Freesurfer

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30084 discussions

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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mri_surf2surf
by Satrajit Ghosh 06 Jul '09

06 Jul '09

Hi, If I have created a direct registration from subj1 to subj2 using 'mris_register -1', is there a way to use mri_surf2surf to transfer labels from subj1 to subj2 using this registration, i.e., without using a registration that goes to a common reference? Alternatively, is there an easy way to create an identity registration for a surface? Cheers, Satra

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Re: [Freesurfer] fsaverage across versions
by Georg Homola 06 Jul '09

06 Jul '09

Can anybody confirm my assumption about fsaverage from last week? Is it ok to rerun mri_surfcluster with the new aparc.annot? Thanks a lot, Georg -------------------------------------- Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Georg Homola Gesendet: Mittwoch, 1. Juli 2009 17:05 An: 'Freesurfer Mailing List' Betreff: Re: [Freesurfer] fsaverage across versions Hi, my follow up question would be, how much has changed regarding fsaverage between freesurfer version 4.1.0 and 4.3.1? Is the added insula label the only change that has been made? Besides, when I load both annotations, the old and the new one, it seems to me almost every border of the parcellation has been shifted slightly. Is it how it's meant to be? I ask because I forgot to update the fsaverage in my separately stored Subjects_dir since version 4.1.0 and made a lot of analysis in the last months. To my mind it's good enough to rerun mri_surfcluster with the new fsaverage to get the updated annotations into my summary tables. Should that do the trick? Thanks again, Georg ---------------------------------------------------------------------------- ------- Iris, the registration targets were derived differently. With version 4, we automatically fill in all the ventricles. In verion 3, they were partially filled in manually. Version 3 creates a surface around the ventrical making it look like a sulcus, and this affects both the target and the registration to the target. So, on most of the surface, the registration will be very close, but it will deviate signifiacntly around the ventricles/medial wall. I think the fsfast in version 4 should work fine with the anatomicals (including fsaverage) of version 3. doug Steinmann, Iris wrote: Hi, we have several reconstructed brains, which were processed by freesurfer 3.0.5. We also kept using the fsaverage data from 3.0.5 in order to be consistent. We wish to do fMRI analysis with freesurfer/fs-fast 4.0.5 and found that talairach coordinates differ slightly when using the fsaverage from version 3.0.5 and the current fsaverage from 4.0.5. Yet, the both volumes appear pretty similar, the newer one maybe a little bit smoother. We would like to know what constitutes the exact difference between these two fsaverage datasets and whether it is possible to use the new version for analysis with the "old" fsaverage data without getting inconsistent results. Thanks a lot, Iris _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Error message starting qdec analysis
by Rosa Steimke 06 Jul '09

06 Jul '09

HI! When I sart the qdec analysis an error message comes up at around 70%. The error message says: Error in Analyze: command failed: mri_glmfit —y/Users/.../qdec/alh/y.mgh —fsgd /Users/.../qdec/alh/qdec.fsgd dods —glmdir /Users/.../qdec/alh —surf fsaverafe lh —label /Users/.../fsaverage/label/lh.cortex.label In my terminal window the last thing it says is Reading in average area /Users/steimke/Rosa_MRTs/fsaverage/surf/lh.white.avg.area.mgh ERROR: no contrasts specified Do you know what the problem is? Thanks in advance! Rosa Steimke Rosa Steimke Student Master of Neuroscience Vrije Universiteit Amsterdam -- Neu: GMX Doppel-FLAT mit Internet-Flatrate + Telefon-Flatrate für nur 19,99 Euro/mtl.!* http://portal.gmx.net/de/go/dsl02

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Freesurfer