Freesurfer

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[Fwd: Re: [Freesurfer] Thickness repeatability]
by Doug Greve 08 May '08

08 May '08

FYI -------- Original Message -------- Subject: Re: [Freesurfer] Thickness repeatability Date: Thu, 8 May 2008 12:27:35 -0500 From: Xiao Han <elehanx(a)gmail.com> To: Doug Greve <greve(a)nmr.mgh.harvard.edu> CC: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> References: <200805081511.40394.martin.kavec(a)gmail.com> <48232A69.1030408(a)nmr.mgh.harvard.edu> <48232AEA.9020801(a)nmr.mgh.harvard.edu> Hi Doug, How are you? I couldn't send email to the list. But regarding that two questions, here are my thoughts: 1. I remember we used about 50 iterations. We also have a formula in the paper (Pg 183, right column) that relates the kernel size to the number of iterations. 50 iterations equals 5.6 mm kernel size by that formula. 2. That 6mm (or 50 iterations) is not totally arbitrary. We studied the effect of thickness variability w.r.t. smoothing kernel size. The result is summarized in Fig. 3 of the paper. Fig. 3 showed that a kernel of 6mm is effective and sufficient to remove noise. Larger kernel will give better repeatability, but may reduce sensitivity in a thickness study. The point we want to make is that FreeSurfer gives very good repeatability even with a very small smoothing kernel (6mm). That 6mm kernel is indeed much smaller than what other group used when reporting their thickness results (30mm!). We made the statement in the 2nd paragraph in the right column of Pg 185. Best wishes, Xiao On Thu, May 8, 2008 at 11:31 AM, Doug Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Sorry, that was supposed to be a reply to this email Damian Jenkins wrote: We have been following the protocol in Han's paper to test repeatability and the following questions cropped up: 1) how many smoothing iterations were run to achieve a smoothing kernel size of 6mm?; 2) what was the reason for choosing this size? Thanks, D Doug Greve wrote: Probably about 26. You can figure it out from this command: mris_fwhm --fwhm 6 --niters-only --s fsaverage --hemi lh dont know how they chose 6 doug Martin Kavec wrote: Hi, is it possible to obtain LGI values of cortices, similarly as curvature indices in ?h.aparc.stats? Could this value possibly be included in the ?h.aparc.stats files? Thanks in advance, Martin -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Thickness repeatability
by Damian Jenkins 08 May '08

08 May '08

We have been following the protocol in Han's paper to test repeatability and the following questions cropped up: 1) how many smoothing iterations were run to achieve a smoothing kernel size of 6mm?; 2) what was the reason for choosing this size? Thanks, D Dr Damian Jenkins Department of Clinical Neurology Oxford University

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--label2path option in mri_path2label
by Michael Harms 06 May '08

06 May '08

Hello, I'm trying to get the vertices of the border/edge/boundary (whatever you want to call it) of a contiguous, closed ROI/label on the surface. I've noticed an option "--label2path" in 'mri_path2label' (FS v4.0.2) that "will treat input as a label and output a path". When I tried this, I got the following output: ----------------- $ mri_path2label --label2path rh.middletemporal.label test.path INFO: Converting rh.middletemporal.label INFO: to test.path INFO: Label to path No encoded paths found in label file ------------------ So, my question is whether the "--label2path" option is supported, and if so, how is it intended to be used? (The output message implies that the path already has to be "encoded" somehow in the label file itself?) thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Cortical thickness percent difference surface maps
by Jonathan Rohrer 06 May '08

06 May '08

Is it possible to generate surface maps for the percent difference in cortical thickness between 2 groups within freesurfer? Best wishes Jon Rohrer

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incorporating PET data
by Lindsay Casmaer 06 May '08

06 May '08

Hello all, Can anyone offer specific suggestions for overlaying PET data on FS processed MRI data? Thanks, Lindsay lcasmaer(a)artsci.wustl.edu

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Extracting complex data from VB15
by mcloos＠nmr.mgh.harvard.edu 06 May '08

06 May '08

Hi all, I'm kind of new to freesurfer, and looking for a way to extract the complex data from a N4 VB15 file. For use in either matlab/mathematica. Any suggestions? Martijn

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Re: [Freesurfer] out of memory issue with selxavg3-sess
by Schadwinkel, Stefan 06 May '08

06 May '08

Hi, as I tried to show in the posting, I tried it on 3 Machines: 1) Linux, 1 GB memory: out of memory during OLS Residual Pass, then Java crashes 2) Linux, 2 GB memory: out of memory during Whitening 3) Mac (Mac OS X 10.5), 4 GB memory: as well: out of memory during Whitening Thanks a lot & best regards, Stefan Schadwinkel -----Ursprüngliche Nachricht----- Von: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Gesendet: Di 06.05.2008 02:25 An: Schadwinkel, Stefan Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] out of memory issue with selxavg3-sess How much memory do you have on that machine? Schadwinkel, Stefan wrote: >Hi, > >I've got a general question about selxavg3-sess. In short, when I try to run the analysis, MATLAB exits with an out of memory issue. ...

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G* S* labels
by Marlisa Isom 06 May '08

06 May '08

Hi All, I'm sure I'm going to sound like an idiot here. We were wondering how the sulcal volumes are calculated, ie what exactly does it measure? Is there any reason to add in sulci with gyri measures for a more complete ROI, etc. Thanks again Marlisa Isom

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niftii file / force command
by Carline van der Pol 06 May '08

06 May '08

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Re: [Freesurfer] qdec error: ERROR reading lh.cortex.label
by Wen, Wei 05 May '08

05 May '08

- Hi Doug, I ran make_cortex_label (that went through) for my average subject which was mas_average and tried qdec again but still the same message: mri_glmfit: could not parse 149955th line in /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label ERROR reading /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label Error in Analyze: command failed: mri_glmfit --y /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10/y.mgh --fsgd /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10/qdec.fsgd --glmdir /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10 --surf mas_average lh --label /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label --C /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10/contrasts/Avg-Intercept-thickness.mat --C /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10/contrasts/Diff-Female-Male-Intercept-thickness.mat I am now rerunning the average step and see what will happen next. Wei Wen Doug Greve wrote: > I think you can just run make_cortex_label for your average subject. > > Wen, Wei wrote: > >> - >> >> Thanks Doug. >> >> Do I need to rerun everything or at least rerun the average step? I >> went straight into qdec but the same error message appears (after >> replacing the old mri-mergelabels with the one just downloaded. >> >> Wei Wen >> >> Doug Greve wrote: >> >>> >>> This may be a problem with the way that the unix tail command is >>> implemented in newer OSs. Try copying this file: >>> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_mergelabe… >>> >>> >>> into $FREESURFER_HOME/bin >>> >>> doug >>> >>> >>> >>> Wen, Wei wrote: >>> >>>> - >>>> >>>> Hi >>>> >>>> FOrgot to attach the file of lh.cortex.label with my last email. >>>> Here it is. >>>> >>>> >>>> My error message is the same as Sky's: see >>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07271.html >>>> >>>> >>>> Looked like there was no solution for it at the time (April 17th, >>>> 2008), what about now please? >>>> >>>> "mri_glmfit: could not parse 149955th line in >>>> /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label" >>>> >>>> here I have attached the file for you to have a look. Also, I got >>>> the same error message while trying to load that file using >>>> tksurfer. I am using your latest version: 4.0.3. >>>> >>>> Many thanks and regards, >>>> >>>> Wei Wen >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> In order to help us help you, please follow the steps in: >>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >>> >> >> >> >> >

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