Freesurfer March 2009

freesurfer@nmr.mgh.harvard.edu

73 participants
100 discussions

Adding papers to the Wiki
by Pedro Paulo de Magalhães Oliveira Junior 11 Mar '09

11 Mar '09

Hi, Can you add this paper to the Wiki page? "Cortical thickness reduction of normal appearing cortex in patients with polymicrogyria" - Oliveira Jr, Pedro Paulo; Leite, Claudia; Valente, Kette; Shergill, Sukhwinder; Amaro Jr, Edson; - Journal of Neuroimaging - 2008 - In Press Tks PPJ ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom

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Re: [Freesurfer] Voxel size smaller than 1x1x1mm?
by Bruce Fischl 11 Mar '09

11 Mar '09

Hi Falk, yes, you can use the "conform to min" (-cm I think) switch in recon-all. Can you cover the whole brain at .7mm iso? That's hard. And 7T is hard for whole brain morphometry because of dielectric effects. Good luck. Bruce On Fri, 6 Mar 2009, Falk Lüsebrink wrote: > Hi Freesurfers, > > I'm currently doing my bachelors thesis in medical engineering and I'm > trying to measure the cortical thickness of scans acquired by a 7T MRT. > > A colleague of mine has used Freesurfer (v4.0.5) before and mentioned that > high resolution scans with a voxel size smaller than 1x1x1mm (like > .7x.7x.7mm) are converted to 1x1x1mm during a processing stage of autorecon > - I think during the mri_convert process. > > Is it possible to keep the native size or does Freesurfer need to change the > voxel size to 1mm in order to do the segmentation correctly? > > Regards, > Falk > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Average MRI
by SHRIKANTH KULASHEKHAR 11 Mar '09

11 Mar '09

Hi, I have 2 sets of MRI measurements with the same measurement sequence per subject. I was wondering if there would be any use of averaging these 2 sets, before the surface reconstructions? If yes how is this averaging achieved in freesurfer. Thanks in advance. Shriks Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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recon surf folder is missing data
by jake＠nmr.mgh.harvard.edu 10 Mar '09

10 Mar '09

Hi All, I was just wondering if anyone has had data missing from the surf directory in the recon folder of a subject, ie- right hemisphere data is missing, or no data at all. Here is the path to a recon where I recently have found missing data: /space/amaebi/35/users/ablood/R01_Botox/R01BTX_recons/CD_R01BTX_pat2_sess4_recon_missing_surfdata Any help would be greatly appreciated, thanks Jake

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Cluster analysis
by Devdutta W 10 Mar '09

10 Mar '09

Hi, We are doing cluster analysis on 16 subjects using the following command: *mri_glmfit-sim --glmdir /data/zonda1/freesurfer_subjects_zonda/qdec/rh.area --sim mc-z 5000 2 mc-z.abs.2 --sim-sign abs --overwrite* * *It has been running for seven days already and seems to have output well over 72000 lines such as this: *Smoothing done, nsteps = 91, tsec = 8.017 * Is this to be expected? How long does this normally take? We ran this a couple of weeks ago with 1000 iterations and it took 2 days to finish. Since we are now running 5000, will it run for 10 days? I appreciate any help. Thanks, Devdutta

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Display-problem
by Pål Gunnar Larsson 10 Mar '09

10 Mar '09

I have just installed Freesurfer 4.2 on 2 different systems both with Ubuntu 8.10. The systems runs nicely except, I can't diplay any images. On on one system a blank frame is display on the other nothing. I can save as .tiff and see the images, but nothing is displayed from tksurfer or tkmedit. Have checked in the archive without seeing this problem mentioned. Do anybody have a suggestion? Regards Pål

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Destrieux or Desikan/Ron Killiany
by Lars M. Rimol 10 Mar '09

10 Mar '09

Hi, I have an area of significance on the mesial surface of the hemisphere (please see attached tiffs). I would like to know if it is exclusively in the cingulate or in cingulate and SFG. The prolbem is that the two atlases don't agree. The upper more than half of this significant area is in SFG according to lh.aparc.annot and in cingulate gyrus and sulcus according to lh.aparc.a2005s.annot. I know there have been some issues before with cingulate and SFG in the Destrieux atals ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05399.html) but it's unlcear to me whether these have been resolved. As you can see from the tiffs, in lh.aparc.annot the significant area is inside the corpus callosum (a small part), caudal and rostral ant. cingulate, and SFG. In lh.aparc.a2005s.annot it is inside pericallosal sulcus, g. cingulate main part, s. cingulate main part, and only a very small part of it extends into SFG. These are substantially different interpretations. Is one atlas more accurate in this region? Thank you! -- yours, LMR

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ROI definition based on cortical parcellation
by Cindy Eckart 10 Mar '09

10 Mar '09

Dear freesurfers, comparing patient groups I found volume differences in specific cortical regions (using aparc_stats), which I would now like to compare to the results of a classical VBM. Concerning the whole brain analyses, the VBM did not yield comparable results (what might partly be a matter of stringent p-values controlling). To rule out that possibility (and to make the methods more comparable), I would like to do a ROI-based analysis specifically in those regions where I found the group differences with freesurfer. Therefore (and this is my question) I would like to create ROIs based on the labels of the Desikan atlas. I did not yet build a specific average subject for my population and would rather prefer to use one basing on bigger population sizes... which one could I use for this purposes? Bert? Or fsaverage? Or might there be an even more appropriate one for the use in cortical parcellations? Thank you for your help! Cindy ______________________________________________________________________________ Nur bis 16.03.! DSL-Komplettanschluss inkl. WLAN-Modem für nur 17,95 EURO/mtl. + 1 Monat gratis!* http://dsl.web.de/?ac=OM.AD.AD008K15039B7069a

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Thickness histogram on labeled region only?
by Pierson, Ronald K 09 Mar '09

09 Mar '09

I sent this a while back, but haven't received any suggestions. Would anyone have any ideas or suggestions? I would like to look at the histogram of cortical thickness for the cingulate cortex because I am concerned that the edges next to the corpus callosum have very low thicknesses (and significant regions that are zero) that may be creating some interesting cingulate results we are seeing. I see there is a matlab script to look at the thickness histogram of the entire cortex, but is there a way to create a histogram for just one labeled region at a time? Thanks, Ronald Pierson Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.

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Re: [Freesurfer] Aseg
by Jose Luis Cantero Lorente 09 Mar '09

09 Mar '09

When you open it for instance with SPM or MRIcro.... --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/ ----- Mensaje original ----- De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Fecha: Lunes, Marzo 9, 2009 5:19 pm Asunto: Re: [Freesurfer] Aseg > Hi Kelly, > > when you open it in what? The volume doesn't contain any > information about > the semantics - just label indices (into the > FreeSurferColorLUT.txt file). > Things like tkmedit are smart enough to go and find that file and > lookup > the label indices to find names and colors, assuming you tell > tkmedit that > it is a segmentaton. > > cheers, > Bruce > > On Mon, 9 Mar 2009, Kelly Silva wrote: > > > Hello, > > I did the conversion of aseg.mgz to analyze format, but when I > open it, > it appears only with the coordinates and not with the "seg ids". > How can I > do that? > > By the way, is there any posibility to open the > "asegstatsLUT.txt" > together with the aseg.hdr/aseg.img? > > Thanks, > > Kelly > > > > > > > > Veja quais são os assuntos do momento no Yahoo! +Buscados > > http://br.maisbuscados.yahoo.com > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer March 2009