Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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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Gaussian random field correction
by Jürgen Hänggi 06 Jul '09

06 Jul '09

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. ----------------------------------------------------------------------------

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recon-all freezing
by Dana W. Moore 06 Jul '09

06 Jul '09

Hi all, I have been trying to process an image, and the reconstruction has been consistently freezing at the same spot. This brain failed the tailarach transform, but I checked it and it looked fine, so I used the -notal-check flag. I have had this happen with several other brains, and there was no problem using this flag until now. I have tried it on 2 different computers where we have FreeSurfer, and it still freezes at the exact same place. I left it overnight to be sure it was really frozen, and the next morning the reconstruction script had not progressed. There is no error message. The place where it freezes is mri_ca_normalize, and I have pasted the script below: #@# CA Normalize Thu Jul 2 18:31:14 EDT 2009 /home/dwm2003/NPH/FS/NPH3/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (56, 38, 29) --> (205, 184, 175) using (106, 87, 102) as brain centroid... mean wm in atlas = 107, using box (88,69,84) --> (124, 104,119) to find MRI wm before smoothing, mri peak at 88 after smoothing, mri peak at 87, scaling input intensities by 1.230 scaling channel 0 by 1.22989 using 244171 sample points... INFO: compute sample coordinates transform 0.926 -0.053 0.111 2.200; 0.005 0.987 0.482 -32.821; -0.126 -0.444 0.940 78.347; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 43, 29) --> (200, 162, 179) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 110.0 115 of 354 (32.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (58, 45, 28) --> (131, 156, 177) This is always where the script stops when the process seems to freeze. (I have tried 3 times with the same result). Any ideas? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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Citing FreeSurfer in Papers - GLM - Thickness Analysis
by Pedro Paulo de Magalhães Oliveira Junior 02 Jul '09

02 Jul '09

I'm co-writing a paper using FreeSurfer and reading the Wiki page regarding how to cite FreeSurfer: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation <http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation>When we cite the mri_glmfit we usually use as reference: Fischl B, Sereno MI, Tootell RB, Dale AM. High-resolution intersubject averaging and a coordinate system for the cortical surface. *Hum Brain Mapp *1999; *8*: 272-284. However we use mri_glmfit-sim for multiple comparisson correction. Is this paper the citation for mri_glmfit-sim ? ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business

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