Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

Troubles witg GLM Surface-based Cluster Summary Table
by Claudia Dacquino 12 Sep '16

12 Sep '16

Hi all, I've run GLM surface analysis and I've got a summary table like this: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2016/09/12-08:47:18-GMT # cmdline mri_surfcluster --in lh.Compr.glmdir/SZSI-SZNO/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/ cortex/fwhm15/pos/th40/mc-z.csd --mask lh.Compr.glmdir/mask.mgh --cwsig lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.mgh --vwsig lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.voxel.mgh --sum lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.cluster.summary --ocn lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.mgh --oannot lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.ocn.annot --annot aparc --csdpdf lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.pdf.dat --cwpvalthresh 0.05 --o lh.Compr.glmdir/SZSI-SZNO/cache.th40.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white # cwd /media/TREKSTOR/SUBJ/CI_Compr_Contrasts # sysname Linux # hostname Piras-TC2 # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh.Compr.glmdir/SZSI-SZNO/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /media/TREKSTOR/SUBJ # SearchSpace_mm2 65416.6 # SearchSpace_vtx 149953 # Bonferroni 2 # Minimum Threshold 4 # Maximum Threshold infinity # Threshold Sign pos # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 4.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 1e+10 at vertex 3 # Overall min 0 at vertex 8 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 10000000000.000 3 76467.08 -22.1 41.5 24.1 0.00020 0.00000 0.00040 149953 rostralmiddlefrontal Is it possible to have a Cluster Size (76467.08 mm2) greater than the Total Cortical Surface (65416.6 mm2). Are there some errors in this? Thanks a lot to all of you. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 51501575 web: http://www.neuropsichiatrialab.com <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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Tracula movement
by Lars M. Rimol 12 Sep '16

12 Sep '16

HI, Is there a rule-of-thumb upper level of acceptable head motion? The tutorial gives these values as examples: AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore 0.489419 0.00398925 0 1 I have a subject with AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore *30.018* 0.209 24 1.6 I plan, of course, to use the index described in Yendiki et al. (2013) but would such high levels nevertheless be considered disqualifying a priori? Thank you!

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Parcelation a2009 as mask for SPM analysis
by Matyáš Kuhn 12 Sep '16

12 Sep '16

Hi FreeSurfer experts, We would like to use Destrieux atlas for masking DLPFC in subjects, who uderwent fMRI and we used SPM to process the data. We want to find peaks in individuals according to some regions from the atlas (create individual mask). The problem I am facing is to get aparc.a2009s+aseg.mgz to MNI space so I could overlay results from SPM and Freesurfer. I followed some discussions on mailing list and tried this: mni152reg --s $SUB mri_label2vol --seg $SUBJECTS_DIR/$SUB/mri/aparc.a2009s+aseg.mgz \ --temp /.../spm/spmT_0001.nii \ --reg $SUBJECTS_DIR/$SUB/mri/transforms/reg.mni152.2mm.dat \ --o aseg.$SUB.mni152.nii The process ended without errors, but while watching results in freeview - the results are not correctly aligned. Is FSL (which is part of mni152reg procedure) using some other MNI template than SPM? Any suggestions will be most appreciated. The freeview snapshot is here: https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question/freeview_a…

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white and pial surface crossin in the lingual gyrus
by Alain Imaging 12 Sep '16

12 Sep '16

Hello everybody, I am gladly starting my freesurfer adventure after the awesome last course in Copenhagen, but I have quickly realized that troubleshooting on your own is not as easy as with experts going around in a room. I was looking for errors after having run the recon all and I stumbled upon this crossing between white and pial surface in the lingual gyrus (see attached Figure1, green arrow). It seems to me that the problem may arise from the fact that in the WM volume (see attached Figure2) there are areas that have been categorized as WM hypointensities, and in particular on the right, the problem could be that the white matter surface, instead of going around these brighter voxels, just goes straight down (I hope I have explained myself). Is the fixing to this problem changing the value of those voxels (part of them, of course) in the WM volume ? If I look at the WM seg I see that indeed they are left out from the mask. Or should I do something else ? I am working with freesurfer version Linux-centos6_x86_64-stable-pub-v5.3.0, with Linux version 3.10.0-327.4.5.el7.x86_64 (Red Hat 4.8.3-9). Thanks in advance for any suggestion Alain

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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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Freesurfer September 2016