Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

Re: [Freesurfer] 回复: 回复: 回复: about ROI to SPSS
by Douglas N Greve 08 Jan '13

08 Jan '13

How do you know it is the volume and not surface area? The values will be whatever are in y.mgh, so if y.mgh has surface area, then the output will be surface area. On 01/07/2013 07:38 PM, xiangbo_2010(a)126.com wrote: > > I used the command: > mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf avg.dat --id 1. Thanks! > > Bo Xiang > 送自我的HTC One SU > > ----- Reply message ----- > 发件人： "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > 收件人： "xiangbo_2010" <xiangbo_2010(a)126.com>, "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> > 主题： [Freesurfer] 回复: 回复: about ROI to SPSS > 日期：周二, 1 月 8 日, 2013 年 01:51 > > > > >> what was your command line? >> >> On 01/05/2013 01:43 AM, xiangbo_2010 wrote: >>> Dear doug >>> Using the command to only obtain the size of volume from every >>> subject, however, I want to obtain the size of surface area from every >>> subject, what should I do? thanks! >>> Bo Xiang >>> >>> >>> >>> >>> >>> At 2013-01-05 13:12:18,"Douglas Greve" <greve(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>> Drawing the ROI as a label is fine. Just don't transfer the label >>> to each individual subject. The y.mgh is all the data for all the >>> subjects in the fsaverage space (where the label is defined). You >>> can use mri_segstats, something like >>> >>> mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label >>> --avgwf avg.dat --id 1 >>> >>> avg.dat will have one column and number of rows equal to the >>> number of subjects >>> >>> doug >>> >>> >>> On 1/4/13 11:20 PM, xiangbo_2010 wrote: >>>> Dear doug >>>> I am sorry to disturb you again, I still do not know how to >>>> direct obtain the label of two significant clusters, is not to >>>> draw the ROI? thanks! >>>> Bo Xiang >>>> >>>> >>>> >>>> >>>> >>>> At 2013-01-05 06:49:14,"Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> wrote: >>>> >yes y.mgh >>>> >On 01/04/2013 05:13 PM,xiangbo_2010(a)126.com wrote: >>>> >> Do you mean input the file of y.mgh to mri_glmfit and run? Thanks! >>>> >> Bo Xiang >>>> >> 发送自我的HTC One SUJ >>>> >> >>>> >> ----- Reply message ----- >>>> >> 发件人： "Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> >>>> >> 收件人：<xiangbo_2010(a)126.com> >>>> >> 抄送： "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> >>>> >> 主题： [Freesurfer] 回复: about ROI to SPSS >>>> >> 日期：周六, 1 月 5 日, 2013 年 05:48 >>>> >> >>>> >> >>>> >> >>>> >> >>>> >>> That technique can yield inconsistent results when the ROI is small (as >>>> >>> in your case). You are better off extracting the data directly from the >>>> >>> input to mri_glmfit. This is created by QDEC and is called y.mgh. This >>>> >>> will be a file with number of frames equal to the number of subjects. >>>> >>> >>>> >>> doug >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> On 01/04/2013 04:13 PM,xiangbo_2010(a)126.com wrote: >>>> >>>> I drawing two ROIs in two clusters, and mapping two labels to all subjects, following extract the average surface area of two ROIs from every subject. Anyway, whether have command to direct obtain the label of two clusters, not to drawing the ROIs from these clusters, then there have exactly data to be obtained. Thanks! >>>> >>>> Ho Xiang >>>> >>>> >>>> >>>> 发送自我的HTC One SU >>>> >>>> >>>> >>>> ----- Reply message ----- >>>> >>>> 发件人： "Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> >>>> >>>> 收件人：<freesurfer(a)nmr.mgh.harvard.edu> >>>> >>>> 主题： [Freesurfer] about ROI to SPSS >>>> >>>> 日期：周六, 1 月 5 日, 2013 年 02:42 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>> Hi Bo, you need to make sure that you have exactly the same design >>>> >>>>> matrix in SPSS. The design matrix for qdec is Xg.dat in the output >>>> >>>>> directory. How did you extract the data out of the ROIs? >>>> >>>>> >>>> >>>>> doug >>>> >>>>> >>>> >>>>> >>>> >>>>> >>>> >>>>> On 01/02/2013 11:46 PM, xiangbo_2010 wrote: >>>> >>>>>> Dear experts >>>> >>>>>> I has obtained two ROIs (corrected FDR) difference between AA and >>>> >>>>>> GG regressing out the effect of age and gender using the QDEC with >>>> >>>>>> attachment, following extract the average surface area of two ROIs to >>>> >>>>>> analysis using SPSS, in which I used the >>>> >>>>>> Univariate Analysis of Variance to find the difference between AA and >>>> >>>>>> GG, gender and age as covariates, but find that there no significant >>>> >>>>>> in these ROIs, I want to know why there were significant difference in >>>> >>>>>> QDEC, but no significant difference in SPSS? I hope that have experts >>>> >>>>>> to help me, thanks! >>>> >>>>>> Bo Xiang >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> _______________________________________________ >>>> >>>>>> 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 >>>> >>>>>greve(a)nmr.mgh.harvard.edu >>>> >>>>> Phone Number: 617-724-2358 >>>> >>>>> Fax: 617-726-7422 >>>> >>>>> >>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >>>>> FileDrop:www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>>> >>>> >>>>> _______________________________________________ >>>> >>>>> 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. >>>> >>>>> >>>> >>>> >>>> >>> -- >>>> >>> 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:www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>> >>>> >>> _______________________________________________ >>>> >>> 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 >>>> >greve(a)nmr.mgh.harvard.edu >>>> >Phone Number: 617-724-2358 >>>> >Fax: 617-726-7422 >>>> > >>>> >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >FileDrop:www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> > >>>> >>>> >>> >>> >> -- >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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 greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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QA Tool Help - Outliers
by Efrat Kliper 08 Jan '13

