Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

Postdoc and Research Assistant openings in cognitive neuroscience at UCSF
by Roeland Hancock 12 Sep '16

12 Sep '16

*Research Assistant Position at UCSF in California, USA on Multilingualism* The Hoeft Lab (http://brainLENS.org <http://brainlens.org/> PI: Fumiko Hoeft MD PhD) is looking for an exceptional research assistant interested in the developmental cognitive neuroscience of multilingualism. This NIH-funded research is in collaboration with Cammie McBride PhD of Chinese Univ of Hong Kong, Ken Pugh PhD of Haskins/Yale/UConn, Linda Siegel of UBC, Manolo Carreiras PhD of BCBL, Ioulia Kovelman PhD of U Michigan, and Yuuko Uchikoshi EdD of UC Davis. The position is suited for a self-motivated, organized and independent thinker, with good interpersonal and multitasking skills, as well as proficiency in the English language and computer software. Neuroimaging, computational, statistical, programming, and neuropsych testing skills are highly desired but not necessary. Native-like proficiency in Spanish or Cantonese is a plus. A major strength of our lab is that there are plenty of opportunities to conduct independent research, to be first author on publications and to give conference presentations as a novice RA (e.g. Myers et al. Psychol Sci ’14, Myers et al. SCAN ’16, Haft et al. Curr Opin Behav Sci ’16). The position begins in January but start date can be sooner and is negotiable. Please email info(a)brainlens.org with a cover letter and your CV. Please add “[RA job]” and your full name in the Subject of the email. Qualified candidates will be asked to have 2-3 letters of reference forwarded. *Joint Postdoctocal Position at UCSF and Stanford University in California, USA* The Hoeft Lab (http://brainLENS.org <http://brainlens.org/> PI: Fumiko Hoeft MD PhD) at the UCSF Dept of Psychiatry and Weill Institute for Neurosciences in collaboration with the Stanford Mood and Anxiety Disorders Lab in the Dept of Psychology (http://goo.gl/dc96CxPI: Ian Gotlib PhD) is looking for an exceptional postdoc in the field of affective neuroscience, with advanced neuroimaging, psychophysiology, computational, programming and organizational skills. Training in genetics is a plus. The primary project that the postdoc will be responsible for is the examination of intergenerational neuroimaging using a ‘natural’ cross-fostering design that allows dissociation of genetic, prenatal and postnatal environment on brain networks that are transmitted across generations. Related articles from our lab can be found here - Yamagata et al. J Neurosci 2016 (http://goo.gl/vMK8iy) Ho et al. Trends in Neurosci 2016 (http://goo.gl/SyXLcK) and Scientific American (http://goo.gl/YTiH6D) There are other funded opportunities to be involved in research that examines the impact of anxiety and stereotype on psychophysiology and cognitive processes. The position can begin immediately. Please email info(a)brainlens.org with your CV, and with brief paragraphs of research interests, career goals and why you feel you are a good fit for the lab. Please add “[Postdoc job]” and your full name in the Subject of the email. Qualified candidates will be asked to have 3 letters of reference forwarded.

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Tkregister2 error, moveable not present just white screen
by A Nunes 11 Sep '16

11 Sep '16

Hi, After doing a bbregistration I visualized the results with tkregister2. The target is alright, however, the moveable is not present, it is just a white screen. What steps could I take to solve this issue? Thanks Adonay

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Re: [Freesurfer] overlapping area question
by Arkadiy Maksimovskiy 11 Sep '16

11 Sep '16

Hi Doug, Thank you for the information about the matlab method. Since asking the question, I found a way to do this with the help of tksurfer and freesurfer commands, and wanted to share with the community, in case someone will find this useful in the future. Basically, after the desired regions are saved as labels (using one of the desired methods in tksurfer), geometric overlap (and other regional interactions) can be calculated using the "mris_label_calc" function. Best, Arkadiy

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Fedora version problem
by wanghaibao 11 Sep '16

11 Sep '16

Hi, every expert i have tried most of new versions, as follows, but there are qdec problems that I cannot change value in the text box. I know that Fedora (fc20.x86_64) 20 (Heisenbug) mismatch with these versions.I want to know which version of Fedora you use successfully without qdec problems. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 freesurfer-Linux-centos6_x86_64-dev thank you very much. haibao wang

