Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

GLUT: Fatal Error in tksurfer.bin
by stdp82＠virgilio.it 20 Jan '16

20 Jan '16

Hi list, I have installed FS on my macbook (el capitain) and this error occur:tksurferGLUT: Fatal Error in tksurfer.bin: could not open displayI have look in previous mail in the forum but, although the error has been already discussed, no solution for my issue I have found.ThanksStefano

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Questions about eTIV
by Niklas Klasson 20 Jan '16

20 Jan '16

Dear FreeSurfer team, I am writing a paper about FreeSurfer's estimates of intracranial volume (eTIV), when using FreeSurfer version 5.3.0, and have two questions that I would be very grateful if you could answer. My understanding is that the alignment (from which the atlas scaling factor is calculated) of the input MR images to the MNI305 atlas is done by the “Avi Snyders 4dfp suite” (see https://surfer.nmr.mgh.harvard.edu/fswiki/talairach and https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_avi) and using this suite FreeSurfer is trying to align the input images to the brain and about a two cm thick layer around the brain in the MNI305 atlas (see https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-September/008370… guess that FreeSurfer uses the function imgreg_4dfp (in the 4dfp suite, see https://searchcode.com/codesearch/view/39432481/) for the alignment with the following arguments: 1) the MNI305 atlas (as the target image), 2) a target image mask (so that the adoption/evaluation of the alignment only will be done towards the brain and the two cm thick layer around the brain), and 3) the input MR images (as the object image). My questions are: 1) Is my understanding and/or guess correct? 2) Is there any paper or manual available that you know of that describe the alignment procedure used in the 4dfp suite? Thanks in advance! Best regards, Niklas

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How to calculate the volume of subcortical structure using my own atlas?
by Tianqi Wang 20 Jan '16

20 Jan '16

Dear freesurfers, I want to calculate the volume of subcortical structure using my own atlas. But my altlas is not in the fsaverage space. In order to achieve my goal, I plan to use the mri_vol2vol command to register my atlas to the fsaverage subject and then register every subject to the fsaverage subject. At last, I want to use the mris_segstats command to calculate the volume of subcortical structure. I have two questions: 1. Is the plan above can get the right results? 2. If the plan above can get the right results, what registration matrix should I use for mri_vol2vol and how can I get the matrix? Thanks! Tianqi Wang

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visualize fsaverage
by Thục Trinh 20 Jan '16

20 Jan '16

Hello freesurfer experts, I'm having a trouble with visualize the first level analysis output of FSFAST on brain surface (fsaverage). When I open tksurfer tool to look at the contrast for the analysis on Right hemisphere space, the result display the contrast on left hemisphere and vice versa when I want to display the contrast on Left hemisphere space. I already checked the registration quality after run pre-processing and the results were quite good. I hope you can help me to figure out this problem. Thank you and have a nice day, Trinh

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Longitudinal analysis with single timepoint scans
by Bronwyn Overs 19 Jan '16

19 Jan '16

Hi Freesurfer Mailing List, We are running a longitudinal analysis (in R) using 2 time points with scans that have been through the Freesurfer longitudinal pipeline. We were also hoping to incorporate individuals with only a single scan into our analysis. Does it make sense to use long images (2 timepoints) with cross images (1 timepoint) in the same analysis, or can they not be used together because the cross sectional images have not undergone the same processing steps? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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How to determine Freesurfer version used for trac-all
by Alicia Thomas 19 Jan '16

19 Jan '16

I’d like to determine which version of Freesurfer was used to recon-all and trac-all for a subject. Half of my subjects were run using version 5.1 and the other half using version 5.3. I want to determine which version was used for which subjects. Thanks for the help! Alicia

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(no subject)
by EJ Nikelski 19 Jan '16

19 Jan '16

Hi all, I'm testing Freesurfer 5.3 and have a question about processing 1.5T versus 3.0T scans. Specifically, is there a switch in recon-all? I've observed some using a "-3T" switch, but I can't see this option documented in the "recon-all -help" output. I've executed test runs on a VM both with and without this option ... which seems to produce different results in the ROI quantification stats, although no change in the nu_correct arguments (I would have expected a different -distance value, but always appears to be set to 50). So, in sum, is there as 1.5T/3.0T switch in recon-all, and what does it do? Thanks, -jim -- ================================= Jim Nikelski, Ph.D. Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University

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glmfit flag --frame-mask
by Victor Montal Blancafort 19 Jan '16

19 Jan '16

Dear FS Experts, I have seen few posts about this mri_glmfit flag, and I would like to know how it works. In an older post, ( https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32412.html) Doug suggested to use this flag when only some subjects should be exclude for each vertex (i, e. differnet number of subjects to exclude per vertex). Could anyone give me an insight on how this works? My intention is to perform a GLM analysis of some DTI metric volumes projected into the surface. However, some of the DWI volumes are cutted, so I would like exclude those vertexs where there is no signal (i,e value 0). Will --frame-mask work for this? Any other suggestion? Any help will be very appreciated! Thank you in advance, Victor Montal

