Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

tksurfer display
by Ray, Siddharth 07 Jan '14

07 Jan '14

Hi, Is there any way in tksurfer GUI display, that I can set a NVtxs threshold to get rid of regions (that came up significant after monte carlo simulation) which have NVtxs less than my input threshold. For eg. In my table below, I don't want postcentral label to appear in my tksurfer view (as I only want to see labels with more than 300 NVtxs). Can I get that label out from my brain pictures? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 3.048 133418 89.23 52.8 -12.9 32.0 0.00020 0.00000 0.00040 186 postcentral 2 2.938 109465 989.46 36.0 17.2 31.1 0.00020 0.00000 0.00040 1066 caudalmiddlefrontal Thanks, -Siddharth

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Re: [Freesurfer] reconall error.
by Bruce Fischl 07 Jan '14

07 Jan '14

Hi Rashmi how did you create this dataset? The non-black background is probably going to cause trouble. Is it an mp2rage or something similar? Could you try replacing the background value (386.997) with 0 and see if that helps. If there are really big defects the topology fixer will take forever, and probably won't generate the correct solution anyway cheers Bruce On Tue, 7 Jan 2014, Rashmi Singh wrote: > Hello FreeSurfer experts, > I am having problem with running reconall. > I am using version 5.1. > Attached is data set on which I ran reconall. > Because I was getting tailrace failure I ran it with –notal-check flag( the > run with -use–mritotal flag failed too, so I used the –notal check flag ) > Recon all ran OK, but its has got stuck at a point (topology detection > stage) and its not moving forward (my terminal shows that its still running) > May you please help me troubleshoot this issue. > > Thanks, > Rashmi > >

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Postdoc fellowships available in engineering at USC - know any good candidates? (fwd)
by Bruce Fischl 07 Jan '14

07 Jan '14

FYI ---------- Forwarded message ---------- Date: Tue, 07 Jan 2014 10:35:41 -0800 From: Richard Leahy <leahy(a)ee.usc.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Postdoc fellowships available in engineering at USC - know any good candidates? USC has a new and generous engineering postdoctoral fellowship program (deadline January 31st, details attached) for PhD students/recent grads planning on an academic career. If you have any students (or know of others) about to or recently graduated who might be interested in working in the area of neuroimaging imaging at USC, can you please forward the attached and ask them to get in touch with me at their earliest convenience. We have a substantial and growing program in brain imaging at USC, with three faculty in EE (myself, Krishna Nayak and Justin Haldar) with primary research interests in medical imaging and a major focus on the brain. We have access to 3T MRI with simultaneous EEG on the main university park campus where the EE dept is housed as well as research and clinical scanners at the health science campus and Childrens' Hospital LA. We will also have a 7T scanner online sometime in the next 12 months. There is excellent potential to collaborate with neuroimaging faculty in gerontology, psychology, neuroscience and the medical school. We are also particularly interested in candidates with interests in statistics, computer vision, machine learning and graph-based analysis and their application to medical image analysis. I would be happy to discuss this opportunity with any students you feel would benefit from this position. Please do encourage any qualified students to apply and to contact me to discuss potential research topics. best regards Richard. -- _____________________________________ Richard M. Leahy, Professor Signal and Image Processing Institute Department of Electrical Engineering University of Southern California 3740 McClintock Ave, EEB400, MC 2564 Los Angeles, CA90089-2564. 213 740 4659 (t) 213 740 4651 (f) http://neuroimage.usc.edu _____________________________________

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seeking a post-doc (fwd)
by Bruce Fischl 07 Jan '14

07 Jan '14

FYI Dear Colleagues, I hope this finds you well! I wanted to pass along an ad for a post-doc position on a motion correction project. We're having a tough time finding someone with both a strong interest in clinical autism research and technical sophistication with data analysis. Please pass this around and let me know if you can think of anyone or if you have suggestions on where to advertise. We did advertise at SFN. The position is available immediately. Thanks for your consideration and best wishes for a happy new year, Dara Dara S. Manoach, Ph.D. Psychiatric Neuroimaging and Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 1.111 Charlestown, MA 02129 email: dara(a)nmr.mgh.harvard.edu phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Cannot run unpacksdcmdir on buckner_data/014-anon
by Anders Olsen 07 Jan '14

07 Jan '14

Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with unpacking DICOM files. When I run: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly ~/fs_subjects/014-anon/scan.info It completes and gives me the following output: 14 anon ok 256 256 128 001.dcm I then try to unpack slice number 14 by running: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -fsfast -run 14 bold nii f.nii And it gives me the message: ERROR: reading ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm tag 28 30 I have done md5sum buckner_data-tutorial_subjs.tar.gz and got the hash: 14618f42ffa6b21d5714f37e159357c4 which matches the md5sum in ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5su… Am I doing something wrong or is there a problem with the dcm files in the test data? -- Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.olsen(a)gmail.com <mailto:anders.d.olsen@gmail.com>

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Transform sig.mgh file from fsaverage space into a subject's native space
by Jürgen Hänggi 07 Jan '14