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ERROR: matrix is ill-conditioned or badly scaled, condno = 22801.1
by Seung Gul Kang 10 Sep '16

10 Sep '16

Hi, I am new learner in freesurfer and analyzing the difference of the thickness between two groups using qdec. There is a error as below. I don't know what is the reason. ERROR: matrix is ill-conditioned or badly scaled, condno = 22801.1 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y /mnt/hgfs/share/kang_fs/qdec/2/y.mgh --fsgd /mnt/hgfs/share/kang_fs/qdec/2/qdec.fsgd dods --glmdir /mnt/hgfs/share/kang_fs/qdec/2 --surf fsaverage lh --label /mnt/hgfs/share/kang_fs/fsaverage/label/lh.aparc.label --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Avg-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-H-I-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-M-F-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-X-diagnosis-sex-Intercept-thickness.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /mnt/hgfs/share/kang_fs/qdec/2/y.mgh --fsgd /mnt/hgfs/share/kang_fs/qdec/2/qdec.fsgd dods --glmdir /mnt/hgfs/share/kang_fs/qdec/2 --surf fsaverage lh --label /mnt/hgfs/share/kang_fs/fsaverage/label/lh.aparc.label --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Avg-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-H-I-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-M-F-Intercept-thickness.mat --C /mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-X-diagnosis-sex-Intercept-thickness.mat matrix Design matrix ------------------ 1.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 2.600 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 2.440 0.000; 1.000 0.000 0.000 0.000 25.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.510 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 26.000 0.000 0.000 0.000 7.000 0.000 0.000 0.000 2.500 0.000; 1.000 0.000 0.000 0.000 35.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.450 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.380 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.430 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.390 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.350 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 33.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 2.400 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 45.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.300 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 38.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.300 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.480 0.000; 1.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.310 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.460 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 39.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 2.230 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 48.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 2.410 0.000; 1.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 2.370 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 2.510 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 31.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 2.380 0.000; 1.000 0.000 0.000 0.000 33.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.390 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 33.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.540 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 44.000 0.000 0.000 0.000 4.000 0.000 0.000 0.000 2.290 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 2.420 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.400 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 43.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 2.420 0.000; 0.000 1.000 0.000 0.000 0.000 21.000 0.000 0.000 0.000 10.000 0.000 0.000 0.000 2.410 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 46.000 0.000 0.000 0.000 13.000 0.000 0.000 0.000 2.410; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000 0.000 0.000 8.000 0.000 0.000 0.000 2.400; 0.000 1.000 0.000 0.000 0.000 29.000 0.000 0.000 0.000 13.000 0.000 0.000 0.000 2.400 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 39.000 0.000 0.000 0.000 12.000 0.000 0.000 0.000 2.380 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 27.000 0.000 0.000 0.000 6.000 0.000 0.000 0.000 2.370 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 57.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 2.330 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 7.000 0.000 0.000 0.000 2.370 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 31.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 2.330; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 2.520; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 34.000 0.000 0.000 0.000 11.000 0.000 0.000 0.000 2.360; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 32.000 0.000 0.000 0.000 10.000 0.000 0.000 0.000 2.570; 0.000 1.000 0.000 0.000 0.000 37.000 0.000 0.000 0.000 2.000 0.000 0.000 0.000 2.570 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 46.000 0.000 0.000 0.000 5.000 0.000 0.000 0.000 2.400; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 48.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.370; 0.000 1.000 0.000 0.000 0.000 42.000 0.000 0.000 0.000 3.000 0.000 0.000 0.000 2.470 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 54.000 0.000 0.000 0.000 8.000 0.000 0.000 0.000 2.450; 0.000 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.480 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 36.000 0.000 0.000 0.000 12.000 0.000 0.000 0.000 2.390; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 34.000 0.000 0.000 0.000 9.000 0.000 0.000 0.000 2.300; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 38.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 2.550; -------------------------------- I attached fsgd file. Thank you. Best, Seung-Gul --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea *Research scholar*; Sleep Disorders Clinical Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA *Collaboration researcher*; Division of Sleep & Circadian Disorders, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115

