Freesurfer

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30132 discussions

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

1 1

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

1 0

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

1 0

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

1 0

Lesion Volume Analysis
by Ledesma, Jason 08 Jan '18

08 Jan '18

Hi, I am aware that the recon-all command ultimately calculates statistics on a given MRI sequence, including what is referred to as "aseg.stats". "Aseg.stats" includes the "WM-hypointensities" calculation, which I was told would be an equivalent to white matter lesion volume. Is there a way to calculate the WM-hypointensity volume without doing the complete "recon-all" analysis to reduce processing time for this particular aspect of study? Thank you. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)labiomed.org<mailto:jason.ledesma@labiomed.org> ________________________________ LA BioMed Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ________________________________

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make_average_subject for skull-stripped data
by Duran, Tugce 08 Jan '18

08 Jan '18

Hi FS Experts, I want to make sure that the make_average_subject on my pre skull-stripped data is accurate. I check the avgsubj volume and surfaces using the following command: tkmedit avgsubject orig.mgz lh.white and as a result, I get the attached. Though the shape looks elongated in other analyses. Any thoughts? Thanks! Tugce Duran, B.S. Research Technologist II [cid:image001.png@01D38882.8FF43A70]<https://medicine.iu.edu/departments/neurology/research/> Indiana Alzheimer Disease Center (iADC) Office: 317-278-7015 durant(a)iupui.edu<mailto:durant@iupui.edu>

1 0

asegstats2table error message
by Hugh Pemberton 08 Jan '18

08 Jan '18

Hi, I'm getting the following error when trying to use the asegstats2table command, I can't see anything similar from previous emails, any ideas what the issue is? Thanks v much in advance. asegstats2table --subjects baseline 12m 24m 36m --meas volume --tablefile aseg_stats.txt File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' SyntaxError: invalid syntax

2 1

viewing the flatten sheet
by N Saf 08 Jan '18

08 Jan '18

Dear experts, I cut the inflated surface in tksurfer and obtain the flatten sheet by mris_flatten but I can not load the $h.flaten.patch.3d not in freeview nor in tksurfer it somehow collapse! my laptop is RAM:6G , core i5 , would you please help me how can I see the 2D flatten sheet ?? many thanks to any help you can provide me. BRG, Nazanin

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