Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

hippocampal subfields in younger populations
by Christian Krog Tamnes 10 Jan '18

10 Jan '18

Dear FreeSurfer and hippocampal subfield segmentation developers, I have noted that the FS6.0 hippocampal subfield segmentation procedure was developed using scans of older adult brains. Has the application of this method to kids, adolescents and/or young adults in any way been validated? Or do you have any thoughts regarding such use of the method? I would think this would be an issue for young kids that have markedly different brain volumes, but not for older kids and young adults that differ less dramatically from older adults. But I would greatly appreciate any input regarding this. Best regards, Christian

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How to output particular area from stats subdir
by Jing Gu 09 Jan '18

09 Jan '18

Dear FreeSurfer Developers, By using the following code, we can get volume data of different areas from stats file. asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txt How can I get information of one or two areas, such as hippocampal? thanks Best, Gina

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Acquiring Exact p Values
by Hannah Claussenius-Kalman 09 Jan '18

09 Jan '18

Hello, I am conducting surface group analyses and would like to acquire exact p values. The FreeSurfer manual notes that the number listed after the peak coordinates and the vertex # is a "significance value," and that the "significance in this display is a -log(10)p value, and not a straight p value." However, if I log this number the "p value" I calculate is not significant (e.g., log(5.68) = .75) so I don't believe I am interpreting their description correctly. Could you please advise on how to acquire exact p values? Thank you for your time.

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Surfaces along midline
by Romella Durrani 09 Jan '18

09 Jan '18

Hi, I'm having problems with the surfaces along the midline for one scan. I have attached pictures of the brainmask with surfaces, wm.mgz, and T1 (before any of my edits). I have tried to fix this by adding control points and also tried to fix it by editing the wm.mgz file to fix the ventricle problem, however, none of these edits have resolved the issue. Thanks!

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Segmentation of hippocampal subfields and nuclei of the amygdala
by Carme Uribe Codesal 09 Jan '18

09 Jan '18

Dear FreeSurfer users, I wanted to run the new script that segments the hippocampus and amygdala (segmentHA_T1.sh: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) but I can't find it in FreeSurfer 6.0. Is it already available? Where can I find it? Thanks in advance! Carme Uribe

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Fail to retrievive data file from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git
by zuxfoucault Wong 09 Jan '18

09 Jan '18

Hi FreeSurfers, I am trying to build freesurfer from source on ubuntu 16.04 in order to run `recon-all -use-gpu` that is compatible with the latest cuda 9.1. I followed the instruction here to build freesurfer http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page. However, in order to `make install` I have to retrieve the data file but failed. Error message: $ git fetch datasrc error: The requested URL returned error: 403 Forbidden (curl_result = 22, http_code = 403, sha1 = 3a63ee606e817bc4c837fbc8330a16e40432f379) error: Unable to get pack index https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git/objec… error: Unable to find 3a63ee606e817bc4c837fbc8330a16e40432f379 under https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git Cannot obtain needed tree 3a63ee606e817bc4c837fbc8330a16e40432f379 while processing commit d300174e056c2e3b0188eba3fadc1d706698edac. error: fetch failed. Any suggestions? Thanks for your time! Best, Foucault

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LME
by Tefera, Getaneh B 08 Jan '18

08 Jan '18

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g0 : 0 1 0 0 0 0 The slope of g1: 0 1 0 1 0 0 The slope of g2: 0 1 0 0 0 1 The slope difference between g0 and g1: 0 0 0 1 0 0 The slope difference between g0 and g2: 0 0 0 0 0 1 The slope difference between g1 and g2: 0 0 0 -1 0 1 1) Is this contrast matrix correct to observe pairwise slope difference? In the tutorial the contrast matrix C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)] 2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial? If so, my contrast matrix can be C=[0 0 0 1 0 0; 0 0 0 -1 0 1] 3) How can we interpret the result for this contrast matrix? 4) How can I obtain B1, B2, ... ? [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr_pr) 5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)? With regards Getaneh

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Question about combine longitudinal analysis and xhemi
by lanbo Wang 08 Jan '18

08 Jan '18

xhemireg.lh.log <https://drive.google.com/file/d/0B8gDmAZ-2iJ6bTBIbF9xQmhrMmcwVTFFNmN0WEo1d1…> Thanks for replying me. But I still have two questions. Firstly, when I try xhemi on pre-possessed longitudinal data, it showed error like this: Performing left-right swap of labels TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-1, 3.72529e-08, 3.35276e-08) j_ras = (-2.6077e-08, -3.72529e-09, -1) k_ras = (-1.78814e-07, 1, 6.98492e-10) writing to /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+a seg.mgz... Wed Dec 20 17:46:35 EST 2017 recon-all -sb subj_02_1.long.s02_base/xhemi -talairach ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists. Secondly, how I can get the change rate after construct left -right registration. Thanks, Lanbo

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Linear mixed model and samplesize calculation
by Tefera, Getaneh B 08 Jan '18

08 Jan '18

1 0

Linear mixed model and sample size calculation
by Tefera, Getaneh B 08 Jan '18

08 Jan '18

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ … The slope of g0 : 0 1 0 0 0 0 The slope of g1: 0 1 0 1 0 0 The slope of g2: 0 1 0 0 0 1 The slope difference between g0 and g1: 0 0 0 1 0 0 The slope difference between g0 and g2: 0 0 0 0 0 1 The slope difference between g1 and g2: 0 0 0 -1 0 1 1) Is this contrast matrix correct to observe pairwise slope difference? In the tutorial the contrast matrix C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)] 2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial? If so, my contrast matrix can be C=[0 0 0 1 0 0; 0 0 0 -1 0 1] 3) How can we interpret the result for this contrast matrix? 4) How can I obtain B1, B2, … ? [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr_pr) 5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)? With regards Getaneh

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Freesurfer January 2018