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30132 discussions

Re: [Freesurfer] QA Tools Snaps Scrambled - Clairification
by Irwin, William 09 Jan '13

09 Jan '13

Hi Louis- I was speaking cryptically and/or imprecisely. Of course there are dependencies for IM-- in fact about 8 libraries which are uniquely required by IM. I was thinking about a higher (or lower) level of dependency. This would suggest a more system-level problem, but I'm not having problems with any of the other apps running on my system. Obviously I'm not asking you to help diagnose the health of my system, but though you might have some thoughts/suggestions. Regards, Wil -----Original Message----- From: Irwin, William Sent: Wednesday, January 09, 2013 5:37 AM To: Louis Nicholas Vinke Cc: freesurfer(a)nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-contained. This is a real mystery -Wil -----Original Message----- From: Louis Nicholas Vinke [mailto:vinke@nmr.mgh.harvard.edu] Sent: Tuesday, January 08, 2013 6:29 PM To: Irwin, William Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA Tools Snaps Scrambled Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: > > Hi- > > > > I’ve come across a peculiar behavior with recon_checker, and am hoping > someone can shed some light on this. > > > > I have used it 100’s of times in the past, but not for about 2 months. > I recently processed a large set of cases I wanted to QC. When I ran > it, some, but not all, of the snaps were corrupted. Specifically the > talairach, aseg, surfs, and all the ‘detailed snaps’, which are > basically additional instances of the aforementioned types. The > inflated, curv, and parc are all just fine. As the process runs, all > images are being displayed in the pop-up windows, and the html page is created. > > > > While there have been no system changes which should affect this, I > upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the > problem. The problem remains. And the problem remains w/ or w/o the > flag for detailed snaps. > > > > If all of the images were corrupted, I would have certainly concluded > something has gone awry with my system. The fact that only some of the > images are corrupted makes me scratch my head. > > > > Thoughts? Suggestions? > > > > Thanks, > > Wil > > > 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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creating picture using 3D slicer
by L. Koenders 09 Jan '13

09 Jan '13

Dear FreeSurfer people, I have a problem creating a picture with my FreeSurfer volumetric data, for which I have been using 3D Slicer. First, let me explain what I am trying to do. We have a list with cortical and subcortical grey matter areas that were significantly different between our patient and control group. I want to make one picture showing all these areas, and the 3D model as can be made with 3D Slicer with a part of the surface 'clipped out' would be perfect. I tried to do this by loading the surfaces and parcellation map in Slicer. I could successfully load the volumes (mri.mgz, aseg.mgz) and the surfaces (lh.pial and rh.pial). But when I load the parcellation map (aparc.annot) as a scalar overlay for the already loaded model, slicer crashes. I emailed the 3D slicer helpdesk with this problem, but I hope you might have some ideas as well. My question is if there is a way to fix this problem, and if not; if there's another way to get the type of picture I want? I really hope you can help me, thanks in advance! Kind regards, Laura ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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QA Tools Snaps Scrambled
by Irwin, William 09 Jan '13

09 Jan '13

Hi- I've come across a peculiar behavior with recon_checker, and am hoping someone can shed some light on this. I have used it 100's of times in the past, but not for about 2 months. I recently processed a large set of cases I wanted to QC. When I ran it, some, but not all, of the snaps were corrupted. Specifically the talairach, aseg, surfs, and all the 'detailed snaps', which are basically additional instances of the aforementioned types. The inflated, curv, and parc are all just fine. As the process runs, all images are being displayed in the pop-up windows, and the html page is created. While there have been no system changes which should affect this, I upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The problem remains. And the problem remains w/ or w/o the flag for detailed snaps. If all of the images were corrupted, I would have certainly concluded something has gone awry with my system. The fact that only some of the images are corrupted makes me scratch my head. Thoughts? Suggestions? Thanks, Wil

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longitudinal processing
by Catherine Bois 09 Jan '13

09 Jan '13

Hi, just to clarify, When beginning longitudinal analysis, the first step is the same as cross-sectional processing, eg just the "normal" recon-all command, for each subject, and each individual time point? Then the norm.mgz files are used? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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ask about demean in GLM model setup
by chenchunhuichina 09 Jan '13

09 Jan '13

Dear experts, I am confused by demean during GLM model setup and would like someone here can help me. Thanks! Suppose I have a continuous behavior data and I want to find out which brain region(s) correlated with it. The simple way is to calculate correltation between brain data and behavior data, or in GLM to set up a model Y=AX+B+e, A is slope, B is constent and e is error, Y is brain data and X is beahvior data. So this design matrix have two collumns: behavior data and ones. or we can think of demean that dX=X-mean(X), dY=Y-mean(Y) Y=A'dX+B'+e', A' should be the same a A and B' differed from B, and B' maybe more interpretatable. I was told that -D opion in FSL randomise will demean X and Y at the same time. one can set up models like dY=A1dX+B1+e1, or dY=A2dX+e2. I simulated a data in SPSS and confirmed that A1,A2 is the same as A, B1 is 0. but t test for A1 A2 differed a little, A1 is the same as above models. So it seems to me that include a constent in the model is always right, right? My confusion is why Y also need to demean and how was it done in randomise? when one says "demean" or "mean centering", he/she means demean X only or demean X and Y both? Thanks for any clarification! 2013-01-09 Chunhui Chen _________________ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875

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Matching stats in SPSS and QDEC
by Maleki, Nasim 08 Jan '13

08 Jan '13

Hi list, I have done an analysis using QDEC and now I would like to do set up similar statistical analysis in SPSS on some parcellated structures. I have the following setup in QDEC: 2 cohorts (patients, healthy control subjects) Continuous variable : demeaned Age Nuisance Factor: demeaned intracranial volume DODS I'm interested in the effect of age i.e. "differences in the thickness-age correlation between the patients and healthy subjects" . Now my question is if I the following set up would be correct for doing the stats on slopes in SPSS: Univariate General Linear Model Dependent variable: ROI Fixed Factor: group (i.e. patient or healthy control) Covariate: demeaned age AND demeaned intracranial volume and then I also add an interaction term of demeaned_age*group to be the equivalent to the difference between thickness-age correlation in patients vs. healthy subjects that I have in QDEC. Is this correct? Thanks, Nasim

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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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