Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

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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fill stats
by Chris Baker 04 May '06

04 May '06

Hi, Is there a way when using 'fill stats' to only select either the positive or negative values rather than taking both? Cheers, Chris.

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Fwd: [Freesurfer] buying computer - machine requirements
by Jacek Jonca-Jasinki 04 May '06

04 May '06

Kayle, > 1. HDD speed: How hard disk (I/O speed) intensive is freesurfer? What kind of > speed difference will having a RAID make? Would there be a big difference > from plain SATA? Gererally RAID would be most beneficial for computers running large number of search and read operations (i.e. database queries in large databases) as it requires number of rapid movements across large surface of the disk and there are some constraints of how quickly search and read can happen. That is one of the reasons why people use raid arrays. However, I doubt if in your case you will see much of the difference in performance. However, I would consider having two RAID mirrored drives that will impove security of you data. In case one of the drives fails some or all data from the other drive can be recovered preventing data loss. > 2. RAM amount: How much memory does running recon-all for one subject generally > require? Is it 0.5-1.5GB? Would 2GB be enough to run two simultaneously or do I > need 4GB? Or 6GB? How much RAM does running a group map for functionals need? Standard seems to be 4GB you may be able to get away with 2GB and I would not recommend less than that. Please note that those are only my wild guesses. > 3. RAM speed: We are buying DDR400 PC3200 RAM. Should I bother paying more for low-latency timings? Don't bother paying for faster memory, your bottleneck is your harddrive not your memory. > 4. Graphics speed: What speed graphics card is good enough for tkmedit and > tksurfer? Is a Geforce 6000 series plenty, or does having a 7000 series make > any difference? See this website for benchmarks of videocards: http://www.tomshardware.com/site/vgacharts/index.html -jacek

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buying computer - machine requirements
by kslays＠bu.edu 04 May '06

04 May '06

Hi, My group is buying a new computer we will use in the Martinos Center. I emailed Paul Raines via help and he gave me some guidelines as to what type I should get, but I still have some questions. 1. HDD speed: How hard disk (I/O speed) intensive is freesurfer? What kind of speed difference will having a RAID make? Would there be a big difference from plain SATA? 2. RAM amount: How much memory does running recon-all for one subject generally require? Is it 0.5-1.5GB? Would 2GB be enough to run two simultaneously or do I need 4GB? Or 6GB? How much RAM does running a group map for functionals need? 3. RAM speed: We are buying DDR400 PC3200 RAM. Should I bother paying more for low-latency timings? 4. Graphics speed: What speed graphics card is good enough for tkmedit and tksurfer? Is a Geforce 6000 series plenty, or does having a 7000 series make any difference? 5. Has anyone tried clustering computers together to spread the processing? Should we look into this for our three P4 1Ghz machines? Maybe you could add this information to the Machine Requirements wiki pages? https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements Thanks, Kayle

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mri_convert: input filetype = nrrd
by Michael Rullmann 04 May '06

04 May '06

hey, i tried to convert a nrrd file to mgz. but i didn't work because mri_convert doesn't support the nrrd filetype. is there any chance to use nrrd as a input file for freesurfer? does anyone knows a converter which converts nrrd files to analyze/dicom/... ? thanks, michael.

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