4 Mar
2016
4 Mar
'16
10:36 a.m.
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 <naniyaah@gmail.com mailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 <naniyaah@gmail.com <mailto:naniyaah@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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 <fischl@nmr.mgh.harvard.edu <mailto:fischl@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 <naniyaah@gmail.com <mailto:naniyaah@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@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:esthekr@nate.com>aniyaah@gmail.com <mailto:aniyaah@gmail.com>
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