Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

mri_fuse_segmentations error in longitudinal stream
by Sandra Preißler 10 Mar '16

10 Mar '16

Dear freesurfer experts, I am running freesurfer “freesurfer-Linux-centos7_x86_64-dev-20150728”. On a Linux terminal: “Linux cortical 3.16.6-2-default #1 SMP Mon Oct 20 13:47:22 UTC 2014 (feb42ea) x86_64 x86_64 x86_64 GNU/Linux” After normal processing of the data cross sectional. Followed by the creation of the within-subject template (DTprae_P01) I get an error message running the longitudinal command (-long). The command line I used was: recon-all -long DTprae_P01 DT_P01 -all The subject directory is: /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT The subprocess ending with the error and the error message were the following: mri_fuse_segmentations -a aseg.presurf.mgz -c aseg.auto_noCCseg.mgz -n norm.mgz DTprae_P01.long.DT_P01 DTprae_P01 DTpost_P01 aseg.fused.mgz mghRead(/mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01/mri/aseg.presurf.mgz, -1): could not open file using aseg.presurf.mgz as aseg volume using aseg.auto_noCCseg.mgz as aseg no-CC-label volume using norm.mgz as norm volume reading /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01.long.DT_P01/mri/norm.mgz and processing 2 timepoints, writing to aseg.fused.mgz loading data for subject DTprae_P01 ... mri_fuse_segmentations: could not read input volume /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01/mri/aseg.presurf.mgz Linux cortical 3.16.6-2-default #1 SMP Mon Oct 20 13:47:22 UTC 2014 (feb42ea) x86_64 x86_64 x86_64 GNU/Linux recon-all -s DTprae_P01.long.DT_P01 exited with ERRORS at Tue Mar 8 17:52:40 CET 2016 I checked the folder (DTprae_P01/mri) and there is no data called aseg.presurf.mgz. in which step is this data produced? How can I fix this problem? I hope you could help me. Kind regards, Sandra

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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, 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>> 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>> 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>> 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>> 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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adc brainstem-subs
by Thomas Potrusil 10 Mar '16

10 Mar '16

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Re: [Freesurfer] Using external software to perform brain extraction, multiple T1s
by Chris Adamson 09 Mar '16

09 Mar '16

There was a post in 2015 from Richard Parker talking about using SPM brainmasks instead of the Freesurfer ones. I would like to do this but in some cases I have multiple T1s and I get the motioncor step to make a registered template. What steps do I need to perform to get a brainmask from one of the images into the template space created by motioncor? Apologies if this has already been asked. [cid:image001.jpg@01D17AC3.302C3530] Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adamson(a)mcri.edu.au www.mcri.edu.au<http://www.mcri.edu.au/> [cid:image002.png@01D17AC3.302C3530]<https://www.facebook.com/MurdochChildrensResearchInstitute>[cid:image003.png@01D17AC3.302C3530]<https://twitter.com/MCRI_for_kids>[cid:image004.png@01D17AC3.302C3530]<http://instagram.com/murdoch_childrens>[cid:image005.png@01D17AC3.302C3530]<http://www.youtube.com/user/MurdochChildrens/videos>[cid:image006.jpg@01D17AC3.302C3530]<https://donate.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Postdoctoral position in brain imaging genetics at UCSD
by Chen, Chi-Hua 09 Mar '16

09 Mar '16

We are looking for a highly motivated individual with PhD to join our team for brain imaging genomics research. Current projects focus on studying the genetic basis of the human brain and psychiatric disorders. The post holder will analyze neuroimaging data and examine relationships among gene, brain, and clinical variables. For qualified candidates there are excellent opportunities to pursue research interests in brain imaging, statistical genetics, and brain disorders in a multi-disciplinary team. We are particularly interested in applicants with strong writing and programming skills. A background in neuroimaging, cognitive science, genomics or computational disciplines, and a strong publication record are preferable. Applicants should send a CV and a list of three references to Dr. Chi-Hua Chen chc101(a)ucsd.edu<mailto:chc101@ucsd.edu>.

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Patch for ribbon.mgz failure
by Philip Deming 09 Mar '16

09 Mar '16

Hi Freesurfer team, I'm having an issue running -autorecon2. The program exits with errors because it is unable to create the ribbon.mgz file. According to the version 5.3 release notes, there is a patch available to fix this issue: Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2 because ribbon.mgz is not present. This has been fixed. Ask for a patch. How can I obtain the patch to fix the ribbon.mgz issue? Thanks, Phil

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System crash by extremely much generated output v6 beta
by Ed Gronenschild 09 Mar '16

09 Mar '16

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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QDEC GUI or in-line command for Monte Carlo simulation?
by Karl Liu 08 Mar '16

08 Mar '16

Dear Freesurfer Experts: I would appreciate your help in clarifying one issue I have when applying Monte Carlo simulation to control for multiple comparisons. First, 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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[freesurfer] selxavg-sess question
by Ji Won Bang 08 Mar '16

08 Mar '16

Dear. Freesurfer experts. Hi. I'm using freesurfer version 5.3.0. I tried: mkanalysis-sess -analysis retino -TR 2 -paradigm para.para -event-related -funcstem fmc -nconditions 4 -timewindow 34 -inorm -gammafit 2.25 1.25 -polyfit 2 -mcextreg -force -fsd bold_retino -per-run -native -refeventdur 8 mkcontrast-sess -analysis retino -contrast HorVer -a 1 -c 2 preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -nosmooth -per-run selxavg-sess -s $SUBJECT -analysis retino -df sessdirfile -noomnibus Then at the selxavg-sess process, I got the error: INFO: WhitenFlag = 0 -------------------------------------------------------------- selxavg-sess logfile is /home/jbang/Projects/replay/log/log/selxavg-sess-bold_retino-retino-160308143510.log -------------------------------------------------------------- ------------------------------------------- /home/jbang/Projects/replay/epi/replay06 Tue Mar 8 14:35:10 EST 2016 ERROR: could not find volume ERROR:. Does it exist? (standard_in) 1: syntax error ERROR: could not find volume ERROR:. Does it exist? inplaneres TR INFO (replay06): RunList = 023 025 027 029 -------------------------------------------------------- /home/jbang/Projects/replay/epi/replay06/bold_retino selxavg2 -TR -parname para.para -o retino/h -i 023/fmc -i 025/fmc -i 027/fmc -i 029/fmc -cfg /home/jbang/Projects/replay/log/retino/analysis.cfg -------------------------------------------------------- --- Parsing Config File: /home/jbang/Projects/replay/log/retino/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 ERROR: Flag 3 unrecognized. -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 -TR -parname para.para -o retino/h -i 023/fmc -i 025/fmc -i 027/fmc -i 029/fmc -cfg /home/jbang/Projects/replay/log/retino/analysis.cfg ERROR (/home/jbang/Projects/replay/epi/replay06): selxavg failed Could you please hlep what's going wrong? Thank you very much! Best, Ji Won

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Message error in qdec analysis‏
by Lisa Delalande 08 Mar '16

08 Mar '16

Hello everyone, I've got some problems with qdec. I have .levels with more than 2 factors. For example a "grpe.levels" with three factors : children (enfant), adults (adultes) and nothing (rien). But if I want to exclude some subjects like children qdec doesn't work anymore (attachment : error message). Is that possible a .levels can not have more than two factors ? Or the problem came from anything else ? Thanks in advance for your help ! Best regards, Lisa

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Freesurfer March 2016