hello experts i have some question to you
Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..? Question 2. Left hemisphere whole vertices were extracted using a matlab. ( i read lh.thickness.fsaverage.mgh) i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png) what is that mean? plz answer me. 2016-02-13 5:19 GMT+09:00 A-reum Min <naniy...@gmail.com>: > 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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