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 ( >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz >> > ) >> > to TP >> 1 ( >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >> > ) >> > >> > -- Original : >> (0.4688, >> 0.4688, >> 0.800001) mm size >> > and (512, 512, 244) >> > voxels. >> > -- Resampled: >> (0.4688, >> 0.4688, >> 0.4688) mm size and >> > (512, 512, 417) >> > voxels. >> > -- Reslicing >> using cubic >> bspline >> > MRItoBSpline degree >> 3 >> > -- Original : >> (0.4688, >> 0.4688, >> 0.800001) mm size >> > and (512, 512, 244) >> > voxels. >> > -- Resampled: >> (0.4688, >> 0.4688, >> 0.4688) mm size and >> > (512, 512, 417) >> > voxels. >> > -- Reslicing >> using cubic >> bspline >> > MRItoBSpline degree >> 3 >> > >> > - Max Resolution >> used: 3 >> > -- gpS ( 64 , >> 64 , 52 ) >> > -- gpT ( 64 , >> 64 , 52 ) >> > - running loop to >> estimate >> saturation >> parameter: >> > Sigma too small: 0 >> (identical >> images?) >> > Sigma too small: 0 >> (identical >> images?) >> > Sigma too small: 0 >> (identical >> images?) >> > Sigma too small: 0 >> (identical >> images?) >> > Sigma too small: 0 >> (identical >> images?) >> > Sigma too small: 0 >> (identical >> images?) >> > Sigma too small: 0 >> (identical >> images?) >> > Sigma too small: 0 >> (identical >> images?) >> > Sigma too small: 0 >> (identical >> images?) >> > Sigma too small: 0 >> (identical >> images?) >> > Killed >> > 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 >> > >> > recon-all -s sub002 >> exited with >> ERRORS at >> Thu Nov 5 >> > 02:37:57 PST 2015 >> > >> > For more details, >> see the log >> file >> > >> >> >> >> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log >> > To report a problem, >> see >> > >> >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> > >> > 2015-10-19 11:05 >> GMT+09:00 >> A-reum Min >> <naniy...@gmail.com >> > >> <mailto:naniy...@gmail.com>>: >> > hello experts. >> > i have a question to >> you.. >> > >> > i'm doing recon-all stage, >> but errors >> show up like >> this >> > >> > >> > >> > >> > >> ects/OSA/14/subj014/mri/orig/002.mgz >> --average 1 >> --template >> > >> >> /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz >> > --satit >> > --inittp 1 --fixtp --noit >> --iscale >> --iscaleout >> > >> >> >> /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt >> > >> >> >> /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt >> > --subsample 200 --lta >> > >> >> >> /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta >> > >> >> >> /usr/local/freesurfer/subjects/OSA/14/subj014/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/14/subj014/mri/orig/001.mgz >> > as >> > movable/source volume. >> > --mov: Using >> > >> >> >> /usr/local/freesurfer/subjects/OSA/14/subj014/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/14/subj014/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/14/subj014/mri/orig/001.mgz'... >> > converting source >> > >> >> >> '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' >> > to >> > bspline ... >> > MRItoBSpline degree 3 >> > reading source >> > >> >> >> '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... >> > converting source >> > >> >> >> '/usr/local/freesurfer/subjects/OSA/14/subj014/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 ( >> > >> >> >> /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz >> > ) >> > to TP 1 ( >> > >> >> >> /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz >> > ) >> > >> > -- Original : >> (0.4688, 0.4688, >> 0.800001) mm >> size >> > and (512, 512, >> > 244) voxels. >> > -- Resampled: >> (0.4688, 0.4688, >> 0.4688) mm >> size and >> > (512, 512, >> > 417) voxels. >> > -- Reslicing using >> cubic >> bspline >> > MRItoBSpline degree 3 >> > -- Original : >> (0.4688, 0.4688, >> 0.800001) mm >> size >> > and (512, 512, >> > 244) voxels. >> > -- Resampled: >> (0.4688, 0.4688, >> 0.4688) mm >> size and >> > (512, 512, >> > 417) voxels. > > > _______________________________________________ > 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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