Freesurfer

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30088 discussions

FW: Topological defect
by Ray, Siddharth 27 Feb '14

27 Feb '14

Hi all, I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject: Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 70557 ambiguous faces found in tessellation segmenting defects... 78 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 0 -merging segment 22 into 0 -merging segment 68 into 49 -merging segment 61 into 55 74 defects to be corrected 0 vertices coincident reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.4264 (-4.2132) -vertex loglikelihood: -5.7733 (-2.8866) -normal dot loglikelihood: -3.6047 (-3.6047) -quad curv loglikelihood: -6.1117 (-3.0559) Total Loglikelihood : -23.9161 CORRECTING DEFECT 0 (vertices=27967, convex hull=5893) Segmentation fault mris_euler_number ../surf/lh.orig mris_fix_topology failed! (euler number != 2) Trying mris_topo_fixer... cp ../surf/lh.orig.nofix ../surf/lh.orig euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes F =2V-4: 234344 != 233464-4 (-884) 2E=3F: 703032 = 703032 (0) total defect index = 442 cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm /work/02510/sray2/Free_Sub/DATA/50011/50011/scripts mris_topo_fixer -mgz -warnings -seed 1234 50011 lh verbose mode on (medium mode): printing warnings setting seed for random number genererator to 1234 Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221) Surface Diagnostics: eno=-440 (nv=116732, nf=234344, ne=351516) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect The surface has 221 loops (X=-440) Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations identify defects... marking ambiguous vertices... 68425 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... INFO: assuming .mgz format reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ] Computing Initial Surface Statistics -face loglikelihood: -5.8578 (-2.9289) -vertex loglikelihood: -5.7524 (-2.8762) -normal dot loglikelihood: -3.6033 (-3.6033) -quad curv loglikelihood: -5.8101 (-2.9050) Total Loglikelihood : -21.0236 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Correcting Topology of defect 1 with euler number -257 (129 loops) computing statistics for defect 1: 33364 vertices location: [ (156,125,84) - average intensity = 92.126 ] -gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 ) -gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 ) -intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ]) -curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 ) -curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 ) MRISalloc(8654176, 520): could not allocate vertices Cannot allocate memory And In some of my subjects the log file stop writing after: "CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)" My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually? Thanks, -Siddharth

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projfrac
by SHAHIN NASR 27 Feb '14

27 Feb '14

Hi Surfers, I want to analyze (preproc-sess + selxavg3-sess) my data using different projfarc depth (e.g. 0.75, 0.5, 0.25 and 0.0). - I know that I can use this parameter with preproc-sess. But is there anyway to use multiple -projfrac(s) within one preproc-sess command? - If no, is there anyway to apply preproc-sess separately to the same dataset with different -projfrac without overwriting? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Binary curvature overlay
by Wesley Burge 27 Feb '14

27 Feb '14

Hi FreeSurfer experts, My question is about the curvature overlay. When we load the curvature files and select binary from the curvature drop down menu in Freeview or change the curvature display to binary gray in tksurfer, what do the the light gray and dark gray mean? I understand the light represents the gyrus and the dark represents the sulcus, but what happens at the light gray and dark gray border? Is that the point where the curvature value is zero? Thanks, -- Wesley Burge Behavioral Neuroscience Graduate Research Assistant UAB Dept of Psychology 1720 2nd Avenue South Birmingham, AL 35294

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Ventral diencephalon measurements
by Stefan Du Plessis 27 Feb '14

27 Feb '14

Hello everyone We are interested in measuring the dimensions of the ventral diencephalon as part of a general metabolic study. We were wondering how accurate people consider freesurfer to be at measuring this region currently? Although some VDC freesurfer results have been published before (Goldman 2008) and look promising, we are not aware of any cross-validation studies in this region with freesurfer. We were wondering what other recommended automated/semi-automated techniques/software packages (Apart from manual tracing of course...) are available to help cross-validate morphological findings in this region specifically? greetings Stéfan *** Stéfan du Plessis Stellenbosch, South Africa

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setenv command not found
by pietro de rossi 27 Feb '14

27 Feb '14

Dear Freesurfers, I am using Freesurfer version 5.1 on Linux-centos4_x86_64. I am trying to set up as SUBJECTS_DIR a folder which is different from freesurfer's predetermined subjects folder..... my command line was setenv SUBJECTS_DIR /path/to/my_folder I get: bash: setenv: command not found How can I solve the problem? It never happened on the Mac I was previously working on... Thanks -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant'Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy 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 90280774 web: http://www.neuropsichiatrialab.com

