Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

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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Subcortical segmentation voxel error
by Selina Wilson 10 Mar '16

10 Mar '16

Hello all, I am new to Freesurfer and learning as I go/encounter problems. This might be an obvious question, but has anyone had issues with black holes in their subcortical segmentation runs? The wiki page it suggests contacting the freesurfer mailing list before attempting to manually fix the issue to see if there is an automatic procedure that could fix it. The second part of my issue is that the black voxels are not incorrectly labeled as another structure/region. When I place the cursor over the black holes, the TkMedit Tools window reads "Sgmtn label: none" . If I do any of the suggested manual fixes (brushing, flood filling, linear selections) on the "none" voxels and label them as hippocampus, would that assign voxels to a structure, increasing the volume of that structure, when those voxels are not actually there? To be more clear, I am worried that these "none" voxels are the result of movement during the scan or an error in how the scan was read by the computer. I do not want to 'fix' this problem by manually labeling those voxels as part of the hippocampus and find out down the line that this scan was actually unusable. That would mean that the data collected from this scan on hippocampal volume would be erroneous and make the final cross-sectional data analysis invalid/inaccurate. Thank you for your help! Selina Wilson Undergraduate Research Assistant Duke University Class of 2017 (317) 430 - 7404 selina.wilson(a)duke.edu

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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, Here it is Cheers, Ed

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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, Let me explain it again. On a 3 TByte disk I've made a partition of 20 GB to run OSX10.7. When I run recon-all all input and output data are on the large partition which has about 1.5 TByte free space. This means that all temporary and intermediate files that are created by recon-all (e.g. in /tmp) are residing on the 20 GB partition which has a free space of 11 GB initially. And all this free space is consumed (I assume by all these temporary/ intermediate files) by mri-topo-fixer. Cheers, Ed On 10 Mar 2016, at 18:00, <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: Hi Ed, I am a bit confused by your two emails. In one you state that you have a MacPro OSX10.7 installed on a partition of 20 GB with FreeSurfer v6 beta Then in the next post you state that the disk you have is 1.5TB (is that the disk or partition?) I'm also confused, because you stated that at the time you ran into trouble the disk had 11GB. You then said you ran out of disk (I assume that means you had 0GB left). Then you said when you rebooted you had 11GB (no files were created at all?). This is a dangerous way in general to run a machine. If a program core dumps you have less disk space then your RAM. General advice is to keep at least 5% of disk space free (or a bare minimum of > RAM size). It may be worth doing this after a fresh reboot and checking your RAM to make sure you don't have apps that autostart sucking up RAM, causing you to swap. If you try to swap, without enough free space that can easily crash your machine. First, What is the full disk partition setup? Next, run df (on the relevant partition) and show the output before running FreeSurfer. Then run recon-all and if possible show the df output at the crash Then run df on reboot. hth d PS it may be worth pointing out that beta 6 was withdrawn for more development. On 3/10/16 5:09 AM, Gronenschild Ed (NP) wrote: Hi, I'm using a MacPro with 32 GByte RAM. The output of FreeSurfer is written to a disk with 1.5 TByte free space. At the time I ran into trouble the free disk space was about 11 GByte. When I wanted to inspect the progress after a few hours I noticed that the disk has ran out of space. I couldn't do anything but restarting the MacPro. Then the disk space was again about 11 GByte. So I reran the subject with recon-all -autorecon2 -autorecon3 and it happened again. Inspecting the log files I noticed that both times the problem occurred at exactly the same stage in the pipeline: mris-topo-fixer. Cheers, Ed On 10 Mar 2016, at 10:41, <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: 20 GB is not a lot for a full macos install + data, how much room was free before you ran recon-all? What is the hardware? CPU, RAM etc. hth d On Wed, Mar 9, 2016 at 12:09 PM, Gronenschild Ed (NP) <ed.gronenschild(a)maastrichtuniversity.nl<mailto:ed.gronenschild@maastrichtuniversity.nl> <mailto:ed.gronenschild@maastrichtuniversity.nl>> wrote: Hi developers, Could you please help me out on this problem. Should I upload the data? Cheers, Ed Begin forwarded message: From: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl<mailto:ed.gronenschild@maastrichtuniversity.nl> <mailto:ed.gronenschild@maastrichtuniversity.nl>> Subject: System crash by extremely much generated output v6 beta Date: 7 March 2016 12:57:57 CET To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>> Hi developers, My environment: MacPro OSX10.7 installed on a partition of 20 GByte; FreeSurfer v6 beta During processing recon-all on 4 subjects in parallel using 4 terminal windows, the 20 GByte partition got full. This happened twice and I managed to trace down the offending stage in the pipeline: topology fixing, in particular the tool mris_topo_fixer. Most probably it went into an endless iteration loop generating so much output the disk got full. Cheers, Ed

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Map label from lh to rh
by Makaretz, Sara Johanna 10 Mar '16

10 Mar '16

Hi, I want to map a label from one hemi to the other (all on fsaverage). I tried mri_label2label: mri_label2label --s fsaverage --srchemi lh --trghemi rh --srclabel lh.a.label --trglabel rh.flipped_lh.a.label --regmethod surface but I think I need to specify a reg file to go between hemispheres, does this exist somewhere? an error message kindly pointed out that this one does not exist: /usr/local/freesurfer/stable5_3_0/subjects/fsaverage/surf/rh.lh.sphere.reg

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Working with non-FreeSurfer derived meshes and labels
by Slater David 10 Mar '16

10 Mar '16

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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v5.3.0 pial crossing into ventricals
by Smaragdi A. 10 Mar '16

10 Mar '16

Hi mailing list, regarding a previous issue with the v5.3.0 and the pial boundary crossing into the ventricles (below), i have run the subjects in the beta version and the problem does not appear. My question to the experts is now, considering it is not advised to switch versions in a data set, how 'bad' would it be to run 7 subjects in the beta version, and the other 190 or so in the v5.3.0 version? It is after all a very small number of the total sample, would this be ok, or would you still advise against it? Many thanks, Areti ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Smaragdi A. [A.Smaragdi(a)soton.ac.uk] Sent: 12 January 2016 18:27 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject) Hi Bruce, thanks for the quick reply, I am running v5.3.0 from a Linux, but more than 2/3 through my data set so don't really want to swap to 6.. Where can I get the beta and how would it help? Thanks, Areti ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: 12 January 2016 16:24 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject) what version are you running? I believe that this is a bug that has been fixed. Hopefully we will get version 6 out soon and upgrading will fix this, but you can download a beta and try to make sure if you want cheers Bruce On Tue, 12 Jan 2016, Smaragdi A. wrote: > Hi mailing list, > > I have encountered this problem in Freesurfer a number of times now and I wondered if any of you had any solutions. > > It seems that sometimes after a recon-all has been run, there is a large overlap of the pial boundary and wm boundary, in the same region each time near the lateral ventricles (it can be on either hemisphere or both). I have attached a print screen of the issue, this time in the LH. As you can see, we have tried adding CPs and have also added WM, but after re-running it, the problem still exists. We have also tried running the randomness, but this has had no effect. > > Any suggestions as to what we could do to fix this would be great - thank you! > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer March 2016