Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Pb with a registration of diffusion images processed with tracula and anat images
by Celine Louapre 28 Feb '14

28 Feb '14

Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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Extracting only hippo campus volume
by Saurabh Thakur 28 Feb '14

28 Feb '14

Hello Freesurfer expert, I have done Hippo campus segmentation using Freesurfer. Can u tell me how to extract the only Hippo campus volume from nu.mgz Why only nu.mgz is used for the main volume--is there some specific reason to use? Thanks in advance , Saurabh Thakur,

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Talairach failure in 5.3 but not in 5.2
by Corinna Bauer 28 Feb '14

28 Feb '14

Hello all, I have 2 subjects that failed autorecon-all at the same Talairach step. Both subjects successfully completed autorecon-all in version 5.2. Here is the output from one of the subjects. Any suggestions? Corinna #-------------------------------------------- #@# Talairach Fri Feb 28 12:39:50 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Feb 28 12:40:51 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/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 Fri Feb 28 12:40:51 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/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/bauer/freesurfer_subjects/symmetry/MWP_04182013/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 bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri Feb 28 12:41:10 EST 2014 tmpdir is transforms/tmp.talairach.30730 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri mri_convert orig_nu.mgz transforms/tmp.talairach.30730/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.30730/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=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.13732e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.45519e-11, -1) k_ras = (2.6057e-10, 1, 1.45519e-11) writing to transforms/tmp.talairach.30730/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.30730/src.mnc transforms/talairach.auto.xfm Fri Feb 28 12:41:27 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Feb 28 12:41:28 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0012, 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 bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MWP_04182013 exited with ERRORS

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Subcortical CVS registration
by Jennifer Eastman 28 Feb '14

28 Feb '14

Hi All, I just wanted to bump this question back up.I am interested in comparing sub-cortical volumes across subjects in my data set. I am wondering if using the CVS registration step is useful in improving the accuracy of the sub-cortical volume measurements independently. I will not be examining the cortical thickness just sub-cortical. I have combed the literature that is available and watched the training video, but I am not clear if there is benefit to using CVS registration if I am just looking at the sub cortical structures. Thank you. Jennifer Sent from my iPhone

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How to clone from T1 to brainmask in freeview to amend a bad skull strip
by Emad Ahmadi 28 Feb '14

28 Feb '14

Hi! I want to know how to clone from T1.mgz to brainmask.mgz in freeview (to amend a skullstript that has removed too much). I couldn’t find the tool in freeview. Thank you very much, Emad Emad Ahmadi, MD ----------------------------------------------- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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Linear Mixed Effects Models
by Eric Cunningham 28 Feb '14

28 Feb '14

Hello Freesurfer Experts, I am currently trying to run the Linear Mixed Effects Models described in the wiki here: http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels And I am running into difficulties that are fairly well described by the last message in this previous mail thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25787.html Can you please clarify the variable "ni"? the following command: *[M,Y,ni] = sortData(M,1,Y,sID);* results in: ??? Error: File: sortData.m Line: 59 Column: 6 Expression or statement is incorrect--possibly unbalanced (, {, or [. do i need to build "ni" ahead of time? You probably don't need to know this, but I am using data generated by Freesurfer version 5.1, on matlab 7.8.0 (R2009a), which I gather will cause a few problems further down the line. Thank you for your help, -Eric

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time course in mri_info lh.gender_age.thickness.10.mgh
by charujing123 27 Feb '14

27 Feb '14

Hi all, I have two questions. 1,If I want to get the value of specific voxel from the lh.gender_age.thickness.10.mgh, which code can I use to perform it? 2,How to graph the time course of specfic voxel from the lh.gender_age.thickness.10.mgh by freeview? Thanks. All the best. Rujing Zha 2014-02-24 charujing123

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PostDoctoral Opportunity
by Mario Ortega 27 Feb '14

27 Feb '14

Dear Freesurfer Community, We have a post-doctoral opportunity available, please send CV and letter of interest to bances(a)wustl.edu Thanks. *Description:* Applications are invited for a post-doctoral position within the Departments of Neurology and Radiology at Washington University in St. Louis. Research focuses on the application of functional MRI methods to neurodegenerative diseases (including Alzheimer's Disease (AD) and HIV Associated Dementia (HAD)). This research investigates the use of functional neuroimaging measures (including arterial spin labeling (ASL) and resting state blood oxygen dependent (BOLD) imaging) as biomarkers for neurodegenerative diseases. Opportunities will be provided for pursuing personal research interests if applicable. Writing manuscripts and applying for independent grants will be strongly encouraged. *Requirements:* The qualified candidate should have a degree in neurosciences, psychology, biomedical engineering, physics, computer science, or other related fields. Previous experience with some of the following computational methods (e.g., linear algebra, time-series analysis, image analysis), programming (e.g., C/C++, MATLAB, R, Python) and neuroimaging programs (e.g. SPM, AFNI, Freesurfer) is preferred and would allow for more individualized studies. Strong facility with statistical analyses is also desired. To apply, please send a letter of interest and CV to bances(a)wustl.edu<https://pod51035.outlook.com/owa/redir.aspx?C=37AOPBO5HUO_j9bos9wYowoaxdzjA…>. Please arrange for three confidential letters of reference to be sent to the address below. Only applicants considered for employment will be contacted. Contact Information: Beau Ances MD, PhD Department of Neurology Washington University in Saint Louis Box 8111 660 South Euclid Ave Saint Louis, MO 63110 bances(a)wustl.edu

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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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Freesurfer February 2014