (Final) >> >> Kernel info: Linux 2.6.9-78.0.13.ELsmp x86_64 >> >> NMR Center info (/space/freesurfer exists): >> >> machine: vantz >> >> SUBJECTS_DIR: /space/ventzl/16/users >> >> PWD: /space/ventzl/16/users >> >> ssh vantz >> setenv SUBJECTS_DIR /space/ventzl/16/users >> cd /space/ventzl/16/users >> >> >> _______________________________________________ >> 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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