Freesurfer July 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
135 discussions

restarting after edits to brainmask.mgz and wm.mgz
by Mira Michelle Raman 07 Jul '09

07 Jul '09

Hi, I was just wondering if I should use -autorecon2-wm or -autorecon2-pial after making adjustments to both the brainmask.mgz and wm.mgz when restarting freesurfer. -Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 940305 (650)498-4538 http://cibsr.stanford.edu

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Citing QDEC
by nmaleki＠mclean.harvard.edu 07 Jul '09

07 Jul '09

Hello, Could you advise me on how to cite QDEC please? Thank you, Nasim

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Within group analysis
by Muhammad Ayaz 07 Jul '09

07 Jul '09

I am trying to run glm for two different scans of same subjects, ie first year scan vs second year scan. I ran the mris_prepoc and mri_surf2surf and it completed without error. When i run mri_glmfit it gives me error ERROR: gdfReadV1: Input line 1, subjid = 0049_05102006 Found 1 variables, expected. 0 FSGDF Format Error: file = CAA_1stScan_VS_2ndScan_Control_thickness.fsgd, tag=Input Ayaz

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How to "Fitting Tensors" in dt_recon?
by 李猛 07 Jul '09

07 Jul '09

Hi, All. The related item of "Fitting Tensors" is listed from the dt_recon. # Fit tensors echo "#@#-------------------------------" | tee -a $LF echo "Fitting Tensors" | tee -a $LF date | tee -a $LF set cmd = (mri_glmfit --y $fec --glmdir $OutDir); if($#bvals == 0) then set cmd = ($cmd --dti $infodump) else set cmd = ($cmd --dti $bvals $bvecs) endif However, I can't find any description about this argument(--dti) in mri_glmfit. Did the mri_glmfit call the dtifit to fit the tensor from fsl?If not, what is it? -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

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citation for appropriateness of using freesurfer with children
by Anthony Dick 07 Jul '09

07 Jul '09

Hello- I am using Freesurfer to obtain cortical parcellations for both children (aged 8-11 years) and adults. A reviewer asked for evidence that the parcellation works equally well in children and adults. Has this been tested empirically and published anywhere? I found a post saying not too worry about it for this age range (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06537.html) but reviewers tend to like references to published evidence :) The closest I get are papers by Burgund et al., 2002 and Kang et al., 2003 (http://tinyurl.com/m6v5s5; http://tinyurl.com/kwckol) but those papers do not use Freesurfer. Anything with Freesurfer? Anthony -- Anthony Steven Dick, Ph.D. Post-Doctoral Fellow Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: adick(a)uchicago.edu Web: http://home.uchicago.edu/~adick/

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ROI
by Natalia Sanchez 07 Jul '09

07 Jul '09

Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for tractography in FSL. First I register the subject to the space I am using (Talairach or MNI), then I save the label from tksurfer and then use mri_vol2roi to create the ROI which is all the precentral motor area. Finally I am downsampling the output from vol2roi in order to use it as an FSL target mask in ProbtrackX. When checking the output in FSL, the mask seems to be missaligned with the original T1 image, is it beacuse an error in the header or is it because I am doing something wrong in the process? Thenk you for your help, let me know if you need anything else. -- Natalia Sanchez

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Re: Melodic results on Freesurfer average subject
by Bruce Fischl 07 Jul '09

