Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Major problems with T2-based pial removal
by Michael Waskom 30 Sep '13

30 Sep '13

Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial ---------------- https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial -------------------- https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic, problems with the pial surface. Any ideas? Michael

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Hippocampal Subfield Segmentation
by Germeyan, Sierra (NIH/NINDS) [F] 30 Sep '13

30 Sep '13

Hi everyone, After running -hippo-subfields, I converted the voxel output of -hippo-subfields to mm^3 based on the instructions given here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031188.html. Then I summed the volumes for all of the subfields (assuming that this would give me the total hippocampal volume), and compared the sum to the hippocampal volume that FreeSurfer gave after running recon-all -all on the same scan. They weren't the same! Why would these differ? Or, is there something I am doing wrong in my comparison of the two hippocampal outputs? Thanks for your help!

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Problems with LME-Setup
by Vivian R. Steiger 30 Sep '13

30 Sep '13

Dear FS-Experts We examined longitudinal t1-based data and used the -long pipeline and mri_glmfit for testing time effects. Now for a more powerful statistical analysis we're trying to set up LME for our data but we struggle while adapting from the tutorials cmd's. ##Problem: We currently struggle with building the CM that compares differences in cortical thicknes between the 2 time points and acts kind of a paired t-test. Could any of you experts might help us setting up the correct parameters for our analysis? ##Basics: - 23 Pre/Post Subjects already processed through the longitudinal pipeline - 2 time points - Comparison of mass univariate data Our qdec.table.dat consists of 5 columns: 1.) fsid 2.) fsid-base 3.) time 4.) group 5.) age ##Cmd History: [Y,mri] = fs_read_Y('/Subjects/LME/lme_setup23/lh.sad23.thickness_sm10.mgh'); lhsphere = fs_read_surf('/Subjects/LME/lme_setup23/lh.sphere.reg'); lhcortex = fs_read_label('/Subjects/LME/lme_setup23/lh.cortex.label'); Qdec_total = fReadQdec('/Subjects/LME/lme_setup23/qdec.table.dat'); Qdec_fsidbase = rmQdecCol(Qdec_total,1); sID = Qdec_fsidbase(2:end,1); Qdec_time = rmQdecCol(Qdec_fsidbase,1); M = Qdec2num(Qdec_time); [Msort,Ysort,ni] = sortData(M,1,Y,sID); X = [ones(length(Msort),1) Msort]; [theta0,residuals] = lme_mass_fit_EMinit(X,[1],Ysort,ni,lhcortex); [regions,RgMeans] = lme_mass_RgGrow(lhsphere,residuals,theta0,lhcortex); lhstats = lme_mass_fit_Rgw(X,[1],Ysort,ni,theta0,regions,lhsphere); F_lhstats = lme_mass_F(lhstats,CM); dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); fs_write_fstats(F_lhstats,mri,'sig.mgh','sig'); Thank you for your assistance Vivian

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Rv: Fwd: Re: LME Guide + Developer Build
by jorge luis 29 Sep '13

