Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Coordinate Transform
by Tianyi Qian 14 Mar '12

14 Mar '12

Dear Freesurfer experts, How can I transfer the coordinate in individual space into MNI space. I don't want to transfer the whole volume, I only need to transfer the coordinate of some points. Thanks, -- Tianyi Qian

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Qdec
by Ahmed, F, Me <fahmed＠sun.ac.za> 14 Mar '12

14 Mar '12

Hello Freesurfer experts, I'm trying to run the tutorial of Qdec and am using the tutorial data set "buckner_data-tutorial_subjs.tar.gz". I started running the Qdec tutorial ok, I managed to load the Qdec.table.dat file ok and everything looked ok. Then when I pressed the tab 'Generate Stats Data Tables' I got this error window popping up below: And in the terminal window it also said: asegstats2table --meas volume --tablefile /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/qdec/stats_tables/aseg.volume.stats.dat --subjects 140 049 141 084 021 093 080 091 040 017 138 106 108 092 124 129 103 130 039 123 095 067 004 133 097 073 149 045 136 144 032 131 145 111 102 074 114 008 128 099 Building the table.. SUBJECTS_DIR : /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs ERROR: cannot find /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/140/stats/aseg.stats Use --skip flag if you want to continue in such cases I can't seem to locate the aseg.stats file in the tutorial data set. Did I not extract the file properly or something? Should it be there? Thanks, Fatima ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

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intersection between ROI masks
by Miranka Wirth 14 Mar '12

14 Mar '12

Dear freesurfers, how can I compute the intersection between binarized masks? Thank you for your support, Miranka

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Freesurfer: surf2vol?
by Florsek 14 Mar '12

14 Mar '12

Dear all, we have performed a cluster analysis in Qdec and found a significant vertex-cluster after correction for multiple testing using the Monte Carlo simulation. Our aim is to map the vertices to an atlas which is different from that of Desikan. To do that we need the volume-based information of the significant cluster. To transform the surface-based information into volume-based information we need to conduct the "surf2volume"-command, right? What I don't understand is what the required flags such as "--surfval" and "--volreg" need to contain. For example what is meant with "source of the surface values and format" (surfval) or "matrix that maps XYZ in the reference anatomical to XYZ in the functional volume" (volreg). Where can I get these files? Do I have to run tkregister2 for each proband? Thank you very much for your help in advance! Best regards, Florian -- Florian Siedek Doctoral Scientist Institute of Human Genetics Department of Genomics Life& Brain Center University of Bonn Sigmund-Freud-Strasse 25 D-53127 Bonn Germany Email: florsek(a)gmail.com

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Vertex index information for a sphere.reg file
by Ji hoon Oh 14 Mar '12

14 Mar '12

Dear FreeSurfer, Hi, I have a label with vertex index, RAS and overlay values, and want to add spherical coordinates to them as presented in tksurfer. I found following archives that are related to this question, but I couldn't find any vertex index (number) information in a sphere.reg file. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00627.html) I converted ?h.sphere.reg file into ?h.sphere.reg.asc using *mris_convert* command, and imported it to MATLAB using *read_asc.m* file (without face data). They had [x,y,z] coordinates in columns, but did not provide vertex index information. I wonder if there is a way to read the vertex index from a sphere.reg file, or there are other methods that read both vertex index and spherical coordinates. Thank you, Jihoon Oh -- --------------------------------------------------------------- Jihoon Oh, M.D. Ph.D. candidate, Bio and Brain Engineering Korea Advanced Institute for Science and Technology (KAIST) E-mail: ojihoon(a)gmail.com ---------------------------------------------------------------

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open PhD position
by Esther Walton 14 Mar '12