08 Jan '13

Dear FreeSurfer expert, I am using Freesurfer version 5.1.0. After I run the QA Tool and check my data, I am getting 39 outliers or more for each subject. When I look at the AsegMeans and DefaultAsegMeans files in the QATool library, i see that the mean values in these file for each anatomical label are 0s. Is that OK? what files are you checking for outliers against? My results are in agreement with the literature and i believe non of them should be outliers. Any suggestion what might be the problem? Thank you in advance, Efrat

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Running recon-all with multiple source files
by Deirdre O Shea 08 Jan '13

08 Jan '13

Hi, I would like to try running recon-all for some subjects using two source images in combination. The first image is a FLAIR with dimensions 288x288x30, while the second is a T1 with dimensions 256x256x165. Furthermore, the each FLAIR voxel has dimensions of 0.79x0.79x4.5 mm, while each T1 voxel has dimensions 1x1x1 mm. I tried running the following command: *recon-all -i FLAIR/FLAIR_P00004210_S0001.nii -i T1/T1_P00004210_S0001.nii -subjid FreeSurfer_FLAIR* But I got the following error message: *ERROR: inputs have mismatched dimensions!* Is there an inbuilt command in FreeSurfer that will override this error message and perform a linear registration of the two images into the same space automatically, or do I need to perform the registration manually before starting with recon-all? Thank you, Deirdre

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mri_glmfit-sim fwhm error
by Gregory Kirk 08 Jan '13

08 Jan '13

run mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos get cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf subset_average lh --cortex --glmdir lh.lgi.glmdir SURFACE: subset_average lh log file is lh.lgi.glmdir/cache.mri_glmfit-sim.log cd /study5/aa-scratch/UTAH/freesurfer_final /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Tue Jan 8 14:21:47 CST 2013 Linux tick.keck.waisman.wisc.edu 2.6.32-279.11.1.el6.x86_64 #1 SMP Tue Oct 16 11:16:02 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux gkirk setenv SUBJECTS_DIR /study5/aa-scratch/UTAH/freesurfer_final FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest Original mri_glmfit command line: cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf subset_average lh --cortex --glmdir lh.lgi.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 38.299834 ERROR: cannot find /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/subset_average/lh/cortex/fwhm38/pos/th20/mc-z.csd i ran mri_surf2surf with --fwhm 10 whats the problem here ? thx greg

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Tracula preprocessing step error
by Allison Gruber 08 Jan '13

08 Jan '13

Dear Freesurfer experts, I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this. Selection from log: mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Users/Desktop/Tracula/diffusion_DTI/... Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 Please let me know if this is not enough information. Thank you for your help. Allison

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Longitudinal stream with special options
by Jürgen Hänggi 08 Jan '13

08 Jan '13

Dear FS experts I run the cross sectional step (step 1) for a longitudinal analysis with the following options: recon-all -s $s -all -talairach -use-mritotal -nuintensitycor-3T I would like to know whether I have also use these options in the creation of the base template (step 2) and in the longitudinal runs (step 3). What is the recommendation when using these special options? Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. 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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Re: [Freesurfer] trac-all bval bvecs bedpostx not running
by Anastasia Yendiki 07 Jan '13

