hello experts i have some question to you
What is the meaning about cortical thickness alteration (increase or decrease) a few days ago i read these sentences Deviations from these patterns can be used as diagnostic indicators for brain disorders <http://en.citizendium.org/wiki/Brain_disorder>: While Alzheimer's disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>, even very early on, is characterized by pronounced cortical thinning[4] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4> , Williams syndrome <http://en.citizendium.org/wiki?title=Williams_syndrome&action=edit&redlink=1> patients exhibit an increase in cortical thickness of about 5-10% in some regions [5] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5>, and lissencephalic <http://en.citizendium.org/wiki/Lissencephalic> patients show drastic thickening, up to several centimetres in occipital regions[6] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6>. from wiki i wonder increased or reduced cortex depended on disorder? plz answer me 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi A-reum > > we use average Euclidean distance from gray to white and visa-versa. There > are other (variational) techniques that we have messed around with, but > none of our experiments have shown that they are any better, so we have > stuck with the simplest thing. > > cheers > Bruce > > > On Fri, 5 Feb 2016, A-reum Min wrote: > > hello experts >> >> i have some question to you >> >> What method do you use when measuring the cortical thickness? >> >> (ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal >> equation?) >> >> plz answer me. >> >> 2016-01-17 0:53 GMT+09:00 A-reum Min <naniy...@gmail.com>: >> Thank you for u r answer. >> I have some question to you. >> >> i compared two groups(patients VS control) >> >> How can i extract the total vertices(ex.#1 vertex : cortical thickness >> value) to 1 subject(patient) and average of patients ? >> I want to compared asymmetry of brain (lateralization). So, i really >> necessary above value(cortical thickness value of vertex). >> >> plz answer me. >> >> Thank you. >> >> >> 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi Areum >> >> every brain will have a somewhat different number of >> vertices depending on size and geometry. If you want them >> to be comparable you need to map them into the fsaverage >> space using e.g. the -qcache switch to recon-all (or >> mri_surf2surf directly if you prefer). >> >> cheers >> Bruce >> >> >> On Sat, 16 Jan 2016, A-reum Min wrote: >> >> Hello expert. >> I'm Areum. >> >> I have some question to you. >> >> A weeks ago, i compared two groups (OSA >> patients VS control) and then the >> number of vertices were confirmed. >> >> Each group has the same number of >> vertices.(176416) -experiment 1. >> >> And yesterday, i compared two groups(partial >> sleep deprivation:PSD VS >> control) and then the number of vertices were >> confirmed. >> >> Each group has the same number of >> vertices(169548) -experiment 2. >> >> >> 1) Why isn't the same number of total >> vertices? is it related rain size? >> >> >> 2) How can i extract the number of total >> vertices(ex.#1 vertex : cortical >> thickness value) to 1 subject(PSD) and average >> of PSD ? >> I want to compared asymmetry of brain >> (lateralization). So, i really >> necessary above value(cortical thickness value >> of vertex). >> >> plz answer me. >> >> Thank you. >> >> >> 2016-01-07 3:52 GMT+09:00 Bruce Fischl >> <fis...@nmr.mgh.harvard.edu>: >> Hi A-reum >> >> did you talk to the Wash U group? If you >> have nifti files they >> can be processed using recon-all (i.e. >> recon-all -i <full path >> to nifti file> -s <subject id> -sd >> <directory to contain all >> subjects> -all) >> >> cheers >> Bruce >> >> >> On Tue, 29 Dec 2015, A-reum Min wrote: >> >> hello experts!my name is areum. >> i have some question to you.i have >> never seen before >> these NIFTI >> format(fig.1.png) >> I want to see these data >> subjects's cortical >> thickness using qdec. >> how can i to do? plz answer me >> >> 2015-12-25 2:16 GMT+09:00 Bruce >> Fischl >> <fis...