Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

Question with QDEC annotations and mri_convert and mri_annotation2label
by Tara Ann Miskovich 22 Jul '14

22 Jul '14

Hello, I am trying to convert my significant cluster from qdec into a .gii file, and I have a couple of questions. My mri_convert is not working, but it is my first time using it so I may be missing something, but it just keeps opening up the usage and gives no errors. mris_convert --annot mc-z.abs.th13.sig.ocn.annot mc-z.abs.th13.sig.ocn.gii Also, I was curious, how would one separate a annotation file created in qdec into separate label files with mri_annotation2label since there is no target subject which is required in he script. Thanks! Tara

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ERROR: Could not open [..]/bvals for reading
by Elia S. 22 Jul '14

22 Jul '14

Dear Freesurfer Community, Running Tracula preprocessing produces this error: ERROR: Could not open /home/elia/scripts/Tracula/LCL/dcmTimePoints_tar/T13D/timePoint1/dmri/bvals for reading I think the error described is the same as here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34169.html And as suggested here (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/035935…) I swapped the dmri_motion from the centos4 updates with the dmri_motion from the centos6 updates, and it works. Now here's the situation, I need to run tracula on machines where is not possibile to install the centos6 updates, since the message i get is this: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Do you have any advice for me? Thanks in advance,Elia. ---------------------------------------------------------------------------------------------------------------------------Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP WedOct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux My Current Working Directory: /home/elia

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DTImap
by Shantanu Ghosh 22 Jul '14

22 Jul '14

Hi FS experts, Is the DtiMap software (www.kennedykrieger.org) compatible with Freesurfer/Tracula? Thanks Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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freeserver versions
by Gianluca Rambaldelli 22 Jul '14

22 Jul '14

Hi, two years ago I processed a lot of data using freesurfer v5.1. Now I'm using v5.3 on a different group of subjects, I'm wondering if I can use together all the subjects from the different versions. Or there is a way to re-run it using the last version? I suppose that I can copy the 'control.dat' file that I saved into the new version but how can I add wm edits if I didn't saved it in a single file (for example edit.dat). Instead of creating an edit file, I saved every variations onto brainmask.mgz changing the original mask created by the recon -all procedure. I need to compare those old subjects because after a machine upgrade it has been installed the new version and I started a new project with v5.3. Thank you Gianluca Rambaldelli

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Extract curvind，folding, gauscurv, meancurv, thickness std in the whole vertices
by Qiongmin 22 Jul '14

22 Jul '14

Dear Experts, I used ‘mri_surf2surf’ to get the area, thickness, volume of all the vertices in the brain. I am wondering what functions can I use to get other information, such as ‘curvind, foldind, gauscurv, meancurv, thicknessstd’ ? I know FreeSurfer provides these statistic data according to two kinds of parcellations of the brain, but I need these information in a vertex-wise way. Thanks very much! Best, Qiongmin

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Thickness measurements on longitudinal data set
by Bastian Cheng 22 Jul '14

22 Jul '14

Dear Freesurfer-Experts, I am currently trying to measure Cortical Thickness of a Volume-defined ROI in a patient measured at 4 timepoints. Basically, I am interested in a ROI resulting from fMRI activation measured on Timepoint 1. I would then like to get thickness values in the same ROI for all Timepoints 1-4. I have read the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness this works. now, my idea is: ROI from TP1 >> register to base image of longit. recon. ("base") ROI from base >> TP1.long (from long recon) ROI from base >> TP2.long (from long recon) ROI from base >> TP3 long (from long recon) ROI from base >> TP4.long (from long recon) OR should I simpy map my ROI to fsaverage and project it back all individual timepoints? ROI from TP1 >> register to fsaverage ROI from fsaverage >> TP1 (not from long recon) ROI from fsaverage >> TP2 (not from long recon) etc. I understand that registration using the long. recon is more robust... Best regards, Bastian

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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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Freesurfer July 2014