Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Neuroimaging Postdoctoral Research Position in Memory, Aging, and Alzheimer's disease
by Scott Hayes 21 Feb '14

21 Feb '14

*Neuroimaging Postdoctoral Research Position in Memory and Aging* Memory Disorders Research Center and Neuroimaging Research Center VA Boston Healthcare System The Boston University Memory Disorders Research Center and Neuroimaging Research Center at VA Boston Healthcare System are seeking an advanced postdoctoral fellow with expertise in Magnetic Resonance Imaging and human memory. The candidate will receive advanced training in multi-modal imaging (fMRI, diffusion tensor imaging, volumetric and surface-based analyses, ASL) in young adults, older adults, and patient populations (Mild Cognitive Impairment and medial temporal lobe amnesics). Studies will focus on human memory, age- and AD-related changes in memory and the brain, and individual differences (e.g., in cardiovascular fitness) that attenuate age-related decline. Dr. Scott Hayes will be the primary mentor, and the fellow will also collaborate on projects with Drs. Mieke Verfaellie and David Salat. The successful candidate will have a doctoral degree in cognitive neuroscience, neuropsychology, biomedical engineering, or a closely related field, and substantial experience in MRI data acquisition and analysis (fMRI preferred, but applicants with experience using other imaging modalities would also be considered). Candidate should have expertise working with MRI analysis software such as AFNI, FSL, SPM, or FreeSurfer, as well as familiarity with unix and Matlab. Experience interpreting neuropsychological data, and previous work with aging or clinical populations are also desirable. The postdoctoral fellow will interact with several research groups at VA Boston examining memory, age and AD-related changes in cognition and the brain and will be part of a rich and stimulating intellectual environment. The candidate should have a keen interest in developing an independent research career. The starting date is flexible. A minimum two-year commitment is required. Salary for highly qualified candidates may be up to $52,000. U.S. citizenship is required for consideration. Potential applicants are encouraged to *immediately* email a letter describing research interests and experience and CV and should arrange to have three letters of recommendation emailed to Dr. Scott Hayes at smhayes(a)bu.edu Lab website: www.bu.edu/brainlab The Department of Veterans Affairs is an Equal Opportunity Employer. -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor Department of Psychiatry Boston University School of Medicine

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ocn?
by Yang, Daniel 21 Feb '14

21 Feb '14

Dear FreeSurfers, I obtained a file from cluster analysis, called "cache.th20.pos.sig.ocn.mgh" Can you tell me what OCN stand for? And what is this file for? I tried to view it but was unable to see anything. Best, 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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interpretation of a 3-way interaction
by Yang, Daniel 21 Feb '14

21 Feb '14

Dear FreeSurfers, I have two discrete and binary factors (Dx: patients vs. controls; Sex: female vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is a 3-way interaction of Dx x Sex x Age, regressing out IQ, is the following interpretation correct? Red/yellow: In females (vs. males), the Age effect of cortical thickening is stronger in patients (vs. controls). Blue/cyan: In females (vs. males), the Age effect of cortical thinning is stronger in patients (vs. controls). Note. by stronger, I mean greater magnitude without sign. Thanks, Daniel

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continusous x continuous interaction?
by Yang, Daniel 21 Feb '14

21 Feb '14

Dear FreeSurfer Experts, In the example here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V, it describes the testing of the main effects of two continuous variables. In order to test the interaction effect, I think we can form an interaction term like age x weight as the third covariate, that is, Regressor1: All ones. Codes intercept/mean for Main Regressor2: age for each subject. Codes age slope for Main Regressor3: weight for each subject. Codes weight slope for Main Regressor4: age x weight for each subject. Codes age x weight interaction effect and then specify a contrast [0 0 0 1]? Is that the way to go? Best, 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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Segmentation process
by Saurabh Thakur 21 Feb '14

21 Feb '14

Hi Freesurfer expert, Thanks for all your help, I have explored the tkmedit ,tksurfer and freeview. How to move ahead with segmentation task. I looking forward to create my own .aseg file for sub cortical region. Is it possible...? And if possible,please share major breakpoint of the process. Thanks in advance. cheers Saurabh Thakur,

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viewing corrected result error
by charujing123 20 Feb '14

20 Feb '14

Hi all, I try to see the cluster wised result by typing "freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.ocn.annot",but it feedback some error infomation as below: Did not find any volume geometry information in the surface ԥhreading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) Thanks. All the best 2014-02-20 charujing123

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questions of clusters defined and sign of the threshold in simulation
by charujing123 20 Feb '14

20 Feb '14

Hi FS experts and users, May I ask some questions about clusterwise correction for multiple comparisons? 1,In mri_glmfit-sim command, there is a --sim(--sim nulltype nsim threshold csdbase) option. Choose the voxel/vertex-wise threshhold used to define clusters. This will be -log10(p), where p is the p-value. Eg, to use all voxels/vertices with p < .01, then set the threshhold = 2.I want to know what is meaning of "using all voxels with p < 0.01". Does it mean that considering all voxels whose p value below 0.01 in every iterations. Then it generates some clusters in every iteration. Is it right? 2,Also there is a --sim-sign option in this command. I want to know meaning of the sign: abs,pos,neg.Does it represent one- and two-tailed tests? Thanks. All the best. Rujing Zha 2014-02-20 charujing123

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mris_convert
by Karen Marie Sandø Ambrosen 20 Feb '14

20 Feb '14

Hi Freesurfer experts, I am trying to run tracktography from freesurfer labels using probtrackx2 in fsl. To convert the labels to surfaces I use the label2surf command as recommended on the fslwiki. To use the label2surf command I need to convert the surface, e.g. lh.white into a fsl-compatible format using mris_convert: mris_convert lh.white lh.white.gii When I load lh.white and the created lh.white.gii into freeview the two are not aligned. Aren't they suppose to be similar when lh.white.gii is use in the label2surf command? Do I need additional arguments in the mris_convert command? Best, Karen

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Fwd: recon-all trouble
by will brown 20 Feb '14

20 Feb '14

Hi all, I'm having a recon-all error that I haven't encountered before with one particular run of scans. I'm a bit too much of a newby to be able to see which stage the error is occurring so any help would be appreciated. I have attached error log. Thanks, Will

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Topological defect
by Ray, Siddharth 20 Feb '14

20 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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Freesurfer February 2014