Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

using T2* weighted scans to assist with dura stripping in a GE scanner?
by Katie Surrence 13 May '13

13 May '13

Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command? Thanks very much for your insight -- and I enjoyed the course! /Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute

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Re: [Freesurfer] Very simple question about Paired Analysis
by Douglas N Greve 13 May '13

13 May '13

Hi Jamie, did you look at the help for mri_glmfit? Run it with --help. doug ps. Please post questions to the list so that others can benefit. thanks! On 05/13/2013 04:12 PM, Jaime Ide wrote: > Dear Douglas, > > Thanks for your helpful page at > https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis > > I am having problems in the last step running mri_glmfit. > It should be a very simple bug to fix... > *"ERROR: you must use '--surface subject hemi' with surface data"* > (the complete message is at the bottom of this email..) > > I wonder to know if you could help me on this. > Thanks very much in advance, > Jaime > > > ***************************************** > cmdline mri_glmfit --glmdir lh.paired-diff --y > lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx > sysname Linux > hostname unifesp-monkey3 > machine x86_64 > user jaime > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y /home/jaime/ji_freesurfer/ji_scripts/lh.paired-diff.thickness.sm05.mgh > logyflag 0 > usedti 0 > FSGD paired-diff.fsgd > glmdir lh.paired-diff > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory lh.paired-diff > Loading y from > /home/jaime/ji_freesurfer/ji_scripts/lh.paired-diff.thickness.sm05.mgh > *ERROR: you must use '--surface subject hemi' with surface data* > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Resting state analysis
by Efrat Kliper 13 May '13

13 May '13

Dear freeSurfer expert, I am trying to perform whole brain functional connectivity analysis Is there a wiki for resting state analysis? I have only found this wiki page https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc So far I have run the following commands: preproc-sess -s TB_482 -fsd Rest -stc odd -surface fsaverage lhrh -mni305 -fwhm 5 -per-run What is the next step? Should I use the mkanalysis-sess command? (mkanalysis-sess -TR 3 -fsd Rest -stc odd -surface fsaverage lh -mni305 2 -fwhm 5 -analysis TB_482_lh -notask)? Running this command it seems to create only an output file with a list of information and nothing more, what am i doing wrong? In addition for resting state analysis, band filter of 0.01-0.08Hz needs to be done. How do i do that and to which of the output files? I don’t find any record about that either. Thanks in advance, Efrat

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LGI radius on outer surface ?
by Gregory Kirk 13 May '13

13 May '13

Hello Im preparing an LGI(local gyrification index) manuscript and seems i don't know the default radius that is used for the circular region defined on the outer surface that the boundary of is then projected onto the pial surface to get the corresponding pial region ? hope im clear, not the radius of the closing operator. thank you Greg

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parcellation boundaries freesurfer atlas
by Oort-4, J. van 13 May '13

13 May '13

Dear freesurfer mailing list, I have got a question with regard to the freesurfer parcellation. I'm using the atlas with 68 cortical areas. I would like to determine where to locate anatomical and functional areas in this atlas. In this way I would like to locate the areas that are involved in processing auditory and visual information. I can't find any article that describes the anatomical boundaries that are used in the parcellation, or which Bradmann area is included in which parcel. Could You recommend an article or other resource where I could find this information? greetings, Jasper van Oort ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Usage of --area option in estimating the vertex-wise maps of surface area
by Xinian Zuo 13 May '13

13 May '13

Hello Doug, I am doing some association studies between functional measures and surface area. In using mris_preproc, there is an option --area. Does this do sth similar to that as Winkler et al. (2012)? Winkler et al., 2012. Measureing and comparing brain cortical surfacearea and other areal quantities. Thank you very much. -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) Google Scholar Citations: http://scholar.google.com/citations?user=a3-gVGMAAAAJ&hl=en

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Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
by Daniel Haehn 13 May '13

13 May '13

Hi Nick, I installed it on Ubuntu 13.04 and all tools seem to work. I didn't test recon-all yet. Cheers, Daniel On Sun, May 12, 2013 at 10:41 PM, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>wrote: > Fedora 18, Ubuntu 13 and Gentoo 64 users, > > another beta of the upcoming v5.3 is available here: > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-… > > this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users > who wished to test that the segfault problem in v5.2 and the prior beta > v5.3 is fixed. Your help in testing this release is appreciated. > > Thanks, > > Nick > > > _______________________________________________ > 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. > > -- Daniel Haehn FNNDSC / BCH +1.857.218.5140

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Correction for multiple comparisons question
by Fotiadis, Panagiotis 13 May '13

13 May '13

Hi Freesurfer experts, I was wondering about three things concerning the use of the mri_glmfit-sim command: 1) I tried running it with the --2spaces flag in order to Bonferroni correct over the two hemispheres but it tells me that the specific flag is not recognized. Is there another way to correct over the two hemispheres? 2) I set the cluster-based threshold to 0.999 in order to see all of the clusters and varied the voxel-based threshold in order to see the differences that it would make on the results. Specifically, i set it to be 1.3, 2.0, 2.3, and 3.0. Between the four different occurring cluster summaries, there was only one common cluster that appeared in all four summaries. As expected, the number of voxels of the specific cluster was decreasing as its voxel-wise threshold was increasing. a) However, the reported cluster-wise threshold varied between 0.05 to 0.96 in those four cases. Does this sound reasonable? Shouldn't the cluster wise p values of the same cluster-between the four cases-be less dispersed? b) If there is a cluster reported in only one of the four summaries (i.e. when the voxel-based threshold is 1.3) that say has a cluster-wise p value of 0.03, do I consider that significant or not, since it does not appear in any other summary with such a low cluster wise p value and since the only published p value is the cluster wise one? Thank you in advance for your time, Panagiotis Fotiadis

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Different freesurfer version
by Oya, Hiroyuki (UI Health Care) 13 May '13

13 May '13

Hello Is it fine to process the anatomical data in v4.5 and analyze the results in v5.1? Thanks, Hiroyuki ________________________________ 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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Binary volume to surface label
by Jonathan DuBois 13 May '13

13 May '13

Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan

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