RE: [Freesurfer] ROI Curvature
when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote: I mainly interested in the mean curvature. This is output for a gyral ROI: % 1001365: 647773 395 12973.145 0.780 0.151 0.027 4.123 0.572 This is for a sulcal ROI; % 1001365: 647773 563 16932.992 0.567 0.121 0.068 48.616 4.783 Cheers, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature which curvature values. Can you send the output? On Fri, 26 May 2006, Fornito, Alexander wrote: Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature Hi Alex, the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check. cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote: Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing? Thanks in advance, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] ROI Curvature
Yup. That looks fine. Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote: > I mainly interested in the mean curvature. > > This is output for a gyral ROI: > > % 1001365: rect. mean curv> > 647773395 12973.145 0.780 0.151 0.027 4.123 0.572 > > This is for a sulcal ROI; > > % 1001365: rect. mean curv> > 647773563 16932.992 0.567 0.121 0.068 48.616 4.783 > > Cheers, > Alex > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > National Neuroscience Facility > The University of Melbourne > Levels 2 & 3, Alan Gilbert Building > 161 Barry St > Carlton South Vic 3053 Australia > Ph:+61 3 8344 1624 > Fax: +61 3 9348 0469 > email: [EMAIL PROTECTED] > > > > -Original Message- > From: Bruce Fischl [mailto:[EMAIL PROTECTED] > Sent: Fri 5/26/2006 8:32 AM > To: Fornito, Alexander > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] ROI Curvature > > which curvature values. Can you send the output? > > On Fri, 26 May 2006, Fornito, Alexander wrote: > >> Sorry, got it wrong way around. >> Either way, when I run mris_anatomical_stats on labels that I have created, >> I tend to get positive values for mean curvature for labels of both gyral >> crowns or sulcal fundi. Are the curvature values provided by >> mris_anatomical_stats unsigned? >> >> Alex Fornito >> M.Psych/PhD (clin. neuro.) candidate >> Melbourne Neuropsychiatry Centre and Department of Psychology >> National Neuroscience Facility >> The University of Melbourne >> Levels 2 & 3, Alan Gilbert Building >> 161 Barry St >> Carlton South Vic 3053 Australia >> Ph:+61 3 8344 1624 >> Fax: +61 3 9348 0469 >> email: [EMAIL PROTECTED] >> >> >> >> -Original Message- >> From: Bruce Fischl [mailto:[EMAIL PROTECTED] >> Sent: Thu 5/25/2006 9:09 PM >> To: Fornito, Alexander >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] ROI Curvature >> >> Hi Alex, >> >> the gyri will should have negative mean curvature and the sulci positive. >> You can overlay the ?h.curv map to check. >> >> cheers, >> Bruce >> On Thu, 25 May 2006, Fornito, >> Alexander wrote: >> >>> Hi, >>> I have some labels that I've drawn, which correspond to the gyral crown and >>> sulcal fundus of a given ROI. From what I understand, mean curvature >>> provides an index of the convexity/concavity of the region. I would >>> therefore have expected high positive values in the gyral ROI to represent >>> a steeper peak in the curvature of the crown, with values closed to zero >>> representing a more flattened gyrus. Converseley, I would have thought low >>> negative values for the fundus ROI would represent a steeper peak in the >>> opposite direction, with values closer to zero again reflecting flattened >>> curvature. >>> In reality, the values I get for both sulcal and gyral labels (using >>> mris_anatomical_stats) tend to be both positive. >>> Hoping someone could tell me what I'm missing? >>> >>> Thanks in advance, >>> Alex >>> >>> >>> >>> >>> Alex Fornito >>> M.Psych/PhD (clin. neuro.) candidate >>> Melbourne Neuropsychiatry Centre and Department of Psychology >>> National Neuroscience Facility >>> The University of Melbourne >>> Levels 2 & 3, Alan Gilbert Building >>> 161 Barry St >>> Carlton South Vic 3053 Australia >>> Ph:+61 3 8344 1624 >>> Fax: +61 3 9348 0469 >>> email: [EMAIL PROTECTED] >>> >>> >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> >> > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] ROI Curvature
and if you click on the gyri do you get negative values? On Fri, 26 May 2006, Fornito, Alexander wrote: Yup. That looks fine. Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote: I mainly interested in the mean curvature. This is output for a gyral ROI: % 1001365: 647773 395 12973.145 0.780 0.151 0.027 4.123 0.572 This is for a sulcal ROI; % 1001365: 647773 563 16932.992 0.567 0.121 0.068 48.616 4.783 Cheers, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature which curvature values. Can you send the output? On Fri, 26 May 2006, Fornito, Alexander wrote: Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature Hi Alex, the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check. cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote: Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing? Thanks in advance, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] ROI Curvature
