Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

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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Control points coordinates
by Andrea Gerardo Russo 08 Mar '16

08 Mar '16

Hi Freesurfer users! We are performing such analysis on Matlab using cartesian coordinates of the control points for the study of cortical thickness. We have some problems to exactly localize control points from matlab viewing to freview or tkmedit: if the localization in Matlab is fine, in freeview are there some trasformations that I'm missing? We' d like to know if is there a file that exactly reports the trasformation matrix to change Cartesian coordinates (row, column, slice) into the "Volume RAS coordinates§" ( i.e. the coordinates used in "control.dat" file)? Any suggestions will be appreciate. Thanks in advance Andrea Gerardo Russo Student at University of Naples "Federico II" (Italy)

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Medial crossing surfaces
by maryam koochaki 08 Mar '16

08 Mar '16

Hi Bruce,I am editing aseg to correct the boundaries that excluded the lateral ventricle. The problem with lateral ventricle has been solved after running the process with -noaseg flag. But the boundaries in the middle, is crossing to the other hemesphere in some cases. I even tried -autorecon2-cp, the problem still exists. aparc+aseg has not been updated after running the process. Does Celine's case apply to mine? Here is your answer to Celine: Hi Celine the only existing way to correct this would be to create two volumes in addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the contralateral hemisphere that are causing problems, then rerun mris_make_surfaces for each hemi, using the appropriate volume. At some point I guess we should put an intersection check into it for the contra hemicheers Bruce Could you help me with the exact command line? Thank you in advance for your help,Maryam

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mean thickness
by Caroline Beelen 08 Mar '16

08 Mar '16

Dear Freesurfer team, Forgive me if this is a foolish question... I wanted to overlook cortical thickness, area and volume measures in Gnumeric file after recon-all (checking edits made). However, for several subjects I noticed that the values of mean thickness (final column) were calculated wrong, whereas this is not the case for their independent cortical thickness values. For instance, this happened to subject A09. I'm including the excel file to show the example. In the gnumeric file the number for this subject was depicted as 2/4964 instead of 2.4 etc.. What could have went wrong? Thank you for your answer in advance. Kind regards, Caroline

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T2pial shrinks pial surface
by Chris Adamson 07 Mar '16

07 Mar '16

The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? [cid:image013.jpg@01D17862.9262C650] 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:image014.png@01D17862.9262C650]<https://www.facebook.com/MurdochChildrensResearchInstitute>[cid:image015.png@01D17862.9262C650]<https://twitter.com/MCRI_for_kids>[cid:image016.png@01D17862.9262C650]<http://instagram.com/murdoch_childrens>[cid:image017.png@01D17862.9262C650]<http://www.youtube.com/user/MurdochChildrens/videos>[cid:image018.jpg@01D17862.9262C650]<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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