Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

Save-the-Date: Feb 12-13, 2015, Real-time Functional Imaging and Neurofeedback Conference, Gainesville, Florida
by Frank Scharnowski 21 Jul '14

21 Jul '14

Dear Real-Time Functional Neuroimaging Community, It is our pleasure to announce the conference on real-time Functional Imaging and Neurofeedback (rtFIN) in Gainesville, Florida on February 12-13, 2015 at the University of Florida, hosted by Prof. Ranganatha (Ranga) Sitaram. This conference is the second iteration following the first conference on rtfMRI neurofeedback held in Zurich in 2012. We currently have four keynote speakers: Niels Birbaumer, University of Tuebingen Eberhard Fetz, University of Washington John Gabrieli, MIT Mitsuo Kawato, ATR Japan Please fill out the survey below if you're interested. Website, venue, registration and abstract submission information will be announced at a later date on the rtfMRI email list. Please sign up at the link below if you'd like to be kept updated. Survey link: https://www.surveymonkey.com/s/7NVVQZH Best regards, your co-organizers, Ranganatha Sitaram, University of Florida Sven Haller, University of Geneva Jarrod Lewis-Peacock, University of Texas at Austin Frank Scharnowski, University of Geneva Luke Stoeckel, Harvard University / National Institutes of Health James Sulzer, University of Texas at Austin Nikolaus Weiskopf, University College London -- Dr. Frank Scharnowski, Lecturer Swiss Institute of Technology Lausanne & University of Geneva, Switzerland +41 78 76 76 749 www.neurofeedback-research.org

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Repost | Re: mni152reg error
by JacobML＠nmr.mgh.harvard.edu 21 Jul '14

21 Jul '14

Hello Doug, Ideally, I am trying to take subject tstat maps from FsFast (stable3 environment) and register these native structural space maps to the MNI152_2mm standard brain. The t_000.bfloat file is what was generated relative to my contrast that was set up in FsFast stable3. There are a series of these files ranging from t_000.bfloat to t_029.bfloat and there are also these same named files with a .hdr extension. t_000.bfloat is the file I designate when I select an overlay within tkmedit. Your help sorting out this registration is very appreciated. Thank you, Jacob >> I'm not sure what you are trying to do, but that command line looks like >> things are not set up properly. What is t_000.bfloat? (And why are you using bfloats?) >> doug >> On 7/17/14 1:14 PM, JacobML(a)nmr.mgh.harvard.edu wrote: >>> Hello again Doug, >>> Thank you for sending the updated version of mri152reg. It ran without error and generated the reg.mni152.2mm.dat registration matrix. Unfortunately though, when I tried to apply the transformation to the same >>> subject's t_000.bfloat, the registration is not correct (command below). >>> mri_vol2vol --inv --targ /.../t_000.bfloat --mov >>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o >>> CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat On a positive note, I was able to load the output image and >>> MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be >>> shifted too far anterior. >>> With my next attempt, I used mri_convert to make the t_000.bfloat into a >>> .mgz and than ran mri_vol2vol, but the same misalignment occurred (see attached photo). >>> Using tkmedit, I have confirmed that this file aligns properly on this subject's native structural image, so I am not quite sure why the registration matrix may be off. Given that the reg.mni152.2mm.dat file reflects the transformation of the native struc to MNI, I wonder if I need >>> to account for the reg file between the func data and the native struc? >>> Can you please let me know what I may be doing incorrectly? >>> As always, your help is very appreciated. >>> Jacob >>>> Yea, i fixed this problem. I've attached a new version with the fix. doug >>>> On 07/17/2014 10:35 AM, JacobML(a)nmr.mgh.harvard.edu wrote: >>>>> Hello Freesurfer Experts, >>>>> I am trying to view stats generated with FsFast in fslview/MNIspace, >>> and >>>>> in doing so I have run mni152reg to generate the registration matrix. >>> That said, mni152reg did not complete correctly and below I have pasted >>> the terminal output: >>>>> Thu Jul 17 09:58:10 EDT 2014 >>>>> setenv SUBJECTS_DIR >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons >>>>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons >>> /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s >>>>> CD_cerv_pat4_sess1_recon >>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 >>> UTC >>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux >>>>> fslregister --mov >>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz >>> --s CD_cerv_pat4_sess1_recon --reg >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat >>> --dof 12 >>>>> mkdir: cannot create directory >>>>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': >>> Permission denied >>>>> Log file is >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log >>> Thu Jul 17 09:58:11 EDT 2014 >>>>> --mov >>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz >>> --s CD_cerv_pat4_sess1_recon --reg >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat >>> --dof 12 >>>>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ >>>>> purkinje >>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 >>> UTC >>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux >>>>> nIters 1 >>>>> -------------------------------------- >>>>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons mri_convert >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz >>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii mri_convert >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz >>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii niiWrite(): error opening file >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii >>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... >>> TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 >>>>> i_ras = (-1, 0, 0) >>>>> j_ras = (-0, -0, -1) >>>>> k_ras = (0, 1, 0) >>>>> writing to >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... >>> ERROR: failure writing >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii >>> I tried to run the fslregister command from within the subject's directory >>>>> (in hopes to possible correct what may be a permissions issue), but >>> this >>>>> produces the same final error, "ERROR: failure writing >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." >>> Lastly, probably to no surprise, the >>>>> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any >>> ideas how I may be able to correct these errors? >>>>> Thank you for the help! >>>>> Jacob >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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White matter completely filled in
by Jonathan Holt 21 Jul '14