p.s. sorry, the mean and Gaussian curvatures displayed in mris_anatomical_stats are absolute value. I forgot this, sorry. The integrate Gaussian curvature is actually a topological invariant, so doesn't tell you much about the surface. Do you really need signed mean curvaature averaged over a region? If so, you could specify -T curv, so that the "thickness" is actually the curvature, and it will give you the mean and std. Bruce On Fri, 26 May 2006, Fornito, Alexander wrote: Yup. That looks fine. Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote: I mainly interested in the mean curvature. This is output for a gyral ROI: % 1001365: 647773 395 12973.145 0.780 0.151 0.027 4.123 0.572 This is for a sulcal ROI; % 1001365: 647773 563 16932.992 0.567 0.121 0.068 48.616 4.783 Cheers, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature which curvature values. Can you send the output? On Fri, 26 May 2006, Fornito, Alexander wrote: Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature Hi Alex, the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check. cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote: Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing? Thanks in advance, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ROI Curvature
On Thursday 25 May 2006 17:44, Fornito, Alexander wrote: > Sorry, got it wrong way around. > Either way, when I run mris_anatomical_stats on labels that I have created, > I tend to get positive values for mean curvature for labels of both gyral > crowns or sulcal fundi. Are the curvature values provided by > mris_anatomical_stats unsigned? 'mris_curvature_stats' provides signed statistics on Gaussian and Mean curvatures. By default it does not calculate the principle curvatures, so it has to be explicitly told: $>mris_curvature_stats -m -h 11 -G -F smoothwm where -m Show the min and max values of each curvature calculation -h 11 Show a histogram of curvatures sorted into 11 bins -G Calculate Gaussian statistics -F smoothwm Use the 'smoothwm' surface for Gaussian statistics (otherwise default to the 'orig' surface which is probably what you don't want). The subject to process Hemisphere to process Curvature file to process (does not affect the Gaussian / mean stats). Cheers -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] colortable
Satrajit Ghosh wrote: 1. Is there a matlab function to read the colortable from an annot file? Not that I know of. 2. Is there a reason why several of the annotvalues generated by the classifier using rh.atlas2005_simple.gcs do not have corresponding names in surface_labels.txt? I remember there was a release where there was a separate colortable for that atlas, but it doesn't exist in the current download, so I was assuming they have been merged into a single file. I'm not sure why there is a difference. The colortable associated with an annot can be found in the stats dir (eg, stats/aparc.annot.a2005s.ctab doug Thanks, Satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] regarding slice timing
Dear fellow FreeSurfers, does anybody know how to account for interleaved slice acquisition of functionals in fs-fast? Basically all my scans were taken interleaved instead of linear ordered, so I think it might be a good idea to tell the system (even though the block design used should not be too sensitive). selxavg2 does sort of know a parameter acqorder that will be passed to fast_selxavg.m, but selxavg-sess does not allow to specify this parameter, and on first impression there seems to be no auto-detection. And the 3.0.2 version of fast_selxavg does not use the SliceDelay in any way. Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] ROI Curvature
No, I don't need signed values necessarily. So just to double-check then, higher mean curvature for averaged across a gyral ROI label would mean the gyrus has a more steeply peaked appearance, whereas high values for a sulcal label would, conversely, mean the sulcus resembles a shraply bended valley? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 10:21 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature p.s. sorry, the mean and Gaussian curvatures displayed in mris_anatomical_stats are absolute value. I forgot this, sorry. The integrate Gaussian curvature is actually a topological invariant, so doesn't tell you much about the surface. Do you really need signed mean curvaature averaged over a region? If so, you could specify -T curv, so that the "thickness" is actually the curvature, and it will give you the mean and std. Bruce On Fri, 26 May 2006, Fornito, Alexander wrote: > Yup. That looks fine. > > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > National Neuroscience Facility > The University of Melbourne > Levels 2 & 3, Alan Gilbert Building > 161 Barry St > Carlton South Vic 3053 Australia > Ph:+61 3 8344 1624 > Fax: +61 3 9348 0469 > email: [EMAIL PROTECTED] > > > > -Original Message- > From: Bruce Fischl [mailto:[EMAIL PROTECTED] > Sent: Fri 5/26/2006 9:44 PM > To: Fornito, Alexander > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] ROI Curvature > > when you overlay the ?h.curv file on the inflated surface does it look > correct? Are there both red and green regions? > On Fri, 26 May 2006, Fornito, > Alexander wrote: > >> I mainly interested in the mean curvature. >> >> This is output for a gyral ROI: >> >> % 1001365: > rect. mean curv> >> 647773 395 12973.145 0.780 0.151 0.027 