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30084 discussions

Using qdec to view cluster results
by Sahil Bajaj 11 Mar '16

11 Mar '16

Dear all, I have a very basic question regarding the usage of qdec. I am using qdec to view cortical thickness for a set of patients vs. controls. I am able to create table.dat, design the comparison and display the results. After that, my results are saved as sig.mgh in qdec folder. Now when I try to reopen the same results by loading surface and overlaying with sig.mgh, although it shows me the results but when I click on 'Find Clusters and go to max' it gives me following error: Error generating cluster stats GeneratingClusterStats: white surface was not found and it doesn't display any cluster results in terminal window. If I do everything from very first step, starting from loading table.dat, creating design once again, everything is working fine. I would really appreciate any help. Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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selxavg3-sess question
by Ji Won Bang 11 Mar '16

11 Mar '16

Dear. Freesurfer experts. Hi. i appreciate your help in advance! I'm using freesurfer version 5.3.0. I tried selxavg3-sess and got the error dimension mismatch between mask and 2th run. Actually, the number of slices of the 1st run and the rest are different. Is it the reason why I get this error message? Please let me know what I should do to correct this error! Below are command and error lines. command: selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile error: -------------------------------------------------------------- selxavg3-sess logfile is /home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino-160309115326.log -------------------------------------------------------------- ------------------------------------------- /home/jbang/Projects/replay/epi/replay06 Wed Mar 9 11:53:33 EST 2016 anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /home/jbang/Projects/replay/log >> sxa3cmd = /usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06 -analysis retino -df sessdirfile >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# replay06 ############################### /home/jbang/Projects/replay/epi/replay06 ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m ------------------------- outtop = /home/jbang/Projects/replay/epi Extension format = nii.gz 1 HorVer.mat 2 UpperLower.mat nruns = 4 autostimdur = outanadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino Found 62211/180708 (34.4) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 0 ntptot = 480, nX = 28, DOF = 452 Saving X matrix to /home/jbang/Projects/replay/epi/replay06/bold_retino/retino/Xtmp.mat XCond = 199.451 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.499283 (t=0.024843) 2 -0.25 -0.268756 (t=0.047925) 3 0 -0.0441607 (t=0.069497) 4 0.25 0.16942 (t=0.093633) 5 0.5 0.359032 (t=0.117433) AR1 Correction M: 0.0657489 1.15858 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean 855.07 run 2 t= 3.1 ERROR: dimension mismatch between mask and 2th run >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you very much! Best, Ji Won

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Fsaverage
by Kasper Jessen 11 Mar '16

11 Mar '16

Dear FreeSurfer experts, In regard to fsaverage, we are wondering whether it is recommended to use the default fsaverage or if a new fsaverage should be created for the individual dataset. If there are no recommendations, what are the advantages and disadvantages? Best regards, Kasper Jessen MD, PhD student -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk

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FA maps surface based analysis
by John Anderson 11 Mar '16

11 Mar '16

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mri_glmfit
by John Anderson 11 Mar '16

11 Mar '16

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For Monte Carlo simulation, QDEC GUI or in-line command?
by Karl Liu 11 Mar '16

11 Mar '16

Dear Freesurfer Experts: I repost a question I have when applying Monte Carlo simulation to control for multiple comparisons. Your help is much appreciated. I did the correction via QDEC GUI. In the section of Monte Carlo Null-Z simulation, I set Threshold: 2.0 (0.01) and Sign: neg. This generates a "mc-z.neg.th20.sig.cluster.summary" file in each contrast folder. Later, I use the in-line: command mri_glmfit-sim instead. My input is: ri_glmfit-sim --glmdir Untitled --cwpvalthresh .05 --cache 2 neg --2spaces. This generates a "cache.th20.neg.sig.cluster.summary" file for each contrast. My question is : are these two summary files the same, one from QDEC GUI with name " mc-z..." and the other from in-line command with name "cache..."? My next question is: In QDEC GUI, when the simulation is finished, the GUI automatically illustrates the clusters/brain, based on a file named "mc-z.neg.th20.sig.cluster.mgh". But I doubted if this is post-correction results. What is the right way to view results after correction? Thank you very much. Karl

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FS 6
by John Epiktitos 11 Mar '16

11 Mar '16

Dear fs experts, Is there a version of fs 6 for Windows to download. Thank u John On Tuesday, March 8, 2016, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi David > > I'm pretty sure that the Wash U HCP group has sorted this out. Have you > asked them? > > cheers > Bruce > > > On Tue, 8 Mar 2016, Slater David wrote: > > >> Hi, >> >> >> >> I have some mesh and label files I would like to use with my Freesurfer >> data >> however they are in an alternative format (connectome workbench). >> >> >> >> I would like to get the labels into the space of a typical Freesurfer >> subject (e.g. fsaverage), followed by pushing the labels to subject native >> space and creating volume label files (similar to the aparc native space >> parcellations). >> >> >> >> Is it possible to register an isolated mesh file to the fsaverage subject? >> How can I convert labels on a .gii mesh file to a standard Freesurfer >> subject? >> >> >> >> Thanks, >> >> David >> >> >> >> p.s. The goal of this would be to use the following parcellation scheme >> with >> my freesurfer data: >> >> Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., >> Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area >> Parcellation from Resting-State Correlations. Cereb. Cortex bhu239–. >> >> >> >> >>