21 Jul '14

The problem is detailed in pictures, I'm emailing to find out how to avoid this problem in the future.

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Edits to Pial and CP at the same time?
by Mark Fletcher 21 Jul '14

21 Jul '14

Dear FreeSurfers, In the training that I attended in May, I believe it was demonstrated by Allison that you could fix multiple problems at the same time. I understand how to make the edits at the same time, but am unsure what command to run to integrate all of these changes concurrently. Since I currently do not know how to do this, it is taking me multiple days to fix some problems on subjects with multiple types of errors. Currently I first manually delete some dura on the brainmask.mgz (thus I would run recon-all -autorecon-pial -subjid xxxx). After examining the output the next day, I then add control points in the anterior temporal lobe or other places if needed on the same subject ( recon-all -autorecon2-cp -autorecon3 -subjid xxxx ). I was wondering how to both manually delete the dura, and add cp at the same time for one processing event (thus saving me a lot of time)? Would the correct command line be: recon-all -autorecon-pial autorecon2-cp -autorecon3 -subjid xxxx ? Also, is it possible to edit the pial, add white matter, and control points all at the same time for one recon-all processing event? Would the correct command line be recon-all -autorecon-pial autorecon2*-cp-wm* -autorecon3 -subjid xxxx or recon-all -autorecon-pial *autorecon2-cp* *autorecon2-wm* -autorecon3 -subjid xxxx Thanks for your help :) Sincerely, Mark Fletcher

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freeview brush value problem
by Tracy Riggins 21 Jul '14

21 Jul '14

Hello Freesurfer experts I am trying to edit an aseg file. I want to set my brush value to a value that does not exist in the default lookup table (e.g,. 570). So, I edited the lookup table, saved this , and loaded it in freeview. My new label and brush value is now visible. However when I set the brush value to this value/label (both the main GUI window and edit voxel window say "Brush value = 570") and draw on the aseg file it does not use this brush value. It uses a different value (eg 48). I can't seem to figure out why. Any thoughts? Thanks in advance, Tracy Tracy Riggins, Ph.D. Assistant Professor Department of Psychology BPS 2147J University of Maryland College Park, MD 20742 Office: (301) 405-5905 Fax: (301) 314-9566 http://ncdl.umd.edu<http://ncdl.umd.edu/> riggins(a)umd.edu<mailto:riggins@umd.edu>

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Tools for FreeSurfer group analysis in R
by Andreas Berger 21 Jul '14

