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:
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:
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.
Why isn't the same number of total vertices? is it related rain size?
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: 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>: 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>: 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>: 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>>: > > 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>>: > > 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 <naniyaah@gmail.com > <mailto:naniyaah@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.
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-- *------------------------------------------------------------* *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 esthekr@nate.comaniyaah@gmail.com