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question about selxavg3-sess
by Ji Won Bang 10 Mar '16

10 Mar '16

Dear. Freesurfer experts. Hi. I'm trying retinotopy analysis using freesurfer version 5.3.0. I'm having a problem when running selxavg3-sess... Could you please help me with this issue? I have 3 runs under bold_retino and all 3 scans have the same dimension.. The command line that I entered are: mkanalysis-sess -analysis retino.lh -TR 2 -paradigm para.para -event-related -funcstem fmcpr.sm0.self.lh -nconditions 4 -timewindow 34 -inorm -gammafit 2.25 1.25 -polyfit 2 -nuisreg mcprextreg 3 -force -fsd bold_retino -per-run -surface self lh -refeventdur 8 mkcontrast-sess -analysis retino.lh -contrast HorVer -a 1 -c 2 mkcontrast-sess -analysis retino.lh -contrast UpperLower -a 3 -c 4 preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-run -force -surface self lhrh -fwhm 0 selxavg3-sess -s $SUBJECT -analysis retino.lh -df sessdirfile Then I get the error: Surface data self lh -------------------------------------------------------------- selxavg3-sess logfile is /home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino.lh-160310164355.log -------------------------------------------------------------- ------------------------------------------- /home/jbang/Projects/replay/epi/replay06 Thu Mar 10 16:43:56 EST 2016 anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /home/jbang/Projects/replay/log >> sxa3cmd = /usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06 -analysis retino.lh -df sessdirfile >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# replay06 ############################### /home/jbang/Projects/replay/epi/replay06 ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m ------------------------- outtop = /home/jbang/Projects/replay/epi Extension format = nii.gz 1 HorVer.mat 2 UpperLower.mat nruns = 3 autostimdur = outanadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh Found 140089/148112 (94.6) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 360, nX = 22, DOF = 338 Saving X matrix to /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/Xtmp.mat XCond = 200.812 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.500111 (t=0.013194) 2 -0.25 -0.270166 (t=0.024429) 3 0 -0.0463709 (t=0.035203) 4 0.25 0.166079 (t=0.04517) 5 0.5 0.354234 (t=0.055571) AR1 Correction M: 0.0689761 1.16382 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean 862.23 run 2 t= 2.0 Global Mean 864.13 run 3 t= 4.1 Global Mean 864.40 Global In-Mask Mean = 863.588 (889.887) Rescale Target = 100 RescaleFactor = 0.115796 OLS Residual Pass run 1 t= 0.0 Saving rho1 run 2 t= 3.4 Saving rho1 run 3 t= 7.1 Saving rho1 Smoothing ACF /usr/local/freesurfer//bin/mris_fwhm --mask /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/mask.nii.gz --i /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.nii.gz --o /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s replay06 --hemi lh --sd /home/jbang/Projects/replay/mri/ /usr/local/freesurfer//bin/mris_fwhm: /usr/local/matlab.r2009a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer//bin/mris_fwhm) ERROR: /usr/local/freesurfer//bin/mris_fwhm --mask /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/mask.nii.gz --i /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.nii.gz --o /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s replay06 --hemi lh --sd /home/jbang/Projects/replay/mri/ >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I'm getting confused what's causing this issue. Please help! I appreciate your advice in advance. Thanks, Ji Won

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Freesurfer 6 beta error on OSX 10.7
by James Bennett 10 Mar '16

10 Mar '16

Dear Freesurfer developers I've just tried out the beta version of Freesurfer 6.0 on my Mac, which I downloaded from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/, mainly because I need to use the mris_decimate function. However, issuing mris_decimate -d 0.25 inputfile outputfile returns this error: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Trace/BPT trap: 5 I'm running OS X 10.7, and I've seen similar errors reported on the mailing list relating to OS X compatibility problems. Is this the case here, and is there a mris_decimate binary that works on 10.7 that could be made available? Many thanks in advance for your help James

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Re: [Freesurfer] System crash by extremely much generated output v6 beta
by Gronenschild Ed (NP) 10 Mar '16

10 Mar '16

Hi Bruce, Is that the reason why >10GB of disk space is consumed? I hope that it is possible to limit the amount of this type of output by some means to prevent the problem I ran into. Cheers and good luck with improving v6. Ed On 10 Mar 2016, at 19:22, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Hi Ed, the problem is that you have a defect that has >40K vertices - about 1/3 the total size of a typical hemi. 6.0 when it is out will complete for this kind of thing but even it is unlikely to generate an accurate surface with that big a defect. You should try down the source of it and fix it then rerun. cheers Bruce On Thu, 10 Mar 2016, Gronenschild Ed (NP) wrote: Hi Bruce, Here it is Cheers, Ed

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