21 Jul '14

Hello FreeSurfers, during the course of my diploma thesis i wrote a few R functions around FreeSurfer, mainly for group analysis of FreeSurfer surface data in R. I thought i'd just contribute the code here, on the off chance that someone may find it useful, and despite the code quality (i wrote this as part of me learning R, so it may actually set your house on fire and so on). It could be of use for someone already working in R and looking to bring FreeSurfer data into it, or someone looking for an alternative to QDEC and the plots created by QDEC. Hardware requirement is not entirely modest unfortunately; it eats up about 8G of memory and takes about 15 minutes around here. Here's an example of how it is used: ############################ BEGIN R CODE ############################## # Presupposing that you have a dataframe 'data' containing your group # description and that all subjects have been processed in ~/subjects ### Group analysis with lm ### # Run the model. This takes some time and memory. lm <- freesurfer.group.analysis.lm(data = data, formula = thickness ~ Age + Gender + Diagnosis, hemi = "lh", fwhm = 10, template = "fsaverage", freesurfer_subjects_dir = "~/subjects") # Extract t values from the model, do FDR correction t <- freesurfer.group.analysis.lm.stats(lm, type.of.value = "t", correction="fdr") # Write the t values to mgh files and open them in FreeSurfer's freeview freesurfer.group.analysis.lm.stats.to.mgh(t, hemi = "lh", template = "fsaverage", freesurfer_subjects_dir = "~/subjects", launch.freeview = TRUE) # Write the t values to .dset ASCII files and open them in AFNI's SUMA freesurfer.group.analysis.lm.stats.to.suma(t, hemi = "lh", template = "fsaverage", freesurfer_subjects_dir = "~/subjects", launch.suma = TRUE) # Make nice plots for vertex #1000 freesurfer.group.analysis.lm.plot(lm, vertex = 1000, interactive = TRUE) ### Group analysis with QDEC ### # Call QDEC freesurfer.group.analysis.QDEC(data = data, freesurfer_subjects_dir = "~/subjects") ### Extract stats ### # Get segmentation stats segstats <- freesurfer.get.segstats(subjects = data$ID, freesurfer_subjects_dir = "~/subjects") ############################## END R CODE ############################## i uploaded the R package here, i called it freesurfR: https://www.nitrc.org/projects/freesurf_r/ thanks also goes to Heath Pardoe, whose code for reading and writing MGH files (also posted on this list) i was allowed to include. regards, Andreas

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Why conn't find subject in Segmentation of hippocampal subfields
by wang kangcheng 20 Jul '14

20 Jul '14

Dear experts When I do Segmentation of hippocampal subfields, it report that ERROR:connot find /nfs/preproc/muti_first/s.... What should I do next? THe scripts was following: SUBJECTS_DIR=/nfs/preproc/multi_first subject_list=${SUBJECTS_DIR}/scripts/check/hipp.list ## Get subjects to run subjects=$( cat ${subject_list} ) ## A. SUBJECT LOOP for subject in $subjects do echo -------------------------- echo running subject ${subject} echo -------------------------- recon-all -s ${subject} -hippo-subfields done echo All have finished Wangkangcheng

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R: Re: Yeo parcellation
by stdp82＠virgilio.it 20 Jul '14

20 Jul '14

Hi list and Thomas, I'm running the first step to use Yeo's parcellation. The running is wrong. mri_surf2surf --s Control01 --hemi lh --sval-tal-xyz white --tval lh.white.Control01 --tval-xyz --trgsubject fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz Reading target surface reg $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.regMRISread( $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg): could not open fileNot a directorymri_surf2surf: could not read surface $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg Thanks, Stefano ----Messaggio originale---- Da: ythomas(a)csail.mit.edu Data: 7-feb-2014 9.49 A: <stdp82(a)virgilio.it> Cc: "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Yeo parcellation Hi Stefano, A) From FreeSurfer 5.2 onwards, the Yeo parcellation files can be found inside $FREESURFER_HOME/subjects/fsaverage/label/, so you can simply use those files there instead of downloading from the wiki. B) You can use mri_surf2surf to transform the annot files from the fsaverage "subject" to the individual subjects' surface. There is an example of how to do it if you run "mri_surf2surf --help" C) Once you have created the subject's specific annot file from part B, I believe you must first run mris_anatomical_stats, and then run aparcstats2table. However, I am not sure about this, so someone on the list should correct me if I am wrong! Regards, Thomas On Fri, Feb 7, 2014 at 3:58 PM, <stdp82(a)virgilio.it> wrote: > Hi list, > > I have download the files of Yeo parcellation from > ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip. > > I have two questions, please. > > A- Which is the directory where I should put these files? > B-I have already run by recon-all -all all my subjects. How can I added to > them Yeo parcellation? > C-I'd like also calculate the cortical thickness for each Yeo's ROI. Is > possible with aparcstats2table? > > Thanks. > > Regards, > > > Stefano > > _______________________________________________ > 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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Re: [Freesurfer] mri_cor2label revisited
by Douglas N Greve 20 Jul '14

