Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Total Surface Area
by XJ Kang 30 Sep '13

30 Sep '13

Hi Experts, I am trying to figure out the total surface area of a hemisphere. I found out 3 ways to read the area data: 1. Read the lh.area file directly [A, f]=read_curv('lh.area'); Total surface area: sum(A) = 86905.15mm^2 2. Read from the ~/stats/lh.curv.stats (generated by mris_curvature_stats in recon-all): Raw Total Surface Area: 87347.86719 mm^2 3. Read from the results: % mris_anatomical_stats sub lh white total surface area = 91046 mm^2 First, the total area includes the cutting area (unknown region?), right? Secondly, which total area is more reasonable? Thanks. XJ Kang

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Question about preproc-sess -no-subcort-mask
by Leila Reddy 30 Sep '13

30 Sep '13

Hi, I would like to verify (as a sanity check and to make sure that I'm on the right track in my analysis) that preproc-sess runs with -no-subcort-mask by default in freesurfer-Darwin-lion-stable-pub-v5.2.0, but with -no-subcort-mask turned off by default in stablev5.3.0 on snowleopard. I first did an MNI305 analysis in v5.2.0 (mountain lion) and was able to see my slices very nicely overlaid on the average/mni305.cor.mgz brain. However, the same analysis in v5.3.0 (snowleopard) didn't overlay on the brain in a sensible way, and only after I searched the mailing list did I realize that I needed to use -no-subcort-mask. Using this option gave me the same results as with v.5.2.0. Searching through freesurfer/fsfast/bin/preproc-sess I don't see where this flag is set by default to -no-subcort-mask in v5.2.0 (in fact, it seems that ApplySubCortMask = 1; by default). So I'm pretty confused, and I'm just not sure that I'm doing things the right way... Thanks in advance, Leila

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Post-Surgery Volume Analysis
by Germeyan, Sierra (NIH/NINDS) [F] 30 Sep '13

30 Sep '13

Hi all, A couple questions regarding post-surgery scans. 1. Is there a way to run scans of post-surgical brains that takes resections into account and gives more accurate results than "recon-all -all"? 2. Is it possible to obtain resection volumes with FreeSurfer? I tried to do this indirectly by finding the difference between total intracranial volume that FreeSurfer gave for scans pre- and post- surgery. However, I rarely obtained reasonable numbers with this method. Thanks very much for any advice you can give!

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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

1 0

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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Freesurfer September 2013