@nmr.mgh.harvard.edu>: >> Hi A-reum >> >> you should probably ask the >> Wash U HCP group. >> I'll cc Matt >> Glasser who might be able to >> answer your >> question >> cheers >> Bruce >> >> On Thu, 24 Dec 2015, A-reum >> Min wrote: >> >> hello experts!my name >> is areum. >> i have some question >> to you. >> a few days ago i was >> down load HCP(human >> connectom >> project) data. >> but.. how can i use >> these HCP format. >> i have never seen >> before these >> format(fig.1.png) >> I want to see HCP data >> subjects's >> cortical thickness >> using qdec. >> how can i to do? >> plz answer me >> >> 2015-11-10 7:49 >> GMT+09:00 A-reum Min >> <naniy...@gmail.com>: >> Hello experts! >> I have some question >> to you.. >> >> I don't need to show >> up so small blue >> regions(fig.1 >> blue region) >> >> How can i control >> these? >> >> 2015-11-10 7:41 >> GMT+09:00 Douglas N >> Greve >> >> <gr...@nmr.mgh.harvard.edu>: >> Hi, please >> create a new thread >> since this is a >> new topic. >> Also, I don't >> understand your >> question so please >> elaborate. >> >> On 11/09/2015 >> 05:34 AM, A-reum Min >> wrote: >> > Hello experts! >> > >> > i have some >> question to you.. >> > >> > How can i >> control the cluster >> size? >> > >> > My cluster >> threshold is 1. >> > >> > then, too many >> blue regions (as >> shown >> fig.1). >> > >> > so, i want to >> control cluster >> threshold 1--> >> cluster >> threshold 5. >> > >> > 2015-11-08 >> 20:44 GMT+09:00 >> A-reum Min >> >> <naniy...@gmail.com >> > >> <mailto:naniy...@gmail.com>>: >> > >> > Hello >> bruce! >> > >> > I solve >> the problem for your >> answer. >> > >> > And.. i >> have some question >> to you.. >> > >> > How can i >> control the >> cluster size? >> > >> > My cluster >> threshold is 1. >> > >> > then, too >> many blue regions >> (as shown >> fig.1). >> > >> > so, i want >> to control >> cluster threshold >> 1--> cluster >> threshold 5. >> > >> > How can i >> to do? >> > >> > >> > >> > >> > >> > 2015-11-05 >> 22:22 GMT+09:00 >> Bruce Fischl >> > >> <fis...@nmr.mgh.harvard.edu >> >> >> <mailto:fis...@nmr.mgh.harvard.edu>>: >> > >> > are >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >> > and >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >> > images >> from *different* >> series or >> from the >> *same* series? >> If >> > they >> are in the same >> series than >> that explains >> what is >> > >> happening. You should >> only give >> recon-all a >> single file from >> > any >> one acquisition - it >> will figure >> out the >> rest of the >> files >> > that >> are part of it. >> > >> > cheers >> > Bruce >> > >> > >> > On >> Thu, 5 Nov 2015, >> A-reum Min >> wrote: >> > >> > >> hello experts. >> > i >> have some question >> to you... >> > >> > >> when i enter the >> recon-all -i >> /paht~ >> > >> > >> error showed up.... >> like below >> one.. >> > >> > >> how can i to fix it? >> > >> > >> [areum@localhost >> 0165766_1]# >> recon-all -i >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >> -i >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >> > >> -all -s sub002 >> > >> Subject Stamp: >> > >> >> >> >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> > >> Current Stamp: >> > >> >> >> >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> > >> INFO: SUBJECTS_DIR >> is >> > >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1 >> > >> Actual >> FREESURFER_HOME >> /usr/local/freesurfer >> > >> Linux >> localhost.localdomain >> >> 2.6.32-504.el6.x86_64 #1 SMP >> > >> Wed Oct 15 04:27:16 >> > >> UTC 2014 x86_64 >> x86_64 x86_64 >> GNU/Linux >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 >> > >> > >> mri_convert >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >> > >> > >> > >> mri_convert >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >> > >> > >> $Id: mri_convert.c,v >> 1.179.2.7 >> 2012/09/05 >> 21:55:16 mreuter >> > >> Exp $ >> > >> reading from >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... >> > >> Starting >> DICOMRead2() >> > >> dcmfile = >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >> > >> dcmdir = >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1 >> > >> Ref Series No = 3 >> > >> Found 247 files, >> checking for >> dicoms >> > >> Found 244 dicom >> files in series. >> > >> First Sorting >> > >> Computing Slice >> Direction >> > >> Vs: -0.8 0 0 >> > >> Vs: -1 0 0 >> > >> Second Sorting >> > >> Counting frames >> > >> nframes = 1 >> > >> nslices = 244 >> > >> ndcmfiles = 244 >> > PE >> Dir = ROW (dicom >> read) >> > >> TransferSyntaxUID: >> >> --1.2.840.10008.1.2.1-- >> > >> Loading pixel data >> > >> TR=7.70, TE=3.37, >> TI=400.00, >> flip >> angle=12.00 >> > >> i_ras = (0, -1, 0) >> > >> j_ras = (0, 