Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Alignment of non whole-brain functional slabs
by Joakim Vinberg 02 Jan '11

02 Jan '11

Hi everybody, I am working towards multi-modal integration of BOLD data. For some of my data, the entire brain was not recorded (in this case, I have 12 slices covering the superior half of the brain). I have been working to align this data using bbregister and have had very inconsistent results: in 1 subject it worked great; in another 6, the alignment failed (resulting in an alignment that is sometimes close, and sometimes way off). I am creating a .nii using MRICRON/dcm2niiGUI, and using bbregister. I have used this method successfully with a number of other sessions so far (with functional slabs that do cover the entire brain) with outstanding results. Is this troublesome for bbregister, or is there potentially something I'm doing incorrectly? Thanks in advance! If I'm repeating well-worn topics, I apologize, I couldn't find anything following a search through the archives. Joakim

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trgicoorder flag in mri_surf2surf
by Joakim Vinberg 02 Jan '11

02 Jan '11

Hi everybody, I am interested in doing sub-sampling of functional data for some new analyses. Just about the only reference I can find to sub-sampling of data in FreeSurfer is in mri_surf2surf, which has an optional flag trgicoorder. The comment for this flag is: "This specifies the size of the icosahedron according to the formula #vertices=10*4^n+2. In general, it is best to use the largest size available." It would seem that I might be able to use this flag in order to sub-sample surface data by using a smaller n (it seems as if the default for fsaverage is 7 according to the specified formula). Is this correct? Are there any particular guidelines to n? Other surfaces have a variety of vertices, so it seems that n does not have to be an integer? If I computer a surface of functional data for a given subject with a specific 'n' and resulting nVertices, should I also calculate an according anatomical surface with the same number of vertices for display and analysis? Thanks! Joakim

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matlab loading problem (mkcontrast, selxavg3-sess)
by Katherine Sledge Moore 02 Jan '11

02 Jan '11

I am having trouble with the interface between freesurfer and matlab. When I run mkcontrast-sess and selxavg3-sess, matlab opens, but nothing happens (the script does not finish.) When I force it to quit, I get the error "-display: Command not found." In both mkcontrast and selxavg3-sess, the command to call matlab is something along the lines of "matlab -display iconic". Any thoughts as to why the "-display iconic" part is not being interpreted? Katherine Sledge Moore Postdoctoral Associate Visual Cognitive Neuroscience Laboratory Yale University http://camplab.psych.yale.edu/ http://pantheon.yale.edu/~khs8

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the usage of mri_surf2vol program
by qizhu wu 02 Jan '11

02 Jan '11

Dear all, Continue with my previous question in "To use the file thickness.mgh outside Freesurfer". Thanks for Doug's recommedation to use the mri_surf2vol program to convert mgh files into image format, such as NIFTI. But I failed due to wrong setting on several arguments: 1, '--volreg': I do not understand what file it requires. It's declared in --help that "Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume". But I am only dealing with the structural volumes, and has this file been created in any step during the previous processing? Or could anyone tell me clearly how to set this argument? 2, --surfval: if only pthname rather than single file is allowed as input here? 3, --template: couldI use mni305.cor.mgz, or just left these optional arguments empty? thanks in advance. Qizhu Wu

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saving an external mesh in RAS coordinates
by Micheli, C. 01 Jan '11

01 Jan '11

Hi everybody, a very happy new year, with the hope 2011 will bring us near to our goals. I have a very simple question about surfaces in freesurfer. As i posted previously, i am trying to match white matter surface RAS coordinates with the corresponding anatomical volume. My attempt is to save an externally tessellated mesh (in scanner voxel coordinates) into RAS coordinates which match the volume. 1 - I first save the MRI T1 volume with save_mgh routine (i get the info about the vox2ras matrix by doing mri_info --vox2ras mri_file.nii) 2 - Then i save the surface (after transforming the voxel coordinates with the same vox2ras matrix used before for the volume) with write_surf 3 - Then i visualize volume and surface together with the tkmedit tool. Even if surface and volume seem to have correct projection alignment (coronal is coronal for both) there is evidently a mismatch in the superimposition of mesh and volumetric structures. The volume dimensions are 256X256X192 and is a monkey brain. Any suggestion to get me out of this local minimum? Greeting to everybody and congratulations for the nice toolbox Cristiano

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Covariates in Qdec
by Gallen, Courtney (NIH/NIDA) [F] 30 Dec '10

30 Dec '10

Hi, I'm running an analysis in Qdec in which I'd like to control for 3 variables (1 discrete (sex), 2 continuous (age and IQ)). In the output after I run the model: I only see a reference to an effect of my factor of interest controlling for sex (i.e., there is no contrast that also explicitly says controlling for sex, age, and IQ). Is this implied? Or are age and IQ not controlled for here? Is there a way to specify that I'd like to look for an effect controlling for all 3 variables? Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631

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Re: [Freesurfer] inter vertex distance
by YUMI MAEDA 29 Dec '10

29 Dec '10

Yes, I will ask him more information. yumi > did Rudolpha's answer work for you? > On Wed, 29 Dec 2010, YUMI MAEDA wrote: > >> Bruce, >> I meant the distance of 2 nodes along the surface. >> >> YUMI >> >> >>> do you mean on along the surface or in the volume? >>> On Mon, 27 Dec 2010, YUMI >>> MAEDA wrote: >>> >>>> HI, >>>> >>>> I am wondering if there is a way to calculate inter vertex distance on >>>> fsaverage surface with freesurfer. thanks for your help. >>>> >>>> YUMI >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

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Virtualtoolbox
by Liukarl 29 Dec '10

29 Dec '10

Hello, Freesurfer users: I am new to Freesurfer. I have two questions when I tried to install the Virtualtoolbox-Freesurfer into Window-XP system. 1) I downloaded the VirtualBox 4.0 for Windows hosts, but in the step of “Adding the downloaded hard disk image”, there is no “Add” button that I can use add the disk image. Any idea how to fix this? 2) Say, eventually I successfully installed it. I have some other data from another Mac that I need to transfer to this windows computer. What folder I should put in my data that comply with the default SUBJECTS_DIR for further analysis? Thanks a lot! Karl

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inter vertex distance
by YUMI MAEDA 28 Dec '10

28 Dec '10

HI, I am wondering if there is a way to calculate inter vertex distance on fsaverage surface with freesurfer. thanks for your help. YUMI

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FreeSurfer Error(s)
by Tali Swisher 28 Dec '10

28 Dec '10

Hello, Below I've copied the information for 1 case that has repeatedly given me the same error; however, I'm receiving the same error for the entire caselist (which has over 30 cases). Any help would be very much appreciated! Thanks, Tali * [bugr output]* FREESURFER_HOME: /projects/schiz/software/ freesurfer4.2.0_64/ Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 RedHat release: Fedora release 11 (Leonidas) Kernel info: Linux 2.6.30.10-105.2.23.fc11.x86_64 x86_64 *[error log]* #@# Talairach Failure Detection Wed Dec 22 12:48:09 EST 2010 /home/pnlstaff/freesurfer/subjects/casen1623/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux compute-3-9.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Dec 22 12:48:09 EST 2010 * [program]* recon-all -i nifti-files/n1623-t1w-realign-masked.nii.gz -autorecon1 -noskullstrip -subjid casen1623 && cp subjects/casen1623/mri/T1.mgz subjects/casen1623/mri/brainmask.mgz && recon-all -autorecon2 -subjid casen1623 && recon-all -autorecon3 -subjid casen1623 -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

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