Freesurfer

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30099 discussions

bbregister and surf2vol
by 刘东博 07 May '14

07 May '14

Dear Freesurfer I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , the BBR registration matrix is functional to anatomial volume,the surf2vol need anatomical to XYZ And I use bbregister --s sub1 --mov /sub1/mri/orig.nii --init-fsl --reg /sub1/register.dat --t1; mri_surf2vol --surfval /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh --hemi lh --surf pialfs --volreg /sub1/register.dat --outvol ./ --template /sub1/mri/orig.nii the resluts are 256 volumes.Why this happen?Should the voulme be 1 file?

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surf2vol
by 刘东博 06 May '14

06 May '14

I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , the BBR registration matrix is functional to anatomial volume,the surf2vol need anatomical to XYZ

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Help with subject's functional overlay
by Cesar Echavarria 06 May '14

06 May '14

Hello freesurfer experts, The functional overlay for one of our subjects looks like the image attached. You'll notice the "holes" on the overlay that have a value of 0. I'm trying to get ride of these as I expect (as with other subjects) to have values for these vertices that are not 0. Myself and a colleague have tried improving the registration as much as we see possible, but the problem remains. Any tips on how to correct this issue would be greatly appreciated. Thanks in advance for your help! Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012

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Re: [Freesurfer] Question regarding IGI
by Marie Schaer 06 May '14

06 May '14

Hi Virendra, What I don't get is why you would run lGI on the white surface, and specifically on the non topology fixed one? In principle, in mean on the technical side, you could run lGI on the lh.smoothwm which is the corrected surface with no hole and a single component (use mris_compute_lgi --i lh.smoothwm), but biologically I'm not sure it's meaningful. I definitely advise you to look at all coronal sections of the anatomical volume with lh.smoothwm and lh.pial-outer-smoothed / lh.smoothwm-outer-smoothed to get a sense of what you are measuring. Best, Marie On Apr 30, 2014, at 5:39 PM, Virendra Mishra <virendra.mishra(a)utsouthwestern.edu<mailto:virendra.mishra@utsouthwestern.edu>> wrote: Hi Marie, The surface does come after running recon-all but it is not the actual .pial file. It is actually lh.smoothwm.nofix file that I renamed so that I could run IGI. Thank you for that reply. So, in principle, if I go and find the holes and fill them and make it a continuous surface, then I should be able to compute IGI, right? Thank you for your help and time. Sincerely, Virendra ________________________________ From: Marie Schaer [Marie.Schaer(a)unige.ch<mailto:Marie.Schaer@unige.ch>] Sent: Wednesday, April 30, 2014 7:02 PM To: Virendra Mishra Cc: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: Question regarding IGI Hi Virendra, Where does this surface come from? You didn't get this one after running the default recon-all, right? Looking at it I noticed a lots of holes and many small unconnected components on the medial aspect. I ran mris_euler_number and got a total of 68 defects, so I'm afraid you'll not be able to run lGI with this surface as the lGI code expect a single continuous surface with no holes. And beside the issue of running lGI until the end, I'm concerned that neither cortical thickness not cortical folding can be reliably estimated based on this surface, and that you'll have trouble registering it to an average template. Best, Marie On Apr 30, 2014, at 3:08 PM, Virendra Mishra <virendra.mishra(a)utsouthwestern.edu<mailto:virendra.mishra@utsouthwestern.edu>> wrote: Hello Marie and other freesurfer users, I am trying to compute IGI for the attached file but at the step of mri_path2label , the code goes into an infinite loop and it is not able to create .label file even for the first .path file. I will be very thankful if you can help me debug this issue. Thank you, Sincerely, Virendra. ________________________________ UT Southwestern Medical Center The future of medicine, today. <lh.pial>

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mri_glmfit restricted to a label
by Garikoitz Lerma-Usabiaga 06 May '14

06 May '14

Hi, we are trying to run glmfit restricted to a label, with the following commands: mri_glmfit --y lh.p.thickness.10.mgh --label lh.l.label --fsgd f.fsgd --C C.mtx --surf fsaverage lh --cortex --glmdir lh.p.thickness.10.glmdir mri_glmfit-sim --glmdir lh.p.thickness.10.glmdir --sim mc-z 10000 1.3 mc-z.abs --sim-sign abs --cache-label lh.l.label --cwpvalthresh .999 --overwrite but if we check mc-z.abs.sig.masked.mgh and mc-z.abs.sig.cluster.mgh, we found clusters outside the label (see image below). Are we doing it properly? How can we be sure that both the analysis and the correction are done inside the label? thanks! Gari [image: Inline image 1]

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Re: [Freesurfer] When/What to edit?
by O'Shea,Andrew 06 May '14