14 Mar '12

Research position (PhD) in translational developmental neuroscience (with a focus on eating disorders) at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Dresden University of Technology, Germany PLEASE REPOST FOR INTERESTED PARTIES Job Description: The Department of Child and Adolescent Psychiatry, Dresden University of Technology, Germany invites applications for a research position (PhD) in neuroimaging of eating disorders (ED). We are interested in cognitive control, reward system and the processing of emotions in patients with anorexia nervosa. This is a full time position within the Translational Developmental Neuroscience Group. Responsibilities will include the coordination of our ongoing clinical study and the acquisition and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. Imaging sessions will take place on the Neuroimaging Center's 3T Siemens TIM-Trio scanner and data collected includes high-quality structural, diffusion, and functional MRI data. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, physiological and endocrinological information. The successful applicant will work in a team of young investigators and also be responsible to supervise interns and medical students working in the project. Applicants for the position must have completed (a) a Master or Diploma degree in a relevant field (Psychology, Neurosciences or Medicine; if you have additional qualifications a degree in Biology, Biomedicine, Biophysics, Computer Science or Electrical Engineering may also be sufficient), (b) have had some exposure to cognitive and emotional neurosciences, (c) participated in research activities within the past years (d) possess strong organizational skills and (e) be able to communicate in German with non-scientific staff members. Experience in computer programming (Linux/Unix shell scripting, Python and/or MATLAB), neuroimaging analysis methods (FSL, SPM, FreeSurfer), advanced statistical analyses is of advantage but not a precondition. The successful applicant will join a multidisciplinary team of researchers and clinicians and will receive further training in psychometric and endocrinological techniques and the application of analysis tools for neuroimaging data. Psychologists or physicians who wish to advance in their clinical training may be able to dedicate a small amount of their time to work with patients. The position is available for a start date as soon as April 15th 2012 (to be confirmed). Review of applications will begin immediately and will continue until the position is filled. The position is guaranteed for one year with the possibility of renewal after positive evaluation. Salary will be consistent with levels in accordance with the German Research Foundation (50% TV-L: E 13). Compensation includes health insurance, and vacation time. To apply you can use our online portal (http://www.uniklinikum-dresden.de/bildung-und-karriere/stellenangebote/wiss… application should include a cover letter detailing professional objectives and interests, CV (with grades), and the names and email addresses of two references. The application can be written in German or English. Applications from many disciplines may be considered. The position is open to qualified international applicants but the knowledge of some German is necessary since the position includes the coordination of an ongoing clinical study. Applicants with a disability will be given preference in the selection process. Prof. Dr. med. Stefan Ehrlich Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus Dresden an der TU Dresden E-Mail: KJPChefsekretariat(a)uniklinikum-dresden.de Please refer to our homepage: http://www.kjp-dresden.de/en/Eating-disorders, http://www.kjp-dresden.de/en/Schizophrenia and http://kjp-dresden.de/de/Publikationsliste-Prof-Dr-S-Ehrlich for more detailed information.

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wm.mgz "key"
by Michael Harms 13 Mar '12

13 Mar '12

Hello, Is there a "key" for what all the various altered voxel values in wm.mgz represent? For example, I know that if you manually add a voxel, it gets set to 255, and if you delete a voxel it gets set to 1. What is the analogous "key" for values of 200, 215, 230, and 250? thanks, -MH -- 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 6604 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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mri_vol2surf
by Tina Jeon 13 Mar '12

13 Mar '12

Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing "SetSlice $gnVolSlice [set gnVolSlice]" invoked from within ".w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc" (command bound to event) ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Re: [Freesurfer] White matter intensity normalisation
by Bruce Fischl 13 Mar '12