0, -1) >> > >> k_ras = (1, -0, 0) >> > >> writing to >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 >> > >> > >> mri_convert >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz >> > >> > >> > >> mri_convert >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz >> > >> > >> $Id: mri_convert.c,v >> 1.179.2.7 >> 2012/09/05 >> 21:55:16 mreuter >> > >> Exp $ >> > >> reading from >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... >> > >> Starting >> DICOMRead2() >> > >> dcmfile = >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >> > >> dcmdir = >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1 >> > >> Ref Series No = 3 >> > >> Found 247 files, >> checking for >> dicoms >> > >> Found 244 dicom >> files in series. >> > >> First Sorting >> > >> Computing Slice >> Direction >> > >> Vs: -0.8 0 0 >> > >> Vs: -1 0 0 >> > >> Second Sorting >> > >> Counting frames >> > >> nframes = 1 >> > >> nslices = 244 >> > >> ndcmfiles = 244 >> > PE >> Dir = ROW (dicom >> read) >> > >> TransferSyntaxUID: >> >> --1.2.840.10008.1.2.1-- >> > >> Loading pixel data >> > >> TR=7.70, TE=3.37, >> TI=400.00, >> flip >> angle=12.00 >> > >> i_ras = (0, -1, 0) >> > >> j_ras = (0, 0, -1) >> > >> k_ras = (1, -0, 0) >> > >> writing to >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... >> > >> >> >> #-------------------------------------------- >> > >> #@# MotionCor Thu >> Nov 5 >> 02:27:17 PST 2015 >> > >> Found 2 runs >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz >> > >> Checking for >> (invalid) >> multi-frame inputs... >> > >> Checking for >> (invalid) >> multi-frame inputs... >> > >> >> >> >> #----------------------------------------------- >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 >> > >> > >> mri_robust_template >> --mov >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz >> > >> --average 1 >> --template >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz >> > >> --satit >> > >> --inittp 1 --fixtp >> --noit >> --iscale >> > >> --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig >> / >> 0 >> 0 >> 1-iscale.txt >> > >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale >> . >> t >> x >> t >> > >> --subsample 200 >> --lta >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta >> > >> > >> > >> $Id: >> mri_robust_template.cpp,v >> 1.37.2.2 >> 2012/10/10 >> > >> 19:59:06 mreuter Exp >> $ >> > >> > >> --mov: Using >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >> > as >> > >> movable/source >> volume. >> > >> --mov: Using >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz >> > as >> > >> movable/source >> volume. >> > >> Total: 2 input >> volumes >> > >> --average: Using >> method 1 for >> template >> computation. >> > >> --template: Using >> > >> >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz >> > as >> > >> template output >> volume. >> > >> --satit: Will >> estimate SAT >> iteratively! >> > >> --inittp: Using TP 1 >> as target >> for >> initialization >> > >> --fixtp: Will map >> everything to >> init TP! >> > >> --noit: Will output >> only first >> template (no >> iterations)! >> > >> --iscale: Enableing >> intensity >> scaling! >> > >> --iscaleout: Will >> perform >> intensity scaling >> and output >> results >> > >> --subsample: Will >> subsample if >> size is >> larger than 200 >> on >> > >> all axes! >> > >> --lta: Will output >> LTA >> transforms >> > >> reading source >> > >> >> >> >> >> '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... >> > >> converting source >> > >> >> >> >> >> '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' >> > to >> > >> bspline ... >> > >> MRItoBSpline degree >> 3 >> > >> reading source >> > >> >> >> >> >> '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... >> > >> converting source >> > >> >> >> >> >> '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' >> > to >> > >> bspline ... >> > >> MRItoBSpline degree >> 3 >> > >> > >> MultiRegistration::initializing >> Xforms (init >> 1 , maxres 0 >> > , >> iterate 5 , >> > >> epsit 0.01 ) : >> > >> > >> [init] >> ========================= >> TP 2 to TP >> 1 >> > >> ============================== >> > >> Register TP >> 2 ( >> > >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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. > > -- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n <esth...@nate.com>aniy...@gmail.com
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