06 May '14

Thanks for the replies Bruce and Doug. Do either of you know of any publications (or posters) that address the issue of editing effects in healthy controls? Also do you know where I could find some examples of "bad" reconstructions? I have seen screenshots/images on the wiki, but I am looking for whole folders that contain all the files from the recon-all process. I was thinking outliers from a group mean in certain ratios (region A thickness/region B thickness, etc.) may provide some insight. -Andrew --------- I've looked at the actual editing of voxels (ie, erasing and deleting) vs putting control points in terms of their effect on a group analysis of aging. CPs have an appreciable effect. I could not find much of an effect of editing, probably because the edits rarely lined up across subject. I think the jury is still out. I think it is a hard t thing to evaluate because it can be population specific. doug On 05/04/2014 05:26 PM, Bruce Fischl wrote: Hi Andrew I'm not sure I have any useful advise for you. When/what to edit depends in part of your hypotheses, in part on how significant the error is, and in part on how easily fixed it is. You also have to be careful that you don't edit too much and significantly lower inter-rater (or intra-rater) reliability. Maybe Doug can comment as he has looked at the effects of editing vs. not editing in some large scale datasets and I believe hasn't found much of an effect. We've also done a number of inter-rater studies and not found any effect or rater (all unpublished). Sorry, as I said, I'm not sure how useful any of this is cheers Bruce On Fri, 2 May 2014, O'Shea,Andrew wrote: Hello FS experts, I have had a continuing curiosity regarding when/what to edit in FS cortical reconstructions. The wiki does a good job at showing how to deal with large scale problems, (i.e. invalid tal transformation, white matter not being recognized, large portions of the skull included in the surface) however I have yet to come across much that guides edits besides a "trained eye". How do we know when a problem is "big enough" that it needs attention? Are there any tool boxes/ quantitative guidelines that may help someone determine which scans need edits? I know QA tools outputs info on SNR/white matter intensity and I have looked for outliers here. However, I was wondering how else to automate/guide the decision process. Much of the discussion I have seen on this topic in manuscripts is either vague or nonexistent. Does anyone know of any manuscripts that have compared "raw" FS datasets to "selectively edited" datasets? What sort of effects do edits make in the grand scheme of a study? One could imagine problems with someone editing the data when they are knowledgable of the study's hypotheses and groups. Any additional info or guidance on this topic would be much appreciated. -Andrew _____________________________________________

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freeview fails to open
by JacobML＠nmr.mgh.harvard.edu 06 May '14

06 May '14

Hello All, Any idea why freeview fails to open? Below I have included the terminal output. I have checked my quota and I have plenty of available memory. I also tried running the 2 options (-start_in_debugger and -on_error_attach_debugger), but these were not recognized. I was next going to attempt to configure, but I fear I may do more damage if I start messing around with cmds that I do not understand. Thank you for the assistance! Jacob [purkinje:mri] (nmr-stable53-env) freeview [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named purkinje.nmr.mgh.harvard.edu by jacobml Tue May 6 10:07:13 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

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-3T and -mprage flags
by Jason Tourville 06 May '14

06 May '14

Hi there, I am working on a project that involves pediatric data, ages 3-12. We are using Freesurfer to generate cortical surfaces. Information regarding the T1 acquisition is listed below. Is it appropriate to use the -3T and mprage flags for such data? Is there an alternative, pediatric atlas, that can be used for the Talariach and/or normalization steps that would be an improvement over the standard (or Schwartz) atlases? Any input that you can provide would be greatly appreciated. Cheers, Jason Below please see some details on the MPRAGE that is being collected for my study. GE 3T Signa® HDx MR scanner (GE Healthcare, Waukesha, WI) with an 8-channel head coil. During each session, 180 T1-weighted 1-mm3 isotropic volumetric inversion recovery fast spoiled gradient-recalled images (10 minute scan time), with cerebrospinal fluid (CSF) suppressed, were obtained to cover the whole brain with the following parameters: time of echo (TE) = 3.8 ms, time of repetition (TR) of acquisition = 8.6 ms, time of inversion (TI) = 831 ms, TR of inversion = 2332 ms, flip angle = 8°, field of view (FOV) = 25.6 cm × 25.6 cm, matrix size = 256 × 256, slice thickness = 1 mm, and receiver bandwidth = ± 20.8 kHz. -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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qdec question
by Anna Jonsson 06 May '14

06 May '14

Dear group, when using the qdec gui interface, I was wondering where the "button" or the likes is to change the estimation from its standard doss to dods (different osnet, different slope). I believe I can do this somewhere on the qdec gui without changing to mri_glmfit?

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LOOK FOR HELP
by 刘东博 06 May '14

06 May '14

Dear Freesurfer: I have some problems with using mri_surf2vol .I'd like to ask if you could help me with this.--volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. And to get this reg I use bbregister. But the result of bbregister is functional to anatomial volume,so I need to inverse the matrix.When I use convert_xfm in fsl I found the register.dat(which is the reslut of bbregister)is not a 4*4 matrix ,it just like dsub1 1.000000 1.000000 0.150000 9.999998807907104e-01 3.475215926300734e-04 3.422866575419903e-04 1.634627580642700e-02 -3.475832345429808e-04 9.999999403953552e-01 1.798802986741066e-04 -4.015868902206421e-02 -3.422244917601347e-04 -1.799785532057285e-04 1.000000000000000e+00 -2.181045338511467e-02 0 0 0 1 round Is there a command I can use to inverse the register.dat?Or if I use convert_xfm which part of the register.dat should I use? Thank you ! Yours Dongbo Liu

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