Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Re: [Freesurfer] the thickness of manually selected vertex
by Guang Zeng 25 Mar '10

25 Mar '10

Thanks! Yeah, I forgot this. Now, the results look right now. > Date: Thu, 25 Mar 2010 16:17:33 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: freesurfer_zg(a)hotmail.com > Subject: RE: [Freesurfer] the thickness of manually selected vertex > > are you sure you are using 1-based indices in matlab? Also, please post > these to the list so that others can answer! > On Thu, 25 Mar 2010, Guang Zeng > wrote: > > > > > Using mris_anatomical_stats, I got > > > > table columns are: > > number of vertices > > total surface area (mm^2) > > total gray matter volume (mm^3) > > average cortical thickness +- standard deviation (mm) > > integrated rectified mean curvature > > integrated rectified Gaussian curvature > > folding index > > intrinsic curvature index > > structure name > > 537 372 892 2.248 0.455 0.110 0.026 4 0.6 lh.mynew.label > > > > I also calculate the average thickness of the vertices by loading the label file and thickness file into MATLAB, I got some numbers as: > > average cortical thickness: 2.2670 > > standard deviation: 0.5476 > > > > These numbers looks very close, are the difference caused by the partial volume? > > > > Thanks! > > Guang > > > >> Date: Thu, 25 Mar 2010 15:52:34 -0400 > >> From: fischl(a)nmr.mgh.harvard.edu > >> To: freesurfer_zg(a)hotmail.com > >> CC: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: RE: [Freesurfer] the thickness of manually selected vertex > >> > >> nope, mris_anatomical_stats will take either (with -l or -a I think) > >> On Thu, > >> 25 Mar 2010, Guang Zeng wrote: > >> > >>> > >>> Do I need convert the .label file to an annotation file before I run mris_anatomical_stats? > >>> > >>> Could I get the same results if I do something like this: > >>> > >>> 1. create the label file, and load it using MATLAB, > >>> 2. find the corresponding ID of vertices I clicked. > >>> 3. load .thickness file using matlab > >>> 4. find the corresponding thickness value of these vertice > >>> 5. compute the mean > >>> > >>> Thanks! > >>> > >>> Thank! > >>> Guang > >>> > >>>> Date: Wed, 24 Mar 2010 16:15:35 -0400 > >>>> From: fischl(a)nmr.mgh.harvard.edu > >>>> To: freesurfer_zg(a)hotmail.com > >>>> CC: freesurfer(a)nmr.mgh.harvard.edu > >>>> Subject: Re: [Freesurfer] the thickness of manually selected vertex > >>>> > >>>> Q1: yes. > >>>> Q2: do you want each of them individually or the average? You can save a > >>>> label file of the 4 vertices and use mris_anatomical_stats to get the > >>>> average > >>>> > >>>> cheers > >>>> Bruce > >>>> > >>>> On Wed, 24 Mar 2010, Guang Zeng wrote: > >>>> > >>>>> > >>>>> Hi, there, > >>>>> > >>>>> I have two questions about the ?h.thickness file. > >>>>> > >>>>> If I load a subject's surface ?h.inflated using tksurfer, then I load its thickness file ?h.thickness, > >>>>> > >>>>> By clicking mouse on the surface, I can read the corresponding curvature value of a specific vertex. > >>>>> > >>>>> Q1, Here, the value next to 'Curvature' is actually its thickness value, right? > >>>>> Q2, If I select four vertexes on the surface, is there a way that I can save the thickness values of these four vertexes into a txt file? > >>>>> > >>>>> > >>>>> Thanks! > >>>>> Guang > >>>>> > >>>>> _________________________________________________________________ > >>>>> Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. > >>>>> http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:… > >>>> _______________________________________________ > >>>> 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. > >>>> > >>> > >>> _________________________________________________________________ > >>> Hotmail: Trusted email with Microsoft?s powerful SPAM protection. > >>> http://clk.atdmt.com/GBL/go/210850552/direct/01/ > > > > _________________________________________________________________ > > Hotmail: Trusted email with Microsoft?s powerful SPAM protection. > > http://clk.atdmt.com/GBL/go/210850552/direct/01/ _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/210850552/direct/01/

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the thickness of manually selected vertex
by Guang Zeng 25 Mar '10

25 Mar '10

Hi, there, I have two questions about the ?h.thickness file. If I load a subject's surface ?h.inflated using tksurfer, then I load its thickness file ?h.thickness, By clicking mouse on the surface, I can read the corresponding curvature value of a specific vertex. Q1, Here, the value next to 'Curvature' is actually its thickness value, right? Q2, If I select four vertexes on the surface, is there a way that I can save the thickness values of these four vertexes into a txt file? Thanks! Guang _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:…