07 Jul '09

great, thanks Christian. I think Doug has some tools that can be used for this. cheers Bruce On Tue, 7 Jul 2009, Christian F. Beckmann wrote: > Hi Bruce & Martina, > > Yes, the easiest is to run melodic temporal concatenation on data pre- > processed and warped into a common space by freesurfer. Melodic does not care > about the space the data lives in - everything is reshaped into simple > matrices anyways. Have a look at the melodic command line call (in the log > file) to see how to call melodic with data pre-processed outside the FSL > environment. Essentially you just need to create a single ASCII text file > containing the N different input files (one per row) and then use > > melodic -i <inputfilenames> -o <outputdir> -a concat [otheroptions] > > Hope this helps > cheers > Christian > > On 7 Jul 2009, at 12:59, Bruce Fischl wrote: > >> Hi Martina, >> >> the freesurfer average subject lives in a spherical coordinate system >> created using nonlinear surface-based warps, so it's very far from any >> version of the mni. Maybe Steve or Christian can comment on integration, >> but certainly you would want to do the multi-subject ICA in the surface >> coordinate system. >> >> cheers, >> Bruce >> >> On Tue, 7 Jul 2009, Campanella Martina wrote: >> >>> >>> Hi Freesurfer, >>> >>> I've run a multi-subject analysis with MELODIC(FSL), resting-state data. >>> Now I'd like to view >>> the results on the Freesurfer average subject (made with >>> make_average_subject)... But... >>> FSL uses mni152 and Freesurfer mni305. Is it true? If so... any >>> suggestion? >>> >>> Thank you >>> >>> Cheers, >>> >>> Martina Campanella >>> >>> >>> > > _______________________________________________ > Christian F. Beckmann, DPhil > Senior Lecturer, Clinical Neuroscience Department > Division of Neuroscience and Mental Health > Imperial College London, Hammersmith Campus > Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK > Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548 > Email: c.beckmann(a)imperial.ac.uk > http://www.imperial.ac.uk/medicine/people/c.beckmann/ > > Senior Research Fellow, FMRIB Centre > University of Oxford > JR Hospital - Oxford OX3 9DU > Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717 > Email: beckmann(a)fmrib.ox.ac.uk > http://www.fmrib.ox.ac.uk/~beckmann > > > > >

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Re: [Freesurfer] Gaussian random field correction
by jorge luis 07 Jul '09

07 Jul '09

There is a very good implementation of surface-based Gaussian Random Field theory (GRF) correction from Keith J. Worsley at: http://www.stat.uchicago.edu/~worsley/surfstat/ The matlab toolbox there provides functions for reading freesurfer surface data. I have compared the results (by means of simulations) with those from freesurfer permutation testing and I think it is a very good alternative. Cheers Jorge Luis Bernal Rusiel Phd Student. Laboratory of functional Neuroscience. University of Pablo de Olavide. Seville. Spain --- El lun, 6/7/09, Jürgen Hänggi <j.haenggi(a)psychologie.uzh.ch> escribió: > De: Jürgen Hänggi <j.haenggi(a)psychologie.uzh.ch> > Asunto: [Freesurfer] Gaussian random field correction > Para: "Freesurfer Mailinglist" <freesurfer(a)nmr.mgh.harvard.edu> > Fecha: lunes, 6 julio, 2009 12:11 > Dear FS experts > > Is the GRF correction for multiple comparisons implemented > in FS yet and is > there any documentation how to use it? > > Thanks in advance > Best regards > Jürgen > > ---------------------------------------------------------------------------- > Juergen Haenggi > Ph.D. (Dr. des.) > Division Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > j.haenggi[at]psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ > (website) > http://www.juergenhaenggi.ch (private website) > > This e-mail (and any attachment/s) contains confidential > and/or privileged > information. If you are not the intended recipient (or have > received this > e-mail in error) please notify the sender immediately and > destroy this > e-mail. Any unauthorised copying, disclosure or > distribution of the > material in this e-mail is strictly forbidden. > ---------------------------------------------------------------------------- > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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WM-hypointensities
by Anita di Iasio 07 Jul '09

07 Jul '09

Hi all, I don't kown what is WM-hypointensities Is it a volume? I suppose this because WM-hypointensities is in the aseg.stats. thanks Anita di Iasio

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mris_make_face_parcellation
by BumSeok Jeong 06 Jul '09

06 Jul '09

Dear Freesurfer experts, I did microparcellation of annotation files using mris_divide_parcellation like below. mris_divide_parcellation C001 lh lh.aparc.annot 150 lh_annot_100 It made strip shape. I'd rather do microparcellation like Hagmann's work. But I don't know the option of mris_make_face_parcellation at Leopard. mris_make_face_parcellation [options] <input surface> <output surface> Please let me know what I have to do for making microparcellation with even volume. Thanks, Jeong

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Freesurfer July 2009