Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

autorecon2 on rh only
by anthony gallo 08 May '06

08 May '06

Can you please tell me the command line for running recon-all autorecon2 on only the right hemisphere? It isn't entirely clear to me from the wiki. I appreciate it, Anthony

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Noncompletion of autorecon2
by anthony gallo 08 May '06

08 May '06

Hello, I am having some trouble. I have all of the left hemisphere data that autorecon2 makes but not all from the right hemisphere. I have 2 questions: 1. If freesurfer encountered a problem and ended with an "error" would that error appear at the end of the recon-all log? 2. If the computer shut down and that was the problem (some form of auto shutdown) would an error appear in the freesurfer log? Thanks in advance, Anthony

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Re: [Freesurfer] fill stats
by Kevin Teich 08 May '06

08 May '06

Unless Doug has a tool for this, then no; it can't be done within tksurfer. Sorry. On Thu, May 04, 2006 at 06:16:31PM -0400, Chris Baker wrote: > > Yes- we're trying to select labels based on negative regions. If > there's no way to do this, is there a way to change which is the > positive and which the negative contrast in sfa-sess or does it > always take the first condition as being the positive contrast. -- Kevin Teich

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edit surfaces combined with MRI
by Michael Rullmann 08 May '06

08 May '06

hey, i used mri_watershed to produce different surfaces of the brain such as inner/outer skull, outer skin and brain. often the produced surfaces aren't totally correct. tkmedit shows me the surfaces and the MRI at the same time. now i want to edit the shown surfaces with tkmedit. is it possible? for editing i need to see the MRI and the surfaces at the same time. i didn't found an "edit surface tool" there. thanks, michael.

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mri_convert - 256^3 voxels at 1mm^3
by Darren Weber 05 May '06

05 May '06

Hi Bruce etal, It appears that the new 3.0.2 version of freesurfer does no longer require volumes to be 256^3 voxels at 1mm^3 each. Is there a wiki page on revised coordinate systems for the MRI and surface data? I would prefer to continue working with 256^3 @ 1mm^3 voxels (some other software we are using benefits from this reslicing). Can I specify this at the stage of mri_convert? Will it carry through to recon-all? Thanks, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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medial pial rh and lh surfaces crossing
by Josh Snyder 05 May '06

05 May '06

I see this on a ton of datasets. Is it a known issue? Is there an easy correction? Thanks, Josh

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segmentation
by Durastanti, Valentina (NIH/NINDS) [F] 05 May '06

05 May '06

Hi, I have a question: at the end of the segmentation (before the manual editing) I found that there are some voxel exceeding the yellow line and I can't figure out if they will be included in the WM count or if they will be included in the GM count. Have I to remove them even if they go over the line? Thanks Valentina

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mri_ms_fitparms
by adam walczak 05 May '06

05 May '06

At what point in the processing pipeline is mri_ms_fitparms? I am trying to convert data without header information (TE, TR, Flip angle) to data that freesurfer can use using mri_ms_fitparms and entering that info. This creates a T1 and PD image but I want to run it through the entire reconstruction. So I was wondering two things: 1) when should the mri_ms_fitparms be done on the data and 2) what point in the pipeline does it "spit out" the data? Thanks Adam --------------------------------- Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2¢/min or less.

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Mac OSX intel machines
by Moo K. Chung 04 May '06

