Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

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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aseg.stats volume mismatch
by Gabor Perlaki 06 May '14

06 May '14

Dear all, I've loaded the mri/aseg.mgz in slicer3D and done a label statistics on the image. The left caudate was reported to be 4005 mm^3 and the right caudate to be 4011 mm^3 by Slicer3D. However, these numbers are somewhat different from the values reported in aseg.stats: 3757 mm^3 and 3901 mm^3. Could anyone help me how to resolve these findings? Thanks, Gabor

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Two positions are available @ Queensland Brain Institute
by Yong Liu 06 May '14

06 May '14

Dear all, Two positions are available @ Queensland Brain Institute. *POSITION 1:* Postdoctoral Fellow Position in Neuroimaging and Brain Network Analysis at Queensland Brain Institute The Neuroimaging and Brainnetome Laboratory of Queensland Brain Institute (QBI) and Centre for Advanced Imaging (CAI) at the University of Queensland, Australia, solicits applications for postdoctoral fellow positions in neuroimaging and brain network analysis in healthy and neuropsychiatric diseases. We are looking for an excellent and highly motivated candidate with a PhD degree in neuroimaging, physics, mathematics, computer science, neurobiology, experimental psychology or comparable background. Interest and/or previous experience in/with neuroscience, MRI methods, design and image analysis are a plus. Experience with the LINUX/UNIX operating system is a positive add on. The successful candidate will participate in the multidisciplinary project involves developing algorithms of neuroimage processing and brain network analysis and software and applying them to neurosychiatric diseases. The main focus of this project is twofold: (1) developing new algorithms for structural MRI, functional MRI, DTI, and resting state MRI; (2) the assessment of differences between psychiatric patients and healthy controls in brain functioning, anatomy, default mode and functional connectivity. The postdoctoral fellows will be jointly supervised by Professor Tianzi Jiang and other Professors (QBI) who are experts in neuroscience. As at 30 June 2014, an applicant must not have had more than five years full-time equivalent professional research experience since the award of a PhD. The current salary range for the award is on a four-level scale from A$71,528.60 – A$79,708.50 per annum. Commencing salaries are based strictly on the number of full years’ experience since receiving a doctorate. Salary scales are reviewed from time to time. Please contact Professor Tianzi Jiang on tianzi.jiang(a)uq.edu.au for research plan. To submit an application for these positions, please refer to http://www.uq.edu.au/research/research-management/uq-postdoctoral-research-… . The application deadline is *19 May 2014.* *POSITION 2: * Postdoctoral Position in Imaging Genetics at Queensland Brain Institute The Neuroimaging and Brainnetome Laboratory of Queensland Brain Institute (QBI) and Centre for Advanced Imaging (CAI) at the University of Queensland, Australia, solicits applications for postdoctoral fellow positions in imaging genetics of the human and mice. We are looking for an excellent and highly motivated candidate with a PhD degree in neurobiology, genetics, experimental psychology, and neuroimaging or comparable background. Interest and/or previous experience in/with neuroscience, animal MRI, design and image analysis as well as wet lab experience are a plus. The successful candidate will participate in the multidisciplinary project involves developing transgenic mice model of psychiatric and neurological diseases. The main focus of this project is to address how risky genes of schizophrenia and Alzheimer’s disease affect brain networks in the human and mice. The postdoctoral fellows will be jointly supervised by Professor Tianzi Jiang and other Professors (QBI) who are experts in neuroscience. As at 30 June 2014, an applicant must not have had more than five years full-time equivalent professional research experience since the award of a PhD. The current salary range for the award is on a four-level scale from A$71,528.60 – A$79,708.50 per annum. Commencing salaries are based strictly on the number of full years’ experience since receiving a doctorate. Salary scales are reviewed from time to time. Please contact Professor Tianzi Jiang on tianzi.jiang(a)uq.edu.au for research plan. To submit an application for these positions, please refer to http://www.uq.edu.au/research/research-management/uq-postdoctoral-research-…. The application deadline is *19 May 2014.*

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Viewing functional data on the inflated brain
by Sherryse Corrow 05 May '14

05 May '14

Hi all, Earlier today, I posted the message listed below. However, we discovered part of our issue. When we run reg-feat2anat, there is no anat2exf.register.dat file created. Therefore, we have no registration matrix to use. Before, we were inadvertently using the anat2std file instead. Any suggestions on how to get the anat2exf.register.dat file created? Thanks, Sherryse -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre

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Freesurfer