for asymmetryc, see https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 03/04/2016 09:28 AM, A-reum Min wrote: > 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 > <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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> > > > <mailto: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> > > > <mailto: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 > <mailto: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 <mailto:esth...@nate.com>aniy...@gmail.com > <mailto:aniy...@gmail.com> > > > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