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definition of some aseg.stats measures...
by Gonzalo Rojas Costa 25 Mar '10

25 Mar '10

Hi: What is the definition of the following measures that appears at the beginning of "aseg.stats" file: "Brain Mask Volume", "Brain Segmentation Volume Without Ventricles" (BrainSegVolNotVent), "Brain Segmentation Volume" (BrainSegVol), "Intracranial Volume" (IntraCranialVol, ICV) ?... The cerebelum is included in the ICV ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica Las Condes

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Longitudinal processing edits
by Pierson, Ronald K 24 Mar '10

24 Mar '10

I apologize if this has been covered before, but I wanted to make sure I understand the best way to edit at the appropriate times during the longitudinal stream. 1) Run recon-all -all on each scan 2) If needed, control points are chosen on the individual scans, and recon-all using the -cp option 3) Run the -base processing for the subject 4) WM and brain (pial) edits are done on the base, rerun as needed 5) Final longitudinal processing of each scan I assume the final processing of the individual scans should need very little manual intervention, since the control points and edits will be carried through to that stage. Is this correct, or have I oversimplified or missed something? Ronald Pierson Administrative Chair of Imaging, PREDICT-HD Manager, Research and Development Department of Psychiatry, Carver College of Medicine W-278 GH, 200 Hawkins Dr Iowa City, IA 52242

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qdec Font Error
by Jeff Sadino 24 Mar '10

24 Mar '10

Hello, When I get to the last step of qdec 1.2, when I choose the "Description" under "Scalers" on the "Display" tab, I get a couple of errors relating to fonts: ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Rendering/vtkFreeTypeUtilities.cxx, line 1659 vtkTextProperty (0x217178e0): Unable to create font ! (family: 0, bold: 1, italic: 1, length: 36128) ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Rendering/vtkOpenGLFreeTypeTextMapper.cxx, line 366 vtkOpenGLFreeTypeTextMapper (0x21717710): Render - No font I installed vtk 5.2.0, and also the newest vtk, but neither one worked. I also installed all of the windows fonts on my Linux. Haven't looked at OpenGL yet. Am I just missing the right font, or is there a deeper problem? btw, Freesurfer 4.3.1 is installed on a server that I log into. Thank you again! Jeff Sadino

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Research fellow/Postdoc in Pain Research, University of Michigan, Ann Arbor, MI
by alexandr＠nmr.mgh.harvard.edu 24 Mar '10

24 Mar '10

Research fellow/Postdoc in Pain Research, University of Michigan, Ann Arbor, MI The Headache and Orofacial Pain Effort (H.O.P.E.) requests applications for Research fellow/Postdoc at the University of Michigan Ann Arbor. The research ranges from neuroimaging (e.g. PET, MRI-based morphometry, fMRI, DTI, connectivity) to non-invasive brain stimulation for primary headaches and orofacial pain. Knowledge of Linux/UNIX operating systems as well as programming experience is required, as is a good level of comfort with novel computer applications. Previous research experience, including neuroimaging methods and analyses (e.g. Freesurfer, SPM) and statistics, is highly desirable. A background in pain and/or psychology neuroscience is an asset. We are also seeking applicants with well-developed organizational and interpersonal skills, and strong self-motivation to work in a highly innovative, altruistic, and mentoring environment. Hence, the applicant should feel comfortable working with chronic pain patients (e.g. migraineurs, trigeminal neuralgia and TMJD patients) and a multidisciplinary group of clinical and research collaborators. As part of the H.O.P.E. team, responsibilities will include facilitating experiments with subject handling, but mainly data acquirement and analysis. The stipend is commensurate with experience and training. Applications may be submitted at any time; however due to the competitiveness of this position, you are advised to apply early. H.O.P.E. is a multidisciplinary collaborative effort at University of Michigan to investigate the brain as a research and therapeutic target for headaches and orofacial pain disorders. Together with collaborators at University of Michigan and other academic institutions, we use state-of-the-art neuroimaging techniques to study neuroplasticity, and to investigate novel therapeutic approaches and mechanisms in chronic trigeminal pain disorders. Initially a curriculum vitae and letter of intent should be sent to: Alexandre F. M. DaSilva, DDS, DMedSc Director, Headache and Orofacial Pain Effort (H.O.P.E.) TM Assistant Professor, University of Michigan Ann Arbor Biologic & Material Sciences, School of Dentistry Laboratory: The Molecular & Behavioral Neuroscience Institute (MBNI) 205 Zina Pitcher Pl, room 1021 Ann Arbor, MI 48109-5720 Office: 734 615-3807 Fax: 734 763-3453 adasilva(a)umich.edu University of Michigan is one of the top public universities of the world, a diverse institution of higher learning, fostering excellence in research. http://research.umich.edu/

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Segmentation fault during skull-stripping
by Michael Waskom 24 Mar '10