4.123 0.572 >> >> This is for a sulcal ROI; >> >> % 1001365: > rect. mean curv> >> 647773 563 16932.992 0.567 0.121 0.068 48.616 4.783 >> >> Cheers, >> Alex >> >> Alex Fornito >> M.Psych/PhD (clin. neuro.) candidate >> Melbourne Neuropsychiatry Centre and Department of Psychology >> National Neuroscience Facility >> The University of Melbourne >> Levels 2 & 3, Alan Gilbert Building >> 161 Barry St >> Carlton South Vic 3053 Australia >> Ph:+61 3 8344 1624 >> Fax: +61 3 9348 0469 >> email: [EMAIL PROTECTED] >> >> >> >> -Original Message- >> From: Bruce Fischl [mailto:[EMAIL PROTECTED] >> Sent: Fri 5/26/2006 8:32 AM >> To: Fornito, Alexander >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] ROI Curvature >> >> which curvature values. Can you send the output? >> >> On Fri, 26 May 2006, Fornito, Alexander wrote: >> >>> Sorry, got it wrong way around. >>> Either way, when I run mris_anatomical_stats on labels that I have created, >>> I tend to get positive values for mean curvature for labels of both gyral >>> crowns or sulcal fundi. Are the curvature values provided by >>> mris_anatomical_stats unsigned? >>> >>> Alex Fornito >>> M.Psych/PhD (clin. neuro.) candidate >>> Melbourne Neuropsychiatry Centre and Department of Psychology >>> National Neuroscience Facility >>> The University of Melbourne >>> Levels 2 & 3, Alan Gilbert Building >>> 161 Barry St >>> Carlton South Vic 3053 Australia >>> Ph:+61 3 8344 1624 >>> Fax: +61 3 9348 0469 >>> email: [EMAIL PROTECTED] >>> >>> >>> >>> -Original Message- >>> From: Bruce Fischl [mailto:[EMAIL PROTECTED] >>> Sent: Thu 5/25/2006 9:09 PM >>> To: Fornito, Alexander >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] ROI Curvature >>> >>> Hi Alex, >>> >>> the gyri will should have negative mean curvature and the sulci positive. >>> You can overlay the ?h.curv map to check. >>> >>> cheers, >>> Bruce >>> On Thu, 25 May 2006, Fornito, >>> Alexander wrote: >>> Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for bo
RE: [Freesurfer] ROI Curvature
pretty much, although if you have saddle points the mean curvature can disappear (since one direction has positive and the other negative curvature) On Sat, 27 May 2006, Fornito, Alexander wrote: No, I don't need signed values necessarily. So just to double-check then, higher mean curvature for averaged across a gyral ROI label would mean the gyrus has a more steeply peaked appearance, whereas high values for a sulcal label would, conversely, mean the sulcus resembles a shraply bended valley? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 10:21 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature p.s. sorry, the mean and Gaussian curvatures displayed in mris_anatomical_stats are absolute value. I forgot this, sorry. The integrate Gaussian curvature is actually a topological invariant, so doesn't tell you much about the surface. Do you really need signed mean curvaature averaged over a region? If so, you could specify -T curv, so that the "thickness" is actually the curvature, and it will give you the mean and std. Bruce On Fri, 26 May 2006, Fornito, Alexander wrote: Yup. That looks fine. Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote: I mainly interested in the mean curvature. This is output for a gyral ROI: % 1001365: 647773 395 12973.145 0.780 0.151 0.027 4.123 0.572 This is for a sulcal ROI; % 1001365: 647773 563 16932.992 0.567 0.121 0.068 48.616 4.783 Cheers, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature which curvature values. Can you send the output? On Fri, 26 May 2006, Fornito, Alexander wrote: Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature Hi Alex, the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check. cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote: Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing? Thanks in advance, Alex Alex Fornito M.Psych/PhD (clin. neuro.) ca
Re: [Freesurfer] regarding slice timing
Try using stc-sess (it is a front-end for fsl's slicetimer). doug Sebastian Moeller wrote: Dear fellow FreeSurfers, does anybody know how to account for interleaved slice acquisition of functionals in fs-fast? Basically all my scans were taken interleaved instead of linear ordered, so I think it might be a good idea to tell the system (even though the block design used should not be too sensitive). selxavg2 does sort of know a parameter acqorder that will be passed to fast_selxavg.m, but selxavg-sess does not allow to specify this parameter, and on first impression there seems to be no auto-detection. And the 3.0.2 version of fast_selxavg does not use the SliceDelay in any way. Ahoi Sebastian -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] updated tutorial and data
Freesurfers, An updated Freesurfer tutorial is now online at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial and the data that accompanies it (processed by stable v3.0.2) is available through: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data The outline is setup for a two-day course (to align with tutorial sessions typically found at a conference). Each of the four sessions should take no more than 90 minutes to complete. Comments and suggestions are appreciated. The Freesurfer team ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