13 Mar '12

Hi Charlotte the aim of the WM intensity normalization is to center the white matter class mean around 110 and to "flatten" it over space, so that the mean is spatially stationary. It is certainly harder with 1.5T data that will be noisier than 3T (depending on the receive coil you use), but why do you say it didn't work very well? You need to visually inspect the surface accuracy to determine that. cheers Bruce On Tue, 13 Mar 2012, Charlotte Bernard wrote: > Thanks for your answer. But could you explain to me the aim of the white > matter intensity normalisation. What is the incidence if this step doesn't > work very well? > In my subjects, we can see that the quality of this process is not very > well! Maybe due to the acquisition on 1.5T?? > Thanks, > > > Date: Mon, 12 Mar 2012 08:50:02 -0400 > > From: fischl(a)nmr.mgh.harvard.edu > > To: chakeba(a)live.fr > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] White matter intensity normalisation > > > > Hi Charlotte > > > > have you visually inspected them? I would be more concerned about the # of > > voxels in wm which is way too low, but it looks like you eroded the wm > > mask, so maybe it's ok. Take a look at the surfaces over the data in > > tkmedit and see if it appears accurate in subjects like #8. The WM > > intensity won't be exactly 110, and is usually below it due to partial > > volume effects. > > > > cheers > > Bruce > > > > On Mon, 12 Mar 2012, Charlotte Bernard > > wrote: > > > > > Dear Freesurfer users, > > > > > > I run FS on my 670 subjects. All the scans were acquired on a 1.5T > Philips > > > scan. > > > I noticed that my values in the WM are near 100-110 but not exactly 110. > I > > > think it is a problem! Is it link to the 1.5T? How can I fix it? > > > I joined my log file of QA tools: could you help me to undertand the > output? > > > > > > wm-anat-snr results: > > > > > > SNR: Anatomical signal-to-noise ratio in white matter > > > mWM: Mean white matter intensity value > > > stdWM: Standard deviation of white matter intensity value > > > voxWM: Total number of white matter voxels in eroded mask > > > > > > SubjID SNR mWM stdWM voxWM > > > 1 13,37* 104,18 7,79* 24181 <------ > > > 2 14,79* 105,90 7,16* 22148 <------ > > > 3 13,57* 104,75 7,72* 37341 <------ > > > 4 12,67* 104,18 8,22* 29311 <------ > > > 5 14,36* 105,44 7,34* 48083 <------ > > > 6 11,40* 103,92 9,11* 47704 <------ > > > 7 14,52* 104,71 7,21* 25706 <------ > > > 8 9,92 101,42 10,22 40187 > > > 9 11,31* 104,28 9,22* 22967 <------ > > > 10 11,61* 102,92 8,86* 19850 <------ > > > 11 14,78* 105,05 7,11* 26607 <------ > > > 12 11,36* 105,33 9,27* 15465 <------ > > > 13 11,30* 103,69 9,18* 34685 <------ > > > 14 11,73* 105,20 8,97* 40471 <------ > > > 15 11,92* 104,04 8,73* 13777 <------ > > > 16 9,46 102,04 10,79 30314 > > > 17 12,60* 106,40 8,44* 38432 <------ > > > > > > I thought it can help me to quickly identify the subjects who didn't > work > > > for this step. For example, the subject n°8 has a problem? > > > > > > > > > Thanks, > > > Charlotte > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it > is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > >

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recon and qdec error
by Michels Lars 13 Mar '12

13 Mar '12

Dear Freesurfer community I just installed Freesurfer 5.1 on our LINUX machine (Fedora 14) I then tried to construct volume and surface files (autorecon1 only) for the sample data set ('bert') and received the following error: /home/fsl/data/freesurfer/subjects/bert/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: tkregister2_cmdl failed, see transforms/talairach_avi.log Any ideas or suggestions? In addition, I wanted to start qdec and got the following message: qdec.bin: error while loading shared libraries: libvtkverdict.so.vtk5.2.0: cannot open shared object file: No such file or directory Again, any ideas? Thanks for your help Lars Dr. phil. L. Michels, Oberassistent Institute of Neuroradiology University Hospital of Zurich Frauenklinikstrasse 10 CH 8091, Switzerland FON +41-44-255-4965 Fax +41-44-255-8946

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Freesurfer March 2012