Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

error of color bar in freeview
by 郝磊 21 Jul '14

21 Jul '14

Dear experts when I open freeview, it report that "2014-07-21 11:22:28.453 Freeview[10414:303] invalid drawable". Afterwards, when I click on Show Color Scale, the color bar was in black alternating with white. How should I solve this problem? Thank you Hao Lei (new learner of freesurfer)

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Re: [Freesurfer] Freesurfer longitudinal GLM Design question
by Martin Reuter 21 Jul '14

21 Jul '14

Hi Sal, (please send to freesurfer list). Take a look at the cross sectional qdec file. Years will be the average of 0 and 0.1 (= 0.05) for all subjects, so that may be the reason why it fails as a co-variate. Age is also not time-varying, it is the average age per subject. The analysis at this point is completely cross sectional. You compare the atrophy rates (which were created in the first step with long_mris_slopes) across subjects. So everything is exactly the same as if you were running a cross sectional thickness analysis (except you look at thickness change instead of thickness now). I don't know qdec so well. I am not sure if it can do a one-sample-group-mean. If not use mri_glmfit -osgm directly (there is also a wiki tutorial on how to run glmfit). Best, Martin On 07/21/2014 06:34 PM, Salil Soman wrote: > Thank you Martin. > > I created a minimal longitudinal table (fsid, sid-base, age, and > years). Years is either 0 (timepoint 1) or 0.1 (timepooint2). I ran > mri_slopes using this table, and made the cross table. I load qdec > using the cross table, and have 2 continuous variables (years and > age). I try to run an analysis using long.thickness-rate as the > measure, with years as the covariate, and I keep getting an error > screen "Error in Analyze: command failed: mri_glmfit --y ...." > > If I use age as the covariate, the analysis works and I find no > signficant differences (i.e. no relationship between thickness > differences and age). Is there a way I can simply see if there are any > thickness differences without using any covariates (so look at any > areas of significant difference in thickness-rate) while correcting > for multiple comparisons using fdr? > > Thank you all your help. > > Best wishes, > > Sal > > > On Wed, Jul 9, 2014 at 6:13 AM, Martin Reuter > <mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: > > Hi Sal, > > it looks like you have everything together then. You can run your > QDEC analysis on the long.thickness-rate (or one of the percent > change files) to see where the rate is significantly different > from zero. Negative rate means thickness decrease. > > You could also use glmfit with the one sample group mean (-osgm) > to test the same thing. There is a tutorial about that and also > about multiple comparison correction. > > After you create your within subject rate (or percent change) > files. The whole thing turns into a simple cross-sectional > analysis (as if you are analyzing thickness in a cross sectional > design). Instead of thickness you now look at the 'change of > thickness'. If you are unsure how to use qdec or glmfit, look at > those tutorials first. > > Best, Martin > > On Jul 8, 2014, at 11:19 PM, Salil Soman <salsoman(a)stanford.edu > <mailto:salsoman@stanford.edu>> wrote: > >> Hi, >> >> I have been following the tutorial from here: >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial >> and here: >> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel >> >> And I believe I am running into problems with my GLM design. >> >> I have a set of subjects with 2 time points each (all about 0.1 >> years apart). >> >> All I wish to do is see what areas are significantly changed in >> volume, after correcting for multiple comparisons (fdr or >> montecarlo). >> >> Could anyone suggest how I should setup the Design in QDEC?. I >> have included years and age in my cross.qdec.table.dat file (made >> from my long.qdec.table.dat file as described the tutorial, and >> have the measures of long.thickness-avg, long.thickness-rate, >> long.thickness-pc1 and long.thickness-spc avaialble (again from >> the tutorial). >> >> Any advice would be greatly appreciated. >> >> Sal > > --------------------------------- > Dr. Martin Reuter > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 <tel:%2B1-617-724-5652> > Email: > mreuter(a)nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> > reuter(a)mit.edu <mailto:reuter@mit.edu> > Web : http://reuter.mit.edu <http://reuter.mit.edu/> > > 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. > > > > > -- > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care > System -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Diffusion analysis qs - gradient matrix
by Rotem Saar 21 Jul '14

21 Jul '14

Dear freesurfer experts, For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ? Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel

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[Fwd: LGI recon problem]
by angela.favaro＠unipd.it 21 Jul '14

21 Jul '14

Dear FS experts, I had no answer to my question below (log was attached in my previous mail) The error repeated in different subjects and I do not know how to overcome. Can anyone give me some help? Angela Hi all, I had an error message while running LGI recon I am using Freesurfer 5.3 with a MacOS lion 10.7.5 and Matlab 2013b with the Image processing toolbox Any help is welcome. Thank you! Angela the error is: mesh_outer = vertices: [61278x3 double] faces: [122552x3 double] facesOfVertex: [61278x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (315.30 sec). ... creating path file for vertex 1 / 61278 area file for outer ROIs saved at 1 {Improper assignment with rectangular empty matrix. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); } >> ERROR: make_roi_paths did not complete successfully! Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s subj001 exited with ERRORS at Tue Jul 15 10:23:17 CEST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ 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.

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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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