24 Mar '10

Hi Bruce, Nick, I'm getting a segmentation fault that's crashing recon-all at the start of the watershed during skull-stripping. I've tried this three times, once starting the unpacking stream fresh from the raw dicoms, and it keeps happening at exactly the same place. I've been reconstructing brains of other subjects in the same directory all the while, so I don't think it's a permissions issue of any sort. Full recon-all log is atatched, but here's the section where it crashes: *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=116 y=166 z=95 r=51 first estimation of the main basin volume: 585576 voxelsSegmentation fault Linux ba2 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Mar 17 14:22:26 EDT 2010 And here's the OS data from the bugr script: FREESURFER_HOME: /software/Freesurfer/4.4.0 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0 Debian version: squeeze/sid Kernel info: Linux 2.6.31-20-generic x86_64 Do you have any idea what might be going wrong? Thanks! Mike

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DISPLAY error
by Lindsay Ercole 24 Mar '10

24 Mar '10

Hello All, I am running Mac OS 10.5.8. I can set all of my environment variables and then when I enter the line for calling up a session, I get: GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:0.0 I try to set this to my IP address of the computer, and I still get: GLUT: Fatal Error in tkmedit.bin: could not open display: (my ip):0.0 FS v. 4.0.1 is what we are running. The system did an overnight automatic update, and I think this is what has now caused our display issues, since they were not presenting yesterday (or the day prior). Thanks, Lindsay

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Re: [Freesurfer] extract thickness values for vertex
by Pedro Paulo de Magalhães Oliveira Junior 24 Mar '10

24 Mar '10

Maybe your fsaverage directory is not in the default place I've updated the wiki page # Script created December 2007 by Pedro Paulo Jr. # Use with Freesurfer 4.x # Updated: 24/03/2010 set FSAVERAGE_DIR = "../../fsaverage" #set fsaverage dir cd #your directory where qdec data are stored. set numsubject = 17 #your value for i in `seq 1 $numsubject` do mri_convert --frame $i y.mgh $FSAVERAGE_DIR/surf/lh.$i.mgh mris_convert -c $i.mgh $FSAVERAGE_DIR/surf/lh.inflated lh.$i.asc done ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.4 www.Netfilter.com.br --- Novo Netfilter Small Business Em 24 de março de 2010 06:30, Prapti Gautam <Prapti.Gautam(a)anu.edu.au>escreveu: > I run mri_glmfit the usual way, as detailed in the GroupAnalysis tutorial.. > I couldn't get the script to run either with qdec or mri_glmfit output > directory, so figured it must be a permission issue with fsaverage? > > > > -----Original Message----- > From: Pedro Paulo de Magalhães Oliveira Junior [mailto: > ppj(a)netfilter.com.br] > Sent: Wed 3/24/2010 7:27 PM > To: Prapti Gautam > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] extract thickness values for vertex > > Maybe I need to change that script. > > How do you usually run you glmfit analysis? > > 2010/3/24, Prapti Gautam <Prapti.Gautam(a)anu.edu.au>: > > Dear FreeSurfers, > > > > > > Is there a way to extract thickness values for individual subjects for a > > vertex that are obtained after analyses with mri_glmfit? I have seen a > > script that does this with qdec - but most of the analyses I run are on > > mri_glmfit, so was wondering if the script on the user contribution > > section needs to be modified for mri_glmfit. I ran the script where the > > output files are located and get the following error: > > > > > > > > > > > > ERROR: failure writing ./media...../fsaverage/surf/lh.1.mgh > > > > > > > > Reading group avg surface area 864 cm^2 from file > > > > > > > > mghRead( /media/...../fsaverage/suf/lh.1.mgh, -1) : could not open file > > > > > > > > > > > > > > > > Is this simply a permission issue with the fsaverage folder? > > > > > > > > > > > > Thanks for your help, > > > > > > > > > > > > Prapti > > > > > > > > > > > > > > > > > > > -- > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.4 www.Netfilter.com.br > --- Novo Netfilter Small Business > > > >

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extract thickness values for vertex
by Prapti Gautam 24 Mar '10

24 Mar '10

Dear FreeSurfers, Is there a way to extract thickness values for individual subjects for a vertex that are obtained after analyses with mri_glmfit? I have seen a script that does this with qdec - but most of the analyses I run are on mri_glmfit, so was wondering if the script on the user contribution section needs to be modified for mri_glmfit. I ran the script where the output files are located and get the following error: ERROR: failure writing ./media...../fsaverage/surf/lh.1.mgh Reading group avg surface area 864 cm^2 from file mghRead( /media/...../fsaverage/suf/lh.1.mgh, -1) : could not open file Is this simply a permission issue with the fsaverage folder? Thanks for your help, Prapti

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