Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

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trac-all exited with errors
by BigBen2293＠web.de 12 Sep '14

12 Sep '14

1 0

trac-all exited with errors
by BigBen2293＠web.de 12 Sep '14

12 Sep '14

1 0

Qdec "create stats tables" error
by Markus Gschwind 12 Sep '14

12 Sep '14

Dear all, I am trying to make work Qdec on my system ubuntu 12.04. freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 After I have loaded my qdec.table.dat and renamed the analysis folder , when I then try to create the "stats tables", I get an error and it blocks at 20% of the waiting bar. Data table loading completed successfully. > > SUBJECTS_DIR is '~/Documents/ARNAUD/' > > mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ > > mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec': >> Permission denied > > ERROR: In >> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, >> line 230 > > vtkKWQdecApp (0x289a94e0): > > Script: > > vtkTemp2 GenerateStatsDataTables > > Returned Error on line 1: > > Uncaught exception: command failed: mkdir -p >> /usr/local/freesurfer/subjects/qdec/stats_tables/ > > >> Stack trace: > > Uncaught exception: command failed: mkdir -p >> /usr/local/freesurfer/subjects/qdec/stats_tables/ > > >> while executing > > "vtkTemp2 GenerateStatsDataTables" > > > It seems that it tries to write into the default SUBJECT_DIR, thing that I do not understand as I put the actual SUBJECT_DIR in the top line of qdec.table.dat (and it is correctly recognized in the qdec window SUBJECTS_DIR). How could I come around that problem? Thanks in advance! Markus

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FsFast Functional Connectivity Analysis
by Jiahe Zhang 12 Sep '14

12 Sep '14

Hi Doug, I was trying to run functional connectivity analysis following instructions on the FreeSurferWiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth…) I was able to successfully run the following commands (nothing errored as far as I can tell) but the resulting partial correlation and significance maps turned out to be empty. Could you take a look at the commands and let me know if anything can be improved? 1. PREPROC preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh -mni305-2mm -fsd bold -per-run -stc up 2. SEED CONFIG fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config 3. SEED TIMECOURSE fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config (wm.dat and vcsf.dat were similarly created) 4. ANALYSIS CONFIG mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface fsaverage lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 5 -per-run -lpf .1 5. ANALYSIS selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001 Thanks, Jiahe -- Jiahe Zhang Ph.D. Student Department of Psychology Northeastern University 617-373-4789

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FW: Most recent/complete FreeSurfer + Patches?
by Gurney, Jenny 12 Sep '14

12 Sep '14

Hi guys! We would like to install the latest and greatest FreeSurfer on the processing cluster used by the CNDA at Washington University. We're thinking about installing the 5.3.0-HCP, and then over that, the released 5.3.0 patches. We're looking for verification that doing the install this way makes sense and that these two code sets don't conflict in any way. We know that the 5.3.0-HCP version updates the mris_make_surfaces, however, the patches do not include that update, which is why we are thinking about starting with 5.3.0-HCP as the base install. Note that this is being done on CentOS 6.x The currently available patches seem to include: mni152reg mri_mcsim mri_segstats recon-all tksurfer-sess tksurferfv Is that a complete list or did we miss some binaries/scripts? Also, it seems that the 'patch' binaries are dynamically linked, while the release binaries are statically linked. Besides dependency issues, could this cause an issue with results consistency, etc. if other system libraries get updated? Thanks, guys. Hope all is well. Matt House, Jenny Gurney and John Flavin @WU in STL ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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WM segmentation
by Shengwei Zhang 12 Sep '14

12 Sep '14

Hi FreeSurfer list members, I'm working on a white matter hyper-intensity study, and trying to group the segmented WM labels in lobes based on the wmparc.mgz file made by recon. But I found that there's a large part of "unsegmented WM" near ventricles, and wonder if such labels are consistently assigned among subjects, because most of the WM hyperintensity voxels are located within these locations. Or is there other way to segment the 'unsegmented WM' in more details? I'd appreciate any help related to this topic. Shengwei