20 Jul '14

Are you trying to view it in the volume or the surface? When I run freeview viewing the surface and load the label using the "Load Label" button (not File->LoadLabel), it works for me. Can you try the tksurfer command below? It runs for me. You can ignore the warning about 0 nonzero vertices since they are all set to 1. tksurfer fsaverage lh inflated -label ~/tmp/lh_binarymap_area_covar8.label subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /autofs/cluster/con_009/users/greve/ixi-subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/cluster/con_009/users/greve/ixi-subjects/ixi320/mri checking for nofix files in 'inflated' Reading image info (/autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage) Reading /autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage/mri/orig.mgz surfer: Reading header info from /autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: curvature read: min=-0.673989 max=0.540227 surfer: single buffered window surfer: tkoInitWindow(fsaverage) setting percentile thresholds (-1.00, 0.00, 0.00) loading label /homes/4/greve/tmp/lh_binarymap_area_covar8.label reading white matter vertex locations... ******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 surfer: using interface /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tksurfer.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_common.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_wrappers.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/lib/tcl/fsgdfPlot.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... On 07/15/2014 09:04 AM, Lars M. Rimol wrote: > Hi, > > I go to File -> Label -> load label and there I pick > lh_binarymap_area_covar8.label and then I get the error message: > > > % ******************** 0 nonzero vertices found ******************** > label stat field identically zero - setting to 1 > > > That's it! > > I don't know, but it seems to be saying that all vertices are zero, > doesn't it? > > When I cat the file, I see this: > > 163839 -34.195 -22.897 -24.093 0.0000000000 > > 163840 -34.295 -23.062 -23.449 0.0000000000 > > 163841 -35.093 -23.358 -22.788 0.0000000000 > > The leftmost column surely is vertex number, I don't know what the > next two are (if this were a volume, I'd say x,y,z coordinates) and if > the final column is the value of each vertex, I would have to agree > with tksurfer that there are no nonzero vertices. > > When I load the mgh file, thogh, it has some zero vertices and 98877 > that are 100, that is they are larger than 99.999999999999992. > > >> size(find(gt(testing,99.999999999999992))) > > ans = > > 98877 1 > > > Here's the code I used to make the binary map and save it as an mgh file: > > log10pID = significance threshold > > binaryVLBWlhcovar8(find(gt(binaryVLBWlhcovar8,log10pID))) = 100; > binaryVLBWlhcovar8(find(lt(binaryVLBWlhcovar8,log10pID))) = 0; > > fs_save_mgh(binaryVLBWlhcovar8,'lh_binarymap_area_covar8.mgh',mri); > > > So mri_cor2label must be changing some of these vertices from > 99.99999etc. to 0, right? > > > LMR > > > > On Mon, Jul 14, 2014 at 7:33 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > It loads ok for me both in 5.1 and 5.3. Can you give more info on > what is going wrong with tksurfer? > > > On 07/13/2014 05:35 AM, Lars M. Rimol wrote: > > Hi Doug, > > I'm having some problems with the label creation again. When I > run mri_cor2label, it seems OK (please see below), but when I > try to open it in tksurfer, it gives me an error message (bottom). > > Would you mind taking a look at this label to see what's wrong > with it? I'm attaching the binary mgh file and the label. NB! > The binary .mgh file is from matlab, where I have set all > suprathreshold vertices to 100 and all others to 0. Of course, > Matlab doesn't really do this, it sets them to somewhere close > to 99.999999999999992. I don't suppose I could use "greater > than 99" in mri_cor2label? > > ######### > creating label: > > [LMR in ~ ] mri_cor2label --i > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8.mgh > --id 100 --l > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8 > --surf fsaverage lh > $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ > Loading mri > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8.mgh > Loading /home/lmr/subjects/fsaverage/surf/lh.white > Scanning the volume > Found 98877 label voxels > Writing label file > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8 > Centroid: -28.93 -15.97 10.14 > mri_cor2label completed SUCCESSFULLY > > ####### > loading it in tksurfer: > > % ******************** 0 nonzero vertices found > ******************** > label stat field identically zero - setting to 1 > > > > Thank you! > > -- > yours, > > Lars M. Rimol, PhD > St. Olavs Hospital > Trondheim, > Norway > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > > > > -- > yours, > > Lars M. Rimol, PhD > St. Olavs Hospital > Trondheim, > Norway -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Group analysis tutorial
by Vilde 19 Jul '14

19 Jul '14

Dear mailing list, I am doing the group analysis freesurfer tutorial. When I try to open the significance map, I get the error message "unrecognized sub-opton flag 'overlay_threshold'. " The command is freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d I get the same error message doing the tutorial on my mac os x and on a linux, so I doubt there is a problem with the tutorial data. All files needed seem to be in the directory. I very much appreciate any help Best, Vilde

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Freesurfer July 2014