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Little cluster after FDR correction
by stdp82＠virgilio.it 19 Jan '16

19 Jan '16

Hi list, I have performed a seed-based fcMRI analysis by FAST.After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file could be also produced when FDR correction is applied? I'm very confused.Please, could you help me because from several days I'm trying to have a solution.Thank you very much for your work.Kind regards. Stefano

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error in selxavg3-sess
by neha hooda 19 Jan '16

19 Jan '16

Hii I am using freesurfer to find the resting state connectivity. I used selxavg3-sess to analyze the data. But it neither terminates nor gives the error. Any help will be appreciated. Regards Neha -------------------------------------------------------------- selxavg3-sess logfile is /home/neha/projectfolder/log/selxavg3-sess-bold-fc.lpccseed.surf.lh-160109152215.log -------------------------------------------------------------- preproc-sess -s sessionid -d /home/neha/projectfolder -a fc.lpccseed.surf.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ NC_2 setenv FREESURFER_HOME /home/NC_2/shubham/freesurfer/freesurfer/ setenv SUBJECTS_DIR /home/neha/AKE01/PA0/ST0/ Linux tapan 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux /home/neha/projectfolder /home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/preproc-sess -s sessionid -d /home/neha/projectfolder -a fc.lpccseed.surf.lh -nolog Sat Jan 9 15:22:16 IST 2016 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain sessionid Template ----------------------------- mktemplate-sess -s sessionid -d /home/neha/projectfolder -fsd bold -nolog -update Session: /home/neha/projectfolder/sessionid ---------------- Sat Jan 9 15:22:16 IST 2016 Detected input format at nii.gz sessionid Update not needed Run: 004 ---------------- Sat Jan 9 15:22:16 IST 2016 sessionid 004 Update not needed Sat Jan 9 15:22:16 IST 2016 mktemplate-sess completed sessionid Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sessionid -d /home/neha/projectfolder -nolog -update ------------------------------------------------ /home/neha/projectfolder/sessionid Sat Jan 9 15:22:16 IST 2016 sessionid Update not needed for session-level mask sessionid Update not needed for run 004 mask sessionid Update not needed for run 004 meanval Sat Jan 9 15:22:16 IST 2016 mkbrainmask-sess done sessionid Registration ----------------------------- register-sess -s sessionid -d /home/neha/projectfolder -fsd bold -dof 6 -per-run -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Sat Jan 9 15:22:16 IST 2016 setenv SUBJECTS_DIR /home/neha/AKE01/PA0/ST0/ cd /home/neha/projectfolder /home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/register-sess -s sessionid -d /home/neha/projectfolder -fsd bold -dof 6 -per-run -nolog -update freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux tapan 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Session: /home/neha/projectfolder/sessionid ---------------- Sat Jan 9 15:22:16 IST 2016 Run: 004 ---------------- Sat Jan 9 15:22:16 IST 2016 Update not needed Sat Jan 9 15:22:16 IST 2016 register-sess completed sessionid MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sessionid -d /home/neha/projectfolder -fsd bold -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /home/neha/projectfolder/sessionid RunList: 004 sessionid 004 Update not needed Sat Jan 9 15:22:16 IST 2016 mc-sess completed SUCCESSFULLY sessionid To MNI305 ----------------------------- rawfunc2tal-sess -fwhm 5 -s sessionid -d /home/neha/projectfolder -fsd bold -nolog -update -subcort-mask -per-run ------------------------------ 1/1 sessionid 1/1 sessionid 004 ---------------- Sat Jan 9 15:22:16 IST 2016 /home/neha/projectfolder/sessionid/bold/004/masks/brain.mni305.2mm.nii.gz does not need updating sessionid 004 Update not needed Sat Jan 9 15:22:16 IST 2016 rawfunc2tal-sess completed ---------------------------------------- Started at Sat Jan 9 15:22:16 IST 2016 Ended at Sat Jan 9 15:22:16 IST 2016 preproc-sess done ------------------------------------------- /home/neha/projectfolder/sessionid Sat Jan 9 15:22:17 IST 2016 anadir = /home/neha/projectfolder/sessionid/bold/fc.lpccseed.surf.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014b (8.4.0.150421) 64-bit (glnxa64) September 15, 2014 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /home/neha/projectfolder >> sxa3cmd = /home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/selxavg3-sess -s sessionid -a fc.lpccseed.surf.lh >> /home/NC_2/shubham/freesurfer/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sessionid ############################### /home/neha/projectfolder/sessionid ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /home/NC_2/shubham/freesurfer/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/NC_2/shubham/freesurfer/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/NC_2/shubham/freesurfer/freesurfer/matlab/MRIread.m ------------------------- outtop = /home/neha/projectfolder Extension format = nii.gz rm: remove regular file `/tmp/tmp9865807.nii'? 0

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Freesurfer January 2016