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Re: [Freesurfer] Using fieldmap to correct EPI distortions
by Reza Rajimehr 12 Sep '14

12 Sep '14

Hi Doug, So I am using a command like this: epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph ~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_phasediff.nii --exf ~/MonkeyfMRI/oz_fparc/bold/template.nii.gz --exfdw ~/MonkeyfMRI/oz_fparc/bold/b0dc.nii.gz --vsm vsm.nii.gz --tediff 2.46 --esp 0.31 --sigma 2 --perev (note that instead of --o b0dc.nii.gz, I wrote --exfdw b0dc.nii.gz because this command apparently does not have --o option) Before running the above command, I have registered the mag and phasediff volumes to the template volume and I have generated new volumes (fid_mag and fid_phasediff) that are already in register with the template. I have two steps remaining in preproc-sess, which are register-sess and rawfunc2surf-sess. Should I use both -b0dc and -vsm flags for these two commands? I assume that when I use the above flag(s), my EPI fmc volumes will be dewarped first, and then they will get registered to the anatomical and the surface, right? So I hope that when I view/check the result of registration with tkregister2 (for possible manual interventions), I will see the dewarped template ...? Finally what is the effect of specifying -b0dc in mkanalysis-sess? Thanks, Reza > Hi, > > I have a basic question, but the answer can be useful for others as well. > > I am doing a customized preprocessing of monkey functional data in FS-FAST > v5.3. After motion correction and before functional-anatomical > registration, I want to use fieldmap data to correct spatial distortions > of EPI data. So: > > My fieldmap data: dicom files from a fieldmap scan (there are actually two > series of dicom files for that scan) > > My EPI data: fmc.nii.gz files in run folders > > Now I have three questions: > > 1) How can I unpack the fieldmap data? An example command ... I think you get two series out, one magnitude and one phase, just convert those to nifti > > 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an > example command would be very useful. something like epidewarp.fsl --mag mag.nii --dph phase.nii --exf template.nii --o b0dc.nii ... You have to add --tediff and --esp, but those depend on you sequence Put the output (b0dc.nii) into session/bold (or session/rest, or where ever your fmri data are located) > > 3) How will the undistorted volumes be used later on in the FS-FAST > analysis stream? When you run preproc-sess and mkanalysis-sess add -b0dc to the command line > > Your help would be very much appreciated. > > Thanks, > Reza

2 1

Monte Carlo Sim output / sig.masked.mgh
by Eryilmaz, Huseyin Hamdi 12 Sep '14

12 Sep '14

Dear FS experts, I have a question about a MC output file. When I run the MC sim (using mri_glmfit-sim) on the surface, it generates a bunch of files including a 'sig.masked.mgh', which is nice for displaying the significance map limited to the clusters that survive the MC correction. However, when I run it on the volume, it doesn't generate this specific file. Does anyone know the reason for that? Is there an alternative way to display the significance map that show only the clusters that survive the MC correction? Many thanks! Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email: heryilmaz(a)partners.org<mailto:heryilmaz@partners.org>

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social media: Facebook, Twitter and now LinkedIn
by Martin Reuter 12 Sep '14

12 Sep '14

Hi, many of you are aware of (yes, even excited about) our social media presence at Facebook: http://facebook.com/FreeSurferMRI Twitter: http://www.twitter.com/FreeSurferMRI and so we have just added a group on LinkedIn: https://www.linkedin.com/groups/FreeSurfer-8173404 (it's hard to believe, but it's true!) While these are all social media, they each have their special focus. While facebook is more personal with pictures of courses, social events etc, Twitter focuses on sharing news, and LinkedIn is a professional network group which will allow you to connect with other professionals in your field, browse and post related job offers, and even start your own discussions (Wow - they're all great). So, head over to any or all of these and 'follow', 'like' or 'join' us ... Cheers, Martin (how I love social media, it works completely without eye-contact ;-) )

1 0

Lost toolbar in freeview
by 김영국 12 Sep '14

12 Sep '14

2 1

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Freesurfer September 2014