29 Sep '13

Hi Vivian The error you are getting means that the number of elements of your contrast vector is not the same as the number of columns of your design matrix. I think you're trying to apply the contrast matrix shown in the wiki page example to the sample dataset that we distribute with lme. That is incorrect. Note that the example in the wiki has four groups while the sample dataset only contains the data for two groups. Best -Jorge ----- Mensaje reenviado ----- >De: Jorge <jbernal(a)nmr.mgh.harvard.edu> >Para: jbernal0019(a)yahoo.es >Enviado: Domingo 29 de septiembre de 2013 23:24 >Asunto: Fwd: Re: LME Guide + Developer Build > > > > > > > >-------- Original Message -------- >Subject: Re: LME Guide + Developer Build >Date: Sun, 29 Sep 2013 17:55:24 +0200 >From: Vivian R. Steiger <vivianroger.steiger(a)uzh.ch> >To: Jorge <jbernal(a)nmr.mgh.harvard.edu> > >Hi Jorge > > >I think its not a programming bug itself but an error in the text of the mass univariat example on the website: > > >http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels > > >Perfoming all steps until doing fine but: > > >CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)]; >F_lhstats = lme_mass_F(lhstats,CM); > > > generates the following error in matlab: > > >Error using lme_mass_F (line 49) >The number of colums in the contrast matrix CM(1).C is different from the corresponding number of fixed effects in >stats(1).Bhat > > > > > > >Cheers > > >Vivian > > > > > > > > >Am 26.09.2013 um 16:58 schrieb Jorge <jbernal(a)nmr.mgh.harvard.edu>: > >Yes, please send your questions to the Freesurfer's mailing list. >> >> >>Why do you think there is a bug in the inference step? Could you please send me the prompted error that you are getting and a snapshot of the cmd you typed and of the result of “whos” Matlab cmd? >> >> >>To test an omnibus F-contrast containing several rows you simply create the contrast matrix CM.C with one row for each individual contrast and then pass it on to lme_mass_F, eg. >> >>F_lhstats = lme_mass_F(lhstats,CM); >> >>Unlike the univariate setting, in the mass-univariate setting a structure array CM is passed on to the inference function instead of a plain matrix C because someone might be interested in using different contrasts across different vertices like CM(1).C, CM(2).C, ...(though unusual). If you are using the same contrast across vertices then you simply define CM.C and it will be used for all vertices. >> >>Eg. CM.C = [0 0 0 0 1 0 0 0; 0 0 0 0 0 0 0 1] for an F-test and >> >> >>CM.C = [0 0 0 0 1 0 0 0] for a T-test >>Best >>-Jorge >> >> >> >> >>On 09/26/2013 08:06 AM, Vivian R. Steiger wrote: >> >>Hi Jorge >>> >>> >>>First of all thank you for your detailed response. We appreciate that you took time to answer us back. >>> >>> >>>We've already done the tutorial with the ADNI dataset provided on the website, which worked quite well except of the part with CM.C where we think could be a bug. >>> >>> >>>We eager to learn and process the lme for our structural dataset not just the t1-based but the dti as well and therefore we are interested in any new modelling toolboxes and paper dealing with lme survival analysis. We would be more than happy to beta-test such upcoming tools. >>> >>> >>>The problem that we have right now is the adaptational steps from the tutorial to our own dataset and structure. Should we post such questions in the mailinglist or could we might ask you for some support? Normally a more direct path of q+a provides a better, faster and even more successful way to a solution :) >>> >>> >>> >>> >>>Thank you for our time >>> >>> >>>Best, >>> >>> >>>Vivian >>> >>> >>> >>> >>> >>> >>> >>>> >>>> >>>> >>>>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. >>> >> > > > > >

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Rejoindre mon réseau sur LinkedIn
by Leila Ben Hamida Cammoun via LinkedIn 29 Sep '13

29 Sep '13

LinkedIn ------------ Leila Ben Hamida Cammoun a indiqué que vous êtes un(e) ami(e) ------------------------------------------ J'aimerais vous inviter à faire partie de mon réseau professionnel sur LinkedIn. Accepter l'invitation de Leila Ben Hamida Cammoun http://www.linkedin.com/e/-qq80um-hm6p83uo-48/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Leila Ben Hamida Cammoun http://www.linkedin.com/e/-qq80um-hm6p83uo-48/rso/233935656/Hs9R/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hm6p83uo-48/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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the "Configure Overlay Display" dialog is clipped on low resolution monitors.
by Francesco Cardinale 29 Sep '13

29 Sep '13

Dear Freesurfer developers, the "Configure Overlay Display" dialog is clipped on low resolution monitors with FS version 5.3.0 for MAC. This bug affected the version 5.1.0 and you released a fix for it, but now it's not available anymore on the website. Best regards Cico Cardinale

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Problem in final analysis
by carina＠van-vlodrop.de 28 Sep '13

28 Sep '13

Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-4.4.0 and have been experiencing some problems with the final analysis steps. We are using the qdec. Uploading of the data table has been successful. When we try to use the “Analyze” command (design) in the qdec, we get the following error message: Error in Analyze: Couldn’t open file /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thickness.fwhm10.fsaverage.mgh Obviously, the file was never created during preprocessing. We wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and would be very grateful for your comments. Yours sincerely, Carina $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-4.4.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v4.4.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39- 1 –ql-beowulf i686 $ which surfer -> /apps/prod/i486/freesurfer-4.4.0/bin/freesurfer Used command: qdec/design/Analyze Error message: Error in Analyze: Couldn’t open file /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thikness.fwhm10.fsaverage.mgh