07 Jan '13

Great. Just keep in mind that if you use the newer version of FSL, which has a new syntax for bedpostx, you might have to run bedpostx outside of tracula to get it to work. (This is a recurrent topic in the email list archives.) On Mon, 7 Jan 2013, Gerit Pfuhl wrote: > I redid everything from scratch, now it seems to work > having processed 1 slice ... > I cross my finger that this (new) subject and new calling of Terminal > did the "trick" > > thanks > gerit > > On 7 January 2013 08:35, Gerit Pfuhl <gerit.pfuhl(a)gmail.com> wrote: >> unfortunately changing Language of the system did not help, same error message >> attached the log file. >> >> Regards >> Gerit >> >> On 4 January 2013 16:49, Gerit Pfuhl <gerit.pfuhl(a)gmail.com> wrote: >>> thanks, rerunning now, should know the result in a few hours (plus >>> when bedpostx runs, so more like one day) >>> >>> -g >>> >>> On 4 January 2013 16:33, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>> setenv LANG en_US.UTF-8 >> >> >> >> -- >> http://gerit-orientation.blogspot.com >> http://team-arzgebirg.blogspot.com > > > >

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Re: [Freesurfer] Differences between avg33 and avg32 in dpath folders
by Anastasia Yendiki 07 Jan '13

07 Jan '13

You need to rerun the -prior and -path steps, without the trainfile set to anything, so that it uses the default trainfile with the 33 subjects. Do not set the reinit option, that has nothing to do with this. The reinit option is used when initialization fails but his hasn't happened here. On Mon, 7 Jan 2013, Alessia Sarica wrote: > Dear Anastasia,I checked the scripts of those patients with folders named > avg32 and I noticed that there is setted the trainfile ...difftutorial32.txt > I suppose that is the problem. > > Now, can I relauch TRACULA with reinit parameter equals to 1, or is it > better to delete all folders? > > Thanks for you help, > Alessia. > > 2013/1/6 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > That shows you how many subjects were included in the atlas. > There's a total of 33 subjects in the atlas, and for a general > purpose study there's no reason not to use all of them. Did you > change the trainlist parameter in the configuration file at any > point? > > On Sun, 6 Jan 2013, Alessia Sarica wrote: > > Dear Freesurfer Experts,i'm here again, maybe for a > trivial question, but > I didn't find any information about my doubt. > > I'm doing tractography on 36 patients and I noticed > that some of them have > dpath folders named "_avg33_mni_flt" and in other > patients, they are named > "_avg32_mni_flt". > Which is the reason for this? Something has gone > wrong? > > Thanks a lot, > Alessia. > > > -- > Alessia Sarica > Ph.D. Student Biomedical and Informatics > Engineering, > Bioinformatics Laboratory, Department of Surgical > and Medical Sciences, > University "Magna Græcia" of Catanzaro, > Viale Europa (Località Germaneto), 88100 CATANZARO, > ITALY. > Phone: +3909613694193 > > > > 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. > > > > > -- > Alessia Sarica > Ph.D. Student Biomedical and Informatics Engineering, > Bioinformatics Laboratory, Department of Surgical and Medical Sciences, > University "Magna Græcia" of Catanzaro, > Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. > Phone: +3909613694193 > >

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Recon-all 5.2 crashes after 30s
by Jonathan Holt 07 Jan '13

07 Jan '13

Hello all, Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some issues with disappearing white matter. I'm wondering if it is necessary to have Freesurfer 5.2 in order for recon-all 5.2 to work properly? When I say "crash" I mean it runs to completion after 30 seconds. Log files are not revelatory. best, jon

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Crash with full install of 5.2
by Carl Anderson 07 Jan '13

07 Jan '13

Hi Everyone, I did the full install for 5.2 but got the following crash during Talairach: #@# Talairach Failure Detection Mon Jan 7 13:43:33 EST 2013 /Applications/freesurfer/subjects/all_SP_mprage/SP037/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8143, pval=0.8469 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Applications/freesurfer/subjects/all_SP_mprage/SP037/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /Applications/freesurfer/subjects/all_SP_mprage/SP037/mri/transforms/talairach_avi.log \n TalAviQA: 0.97598 z-score: 0 TalAviQA2: (standard_in) 1: parse error (standard_in) 1: parse error if: Expression Syntax. Thanks for all your hard work, Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Freesurfer January 2013