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Convert 4D volume time series to GIFTI surface time series
by Prokopis Prokopiou 09 Sep '16

09 Sep '16

Dear all, I am trying to convert 4D volume time series to GIFTI surface time series. Following the instructions given in a previous post, so far, I have tried using mri_vol2surf and mris_convert, with no success (i.e. when I try to open the surface file in freeview I get Failed to load Surface /home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi i). I would really appreciate if anyone could give me an advise on how to make it work. I give below the logs of each process. Thank you, Prokopis osboxes@osboxes:~$ mri_vol2surf --mov /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet. feat/filtered_func_data.nii --reg $SUBJECTS_DIR/AL_subject/AL_registrations/AL.mat --hemi lh --o /home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh. mgh --projfrac 0.5 --interp nearest srcvol = /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet. feat/filtered_func_data.nii srcreg = /home/osboxes/Desktop/Windows-Share/EEG_fMRI_test//AL_subject/AL_registratio ns/AL.mat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /home/osboxes/Desktop/Windows-Share/EEG_fMRI_test//AL_subject/AL/surf/lh.whi te Done reading source surface Reading thickness /home/osboxes/Desktop/Windows-Share/EEG_fMRI_test//AL_subject/AL/surf/lh.thi ckness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11976 Writing to /home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh. mgh Dim: 139848 1 1 osboxes@osboxes:~$ mri_info /home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh. mgh Volume information for /home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh. mgh type: MGH dimensions: 139848 x 1 x 1 x 400 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 139848.000 dof: 0 xstart: -69924.0, xend: 69924.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 3000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 400 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -3.2031 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 3.2031 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 72.0000 talairach xfm : Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -1.0000 0.0000 0.0000 69920.7969 0.0000 1.0000 0.0000 2.7031 0.0000 0.0000 1.0000 71.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 69920.7969 -0.0000 1.0000 -0.0000 -2.7031 -0.0000 -0.0000 1.0000 -71.5000 0.0000 0.0000 0.0000 1.0000 osboxes@osboxes:~$ mris_convert -f /home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh. mgh $SUBJECTS_DIR/AL_subject/AL/surf/lh.white /home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi i freeview log: osboxes@osboxes:~$ mriseadGIFTIfile: mris is NULL! found when parsing file /home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi i MRISread failed mriseadGIFTIfile: mris is NULL! found when parsing file /home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi i

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overlapping surface
by Fire Tech 09 Sep '16

09 Sep '16

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Viewing Retinotopy In Freeview
by Taylor, Johnmark 09 Sep '16

09 Sep '16

Hello, I am thinking of switching from Tksurfer to Freeview, but I want to make sure that retinotopy visualization still works well. Is it straightforward to view phase-encoded displays? There are a few options on tksurfer (complex color wheel, ability to set number of cycles and angle offset for phase encoded display, ability to smooth overlay) that I am not able to immediately find on freeview. Currently, to visualize retinotopy data we are using the strategy of loading both the real and complex parts of the display on tksurfer. Are there analogous ways of doing all these steps on freeview as of yet, or are they still waiting to be implemented? Thank you very much, JohnMark

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MatrixReadTxT: could not scan value [8][360]
by Smaragdi A. 09 Sep '16

09 Sep '16

Dear mailinglist, I get the following error when I run the mri_glmfit: MatrixReadTxT: could not scan value [8][360] WARNING: matlab elment type is 805908489, which is not a matrix. It seems like problems such as this one are common, but I haven't found an answer in the archive for this specific one, and my design files have worked before (I have just taken out one continuous variable, so no extra rows or anything like that). Many thanks, Areti

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Flattening the surface
by Younghoon Kim 09 Sep '16

09 Sep '16

Hello, We have a volumetric data (mgz file) of a segmented brain region. We want to detect the surface of this segmented brain volume (i.e. deep brain region) and flatten it into a 2D image with its original surface texture. We’ve noticed that Freesurfer supports an algorithm to flatten volumetric data. We wonder if this could be adapted to our data set. Can anyone offer some advice on how to apply FreeSurfer to this more generic task? Thanks, Younghoon Kim -- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab ---------------------------------------------- younghoon.h.kim(a)gmail.com aktivhoon(a)kaist.ac.kr

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