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questions about ROI analysis
by Rujing Zha 26 Feb '14

26 Feb '14

Hi FS experts and others, I have done two group thickness difference analysis based on whole brain. Now I want to do correlation analysis between specific ROI thickness and behavior score. I searched roi in the FS website, but I cannot distinguish the volume ROI and surface ROI very clearly. So I have some questions as below: 1,As I get some clusters in the two group t-test,I want to use one of these clusters to correlate thickness with behavior score. How to generate this mask and how to use this mask in the mri_glmfit and mri_glmfit-sim? 2,If I want to draw ROI manually or set ROI according previous studies, how to create this ROI mask. Any detailed information will be highly appreaciated. Thanks. All the best. Rujing Zha

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two labels in tksurfer/freeview?
by Yang, Daniel 26 Feb '14

26 Feb '14

Dear FreeSurfer experts, Is it possible to display two labels in tksurfer or freeview, where one label is outlined with a certain color and the other label is filled with a different color? I want to show two labels, one is within the other one. If yes, could you please tell me the specific steps..? thanks a lot! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

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(no subject)
by Douglas Wojcik 26 Feb '14

26 Feb '14

Good afternoon; I am hoping you can help me answer a pretty quick & easy question…. I am trying to identify the best MRI protocol to use for Freesurfer analysis… When I look at the FAQ: Data Requirements The processing procedures for the creation of cortical models require good quality T1 weighted MRI data, such as a Siemens MPRAGE (examples of appropriate Siemens scanner protocols) or GE SPGR sequence with approximately 1mm3 resolution (although a variety of quality data sets can be processed with additional manual intervention). Thickness should not exceed 1.5mm (~1mm^3 is ideal). The protocols specified for the ADNI project are excellent examples to follow. The best FreeSurfer processing results come from scans having excellent gray/white matter contrast. The link to the ADNI project protocols is broken…I think that they should be here: http://adni.loni.usc.edu/methods/documents/mri-protocols/ Thanks Douglas

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No labels file in label directory?
by sabin khadka 26 Feb '14

26 Feb '14

Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this. -Sabin

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mris_preproc xhemi
by Daniel Carey 26 Feb '14

26 Feb '14

Dear All, We have been attempting to run a cross hemisphere analysis using .curv files, as per the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi I have outlined the exact steps within our pipeline below. When fitting any glm to the data (simple osgm shown below), we find that across all vertices, the significance values are 0 (despite the vertex by vertex diff values appearing to be very slightly different, based on a cursory inspection of the sig.mgh file overlaid onto lh of fsaverage_sym in tksurfer). Oddly, the vertex by vertex diff values also appear to be lower than we would expect (approximately by a factor of 10). Within the terminal output from glm_fit, we see both F and sig values of 0. We are unsure as to why the analysis isn't working quite as expected. Any advice on this would be greatly appreciated. Many thanks in advance, Dan --- # register subs foreach sub (01 03 04 05 06 08 10 11 12 13 14 15 16 18 19 20 21 22 23 24 25 27 28 29 30 31 32 33 35 36 37 38 39 40) surfreg --s S$sub-synth --t fsaverage_sym --lh surfreg --s S$sub-synth --t fsaverage_sym --lh --xhemi end # mris_preproc mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff --srcsurfreg fsaverage_sym.sphere.reg --meas curv --out lh.lh-rh.curv.sm00.mgh \ --s S01-synth --s S03-synth --s S04-synth --s S05-synth --s S06-synth --s S08-synth --s S10-synth --s S11-synth --s S12-synth --s S13-synth --s S14-synth \ --s S15-synth --s S16-synth --s S18-synth --s S19-synth --s S20-synth --s S21-synth --s S22-synth --s S23-synth --s S24-synth --s S25-synth --s S27-synth \ --s S28-synth --s S29-synth --s S30-synth --s S31-synth --s S32-synth --s S33-synth --s S35-synth --s S36-synth --s S37-synth --s S38-synth --s S39-synth \ --s S40-synth # smooth mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 5 --i lh.lh-rh.curv.sm00.mgh --o lh.lh-rh.curv.sm05.mgh # mris_glmfit mri_glmfit --y lh.lh-rh.curv.sm05.mgh --glmdir glm.lh.lh-rh.curv.sm05.osgm --osgm --surf fsaverage_sym lh --- Daniel Carey Marie Curie Ph.D. Fellow, Centre for Brain and Cognitive Development, 32 Torrington Sq., London WC1E 7HX UK email: d.carey(a)bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey

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