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Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST TONIGHT)
by MCLAREN, Donald 27 Sep '13

27 Sep '13

Dear Colleagues, The Neurobureau is excited to announce a stipend program for Brainhack 2013. The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist. The stipend program will provide at least 6 stipends for partial or full registration fees [if 24 attendees apply, you have a 25% chance of getting a stipend]. The exact breakdown of stipends provided will depend on the number of applicants and the cost of attending the conference for those applicants. The application for stipend requires: (1) A poster abstract (2) A 1-2 page Brainhack project proposal (pdf format) (3) NIH Biosketch/CV (pdf format) The Brainhack 2013 Organizing Committee will decide which applications will receive stipends based on their abstract and proposed brainhack projects. The deadline to apply for one of the stipends is 11:59PM EST on September 27th. All decisions will be made by October 3rd and must be accepted within 24 hours of being awarded. To submit the application. Please email the 3 documents above to Donald McLaren (mclaren.donald(a)gmail.com) by 11:59 PM EST tonight. Good luck.

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Brainhack Registration and Payment
by MCLAREN, Donald 27 Sep '13

27 Sep '13

Brainhack.org is currently offline due to technical issues. We hope to have the website back up and running shortly. Here are the details to register (if you have not already) and to complete the payment process (if you pre-registered). The cost for the entire workshop and lodging for 4 nights is 450 Euros. The cost for the conference alone is about 200 Euros. * First step* : Here is the website : http://dr01.azur-colloque.cnrs.fr.<http://dr01.azur-colloque.cnrs.fr> - Choose your language - Choose our “event” : Brain Hack 2013 - Click on “Pre-registration” - Fill the form (as you have already done for the Brainhack.org website). The standard “Tarification” you must check is “Researcher”. *Second step* : - After this “Pre-registration” (*and our validation*), you will receive an email “Confirm a pre-registration”. This message will invite you to payon-line. Please follow the link you will receive. - Several pages need to be validated : - 1st page – “Please enter your information” : to get logged, please enter the information previously used. - 2nd page – “Personal information” : fill the form - 3rd page – “Organization (origin)” : just click on “next step” - 4th page – “Payment” : If your university or other institution will paythe fee for you, please check the second option “Someone else...” and fill the form. - 5th page – “Invoice” : just validate. - 6th page – “Invoice details”. Two options: Credit Card: simple, fast and best payment option. Transfer: Please do not take into account the message in red “only from French public organizations” – you do have the right to use this option, even if you're living in a foreign country. Moreover, once the paymenttransfered, you will receive a confirmation only several days after – do not panic, this is only a delay due to this option. I apologise for the lateness but our website is down. Please, let me know if you have problem or questions. Sincerely yours, Marlène Etienne Please let Donald McLaren know if you have any questions. He can be reached via email: mclaren.donald(a)gmail.com

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Fwd: Question about talairach.m3z file
by Paul Beach 27 Sep '13

27 Sep '13

---------- Forwarded message ---------- From: Paul Beach <pabeach1(a)gmail.com> Date: Fri, Sep 27, 2013 at 2:39 PM Subject: Re: [Freesurfer] Question about talairach.m3z file To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> So would you suggest, then, that it would be better to use the mri_vol2vol command to transform subject data (anatomical and functional) to MNI space? On Fri, Sep 27, 2013 at 9:36 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Paul > > not really. It is a nonlinear transform to our own atlas, which is loosely > in MNI space. Doug can probably give you a more precise answer > > cheers > Bruce > > On Fri, 27 Sep 2013, Paul Beach wrote: > > Hello Freesurfer community, >> I have a question about the file talairach.m3z, which is found in the >> mri/transforms directory of all subjects that have undergone recon-all. I >> am >> utilizing this file in an mri_convert script to resample AFNI processed >> T1volumes (and time-series data) to MNI space. However, I wanted to >> confirm >> which MNI talairach.m3z represents - it's MNI305, correct? >> >> >> Thanks! >> Paul >> -- >> Paul Beach >> DO/PhD candidate - Year VI >> Michigan State University >> - College of Osteopathic Medicine >> - Neuroscience Program - Bozoki Lab: Neurology/Radiology >> >> >> > > 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<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. > -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

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