04 May '06

Does Mac version work properly for new OSX intel machines? I just d/l the latest mac version and most programs seem to work except "tkmedit", which I can't able to run. Anyone done any freesurfing on a new mac machine? Moo. On 2/17/06, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > 1. Not offhand. > > for the others run: > > set sdir=$SUBJECTS_DIR/$s/surf > mris_curvature -max $sdir/lh.white > > this will write a file named lh.white.max (or use the pial if you want). > Similarly: > > mris_curvature -min will write the min curvature > > and > > mris_curvature -w will write the Gaussian (to lh.white.K) and mean (to > lh.white.H) curvatures. > > cheers, > Bruce > > > > > On Thu, 16 Feb 2006, Roberto Toro wrote: > > > three more quick questions: > > (1). do you know of a paper using the folding index successfully? > > (2). is it possible to access k_max and k_min for every vertex? > > (3). is it possible to access the mean curvature and the gaussian curvature > > for every vertex? (... to obtain (2)...) > > > > thanks, > > roberto > > > > On 15 Feb 2006, at 17:28, Bruce Fischl wrote: > > > >> yes. > >> On Wed, 15 Feb 2006, Roberto Toro wrote: > >> > >>> Hi, > >>> > >>> I found the reference to D. Van Essen's paper: > >>> > >>> Van Essen, D and Drury, H (1997) "Structural and functional analyses of > >>> human cerebral cortex using a surface-based atlas" J Neurosci > >>> 17(18):7079-7102 > >>> > >>> and the folding index is defined (from that paper) as "the integral of the > >>> product of the maximum principal curvature and the difference between > >>> maximum and minimum curvature, divided by 4*pi", ie, > >>> > >>> FI= (1/4pi) \int \int |kmax|(|kmax|-|kmin|) dA > >>> > >>> is this what freesurfer is using? > >>> > >>> thanks, > >>> > >>> roberto > >>> > >>> On 8 Feb 2006, at 16:39, Bruce Fischl wrote: > >>> > >>>> the Gaussian and mean curvature are differential geometric measures and > >>>> you can find them in any standard textbook (e.g. do Carmo). The folding > >>>> indices come from one of David Van Essen's papers - sorry, I don't have > >>>> the reference offhand, but it shouldn't be too hard to find. > >>>> Bruce > >>>> On Wed, 8 Feb 2006, Goradia, Dhruman D wrote: > >>>>> Hi, > >>>>> The output of function "mris_anatomical_stats" contains the following > >>>>> measurements: integrated rectified mean curvature, integrated rectified > >>>>> Gaussian curvature, folding index and intrinsic curvature index. Can > >>>>> someone please give me a brief explanation of what these measurements > >>>>> are or suggest some reading material. > >>>>> -Dhruman > >>>>> Dhruman D. Goradia (M.S.) > >>>>> Research Specialist. > >>>>> Western Psychiatric Institute and Clinic. > >>>>> 3811 O'Hara St. Suite 431 > >>>>> Pittsburgh, PA 15213 > >>>>> Phone: 412-586-9017 > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> This message has been checked for viruses but the contents of an > >>> attachment > >>> may still contain software viruses, which could damage your computer > >>> system: > >>> you are advised to perform your own checks. Email communications with the > >>> University of Nottingham may be monitored as permitted by UK legislation. > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > > > > > > This message has been checked for viruses but the contents of an attachment > > may still contain software viruses, which could damage your computer system: > > you are advised to perform your own checks. Email communications with the > > University of Nottingham may be monitored as permitted by UK legislation. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Moo Chung http://www.stat.wisc.edu/~mchung Assistant Professor Department of Statistics, Biostatistics & Medical Informatics University of Wisconsin-Madison

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Why I would need Boundary Shift Integral or IPCA for computing whole-brain atrophy rates?
by jorge luis 04 May '06

04 May '06

Hello all I have seen in the articles: -Freeborough, P.A., Fox, N.C., 1997. The boundary shift integral: an accurate and robust measure of cerebral volume changes from registered repeat MRI. IEEE Trans. Med. Imaging 16, 623- 629. - Kewei Chen et. all. An automated algorithm for the computation of brain volume change from sequential MRIs using an iterative principal component analysis and its evaluation for the assessment of whole-brain atrophy rates in patients probable with Alzheimer's disease. NeuroImage 22 (2004) That measures are obtained to estimate the whole-brain atrophy rates in patients with probable Alzheimer's disease and controls. Can I get the same thing by using the calculated intracranial volume (whole-brain) obtained from freesurfer after Skull Streaping and computing the differences for these volumes for the sequential images? Could these two analyses be equivalent in the sense that both they would give me whole-brain atrophy rates? So, if I have intracranial volume calculated why I would need BSI?. I have the same doubt for hippocampus volume comparisons for sequential images. Can I use a volume calculated from freesurfer subcortical segmentation or again I will need BSI or some other measure? In advance, thank you Jorge ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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