07 Jan '14

Dear FS expert I tried to transform a sig.mgh file from fsaverage space into a subject's (called SCC1069) native space, but have some problems. I used: tkregister2 --mov fsaverage/mri/brain.mgz --targ SCC1069/mri/rawavg.mgz --regheader --reg register.dat mri_surf2surf --sval-xyz fsaverage/surf/pial --reg register.dat SCC1069/mri/rawavg.mgz --tval SCC1069/surf/pial.native --tval-xyz --hemi lh --s fsaverage If this is right, how can I proceed in order to transform the sig.cluster.mgh file produced by the MC simulations into the native space of subject SCC1069? Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. 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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Are two T1 scans helpful for better recon-all?
by Hai Pan 07 Jan '14

07 Jan '14

Hello, FreeSurfer experts, We made two T1 scans for each subject at each session, will they be helpful for better recon-all results? Shall I average them and process the averaged T1 image? Let me know please. Thank you, Hai

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group analysis of functional data in custom volume space
by Caspar M. Schwiedrzik 07 Jan '14

07 Jan '14

Hi Freesurfer Experts, I would like to do a whole brain group analysis of functional data with mri_glmfit using a custom volume space instead of the MNI space Freesurfer provides. This is for primate data. I was wondering what the best way to do this would be. I have a T1 template in volume space to which I can align my functional data. I was thinking in getting registration files for the EPI to T1 alignment first, then to run mkanalysis-sess in native space per subject, the selxavg3-sess, then isxconcat-sess providing the registration files with the -reg flag, and then mri_glmfit. Does that make sense? Thank you very much, Caspar

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Question about 7T MRI Datasets with isotropic voxels of 0, 7 mm
by Valentin Frank 07 Jan '14

07 Jan '14

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FW: FW: recon-all exited w/errors
by Boric, Katica A. 06 Jan '14

06 Jan '14

Hi Bruce! So it is the whole brain! Unfortunately, this is the available serie with the most number of slices!! At least we tried! Thanks Bruce! Katica ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Monday, January 06, 2014 3:58 PM To: Boric, Katica A. Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: recon-all exited w/errors oh, it's only 62 slices? So is it not whole brain? Or are they thick slices? Either way that is probably a show stopper On Mon, 6 Jan 2014, Boric, Katica A. wrote: > Hi Bruce! > Thank you very much for your response! > > The input image I used was .dcm of a Sagital MPR with 62 slices. > As for the directions, it is really hard to tell! I have attached a screenshot of an horizontal image. > > How do I perform the alternative or manually tailarach? > > Thank you very much, > > Katica > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Sunday, January 05, 2014 8:50 PM > To: Boric, Katica A. > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all exited w/errors > > Hi Katica > > what format was the input image to recon-all? Can you verify that tkmedit > has the directions correct (that is what it labels as anterior is actually > anatomically anterior, etc...). If so, then the talairach just failed and > you will need to either try an alternative (like the MNI or SPM talairachs) > or generate it manually. > > cheers > Bruce > > > > On Thu, 2 Jan 2014, Boric, Katica A. > wrote: > >> Happy New Year freesuerfers! >> I run into this error while doing recon-all : >> >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) >> Manual Talairach alignment may be necessary, or >> include the -notal-check flag to skip this test, >> making sure the -notal-check flag follows -all >> or -autorecon1 in the command string. >> >> I would really appreciate if someone could give me some advice on how to fix >> this error. >> >> Thank you very much! >> >> Katica Boric, >> >> >> ps: Here is the error log: >> >> #@# Talairach Failure Detection Thu Jan 2 14:20:32 EST 2014 >> /home/XX/XXX/subjects/XXX_SurferOutput/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) >> INFO: Attempting MINC mritotal to perform Talairach align >> #-------------------------------------------- >> #@# Talairach Thu Jan 2 14:20:33 EST 2014 >> /home/XX/XXX/subjects/XXX_SurferOutput/mri >> >> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i >> orig.mgz --o orig_nu.mgz >> >> >> talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm >> >> /home/XX/XXX/subjects/XXX_SurferOutput/mri >> /usr/local/freesurfer/bin/talairach >> --i orig_nu.mgz --xfm transforms/talairach.auto.xfm >> $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ >> Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 >> UTC 2013 x86_64 x86_64 x86_64 GNU/Linux >> Thu Jan 2 14:21:30 EST 2014 >> tmpdir is transforms/tmp.talairach.34005 >> /home/XX/XXX/subjects/XXX_SurferOutput/mri >> mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc >> mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from orig_nu.mgz... >> TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 >> i_ras = (-1, -9.03383e-08, 0) >> j_ras = (-1.3411e-07, 2.66591e-08, -1) >> k_ras = (1.59256e-07, 1, -5.93718e-09) >> writing to transforms/tmp.talairach.34005/src.mnc... >> -------------------------------------------- >> mritotal -verbose -debug -clobber -modeldir >> /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm >> transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm >> Legacy library shellwords.pl will be removed from the Perl core distribution >> in the next major release. Please install it from the CPAN distribution >> Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal, >> line 460. >> >> >> Thu Jan 2 14:21:43 EST 2014 >> talairach done >> >> cp transforms/talairach.auto.xfm transforms/talairach.xfm >> >> #-------------------------------------------- >> #@# Talairach Failure Detection Thu Jan 2 14:21:44 EST 2014 >> /home/XX/XXX/subjects/XXX_SurferOutput/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) >> Manual Talairach alignment may be necessary, or >> include the -notal-check flag to skip this test, >> making sure the -notal-check flag follows -all >> or -autorecon1 in the command string. >> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >> Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 >> UTC 2013 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan 2 14:21:45 EST >> 2014 >> >> >> >> >> >>

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Freesurfer January 2014