Re: [Freesurfer] image matrix
Hi,
Thank you for your response! I use the command what you said.
The terminal shows:
euler # = v-e+f = 2g-2: 154901 - 464697 + 309798 = 2 --> 0 holes
F =2V-4: 309798 = 309802-4 (0)
2E=3F:929394 = 929394 (0)
I guess that 929394 is the vertices number of surface which I want to get.
Right? If not, which value is I want to get?
Then, I run lh.orig and another subjects, I find the value is different from
those. So, the vertices number of surface is not a fixed value and changes
with hemispheres and subjects.
Thank you in advance!!
Feng-Xian
On Wed, 8 Jul 2009 17:19:20 -0400 (EDT), Bruce Fischl wrote
> what is noise0.5_0? It isn't a surface file given the output of
> mris_euler_number. Try running
>
> mris_euler_number rh.orig
>
> On Thu, 9 Jul 2009, Feng-Xian wrote:
>
> > Hi,
> > Thank you for your response! But, I canÿÿt find vertices number of a
> > surface through typing the following command:
> > mris_euler_number noise0.5_0
> >
> > When I type the command, the terminal shows some information as follow.
> >
> > euler # = v-e+f = 2g-2: 0 - 0 + 0 = 0 --> 1 holes
> > F =2V-4: 0 != 0-4 (-4)
> > 2E=3F:0 = 0 (0)
> > total defect index = 2
> >
> > But I donÿÿt know what meaning of the numbers is. Would you tell me?
> > And, have any other ways to get the vertices number of a surface?
> >
> > Then, I want to make sure that is image matrix 256 x 256 x 256?
> >
> > Thank you for in advance!!
> >
> > Feng-Xian
> >
> >
> > On Tue, 30 Jun 2009 07:39:31 -0400 (EDT), Bruce Fischl wrote
> >> Hi Feng-Xian,
> >>
> >> the surfaces all live in the surf subdirectory. To see how many
> >> vertices a surface contains you can run either mris_euler_numer of
> >> mris_info. The thickness is in the ?h.thickness ("curv" format file -
> >> one scalar per vertex) and the inflated is in ?h.inflated surface
> >> format. You can visualize the thickness in tksurfer by loading the
> >> inflated surface then loading the thickness from the file menu using
> >> the load curvature option.
> >>
> >> cheers
> >> Bruce
> >>
> >> On Tue, 30 Jun 2009, Feng-Xian wrote:
> >>
> >>>
> >>> Hi,
> >>> I want to check the image matrix after doing autorecon-all. When I
look
> >>> at the text, I see that ÿÿOriginal Data has (1, 1, 1) mm size and (224,
> > 256,
> >>> 160) voxels. Data is conformed to 1 mm size and 256 voxels for all
> >>> directionsÿÿ. This is said that that image matrix is 256 x 256 x 256.
> > Right?
> >>>
> >>> And, I want to know how many voxels do an inflated surface have?
Where
> >>> dir and what text do I to get that?
> >>>
> >>> And, do FreeSurfer have a text that including the value of cortical
> >>> thickness? I want to know the information of cortical thicknessÿÿs
value
> > at
> >>> all pixels of whole brain for each subject. If yes, what text has the
> >>> information of the value of cortical thickness and where do I find that
> >>> text? If no, how can I get the information?
> >>>
> >>> Thank you in advance!
> >>>
> >>> Feng-Xian
> >>>
> >>>
> >>> -
> >>> Chang Gung University Mail Server Web Mail system
> >>> By Chang-Gung University Information Center
> >>> (http://www.cgu.edu.tw/ic/)
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>>
> >
> >
> > -
> > Chang Gung University Mail Server Web Mail system
> > By Chang-Gung University Information Center
> > (http://www.cgu.edu.tw/ic/)
> >
> >
> >
-
Chang Gung University Mail Server Web Mail system
By Chang-Gung University Information Center
(http://www.cgu.edu.tw/ic/)
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Re: [Freesurfer] 4D to 3D
Hi Mayuresh, I think if you do: mri_convert lh.gender_age.thickness.00.mgh#0 lh.thickness.subject0.mgh you will extract the first frame (or #1 for the second, etc...). cheers, Bruce On Thu, 9 Jul 2009, Mayuresh Korgaonkar wrote: Dear Freesurfer authors, I have been working with the command line group analysis tutorial from the freesurfer wiki website. Unfortunately I did not "qcached" my data with recon-all. So I ran the "mris_preproc" and "mri_surf2surf" commands from the tutorial (see below) at the end of which I get a single 4D file "lh.gender_age.thickness.10B.mgh" concatenated over all subjects Is there a way to split this file into 3D files so that I have a thickness file for each individual subject? Thanks, Mayuresh mris_preproc --fsgd gender_age.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.gender_age.thickness.00.mgh mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.gender_age.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.gender_age.thickness.10B.mgh Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Surface based volumetry vs Voxel based morphometry
no, all that stuff helps the surface positioning. The MRF is a separate thing that happens before most of that On Thu, 9 Jul 2009, Pedro Paulo de Magalhães Oliveira Junior wrote: So the topology fix, spherical registration, etc. help the positioning for the random markov field algorithm? And in the VBM we don't have this aid. Is that correct? 2009/7/9, Bruce Fischl : Hi PPJ we don't use surface-based stuff for subcortical structures, although at some point we probably will. In general the surfaces are more accurate cortically as they let you do subvoxel positioning. I think the advantage for subcortical structures is that we have strong priors on both the intensity distributions and the spatial locations of structures such as putamen, pallidum, etc cheers, Bruce On Thu, 9 Jul 2009, Pedro Paulo de Magalhães Oliveira Junior wrote: It's more a methodological question, and I have asked this before, but I think it could be better discussed in the FreeSurfer community. Several times people ask me what's the advantage of Surface based methods like the ones used in FreeSurfer over VBM in estimating volumetric parameters of subcortical structures. The plain question people ask me is: what`s the advantage of FreeSurfer over SPM in terms of volumetric measures. I have some answers for this. I have wrote something about in the FAQ of FreeSurfer but I was wondering if there's some comparative study or some better idea on this. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 4D to 3D
Dear Freesurfer authors, I have been working with the command line group analysis tutorial from the freesurfer wiki website. Unfortunately I did not "qcached" my data with recon-all. So I ran the "mris_preproc" and "mri_surf2surf" commands from the tutorial (see below) at the end of which I get a single 4D file "lh.gender_age.thickness.10B.mgh" concatenated over all subjects Is there a way to split this file into 3D files so that I have a thickness file for each individual subject? Thanks, Mayuresh mris_preproc --fsgd gender_age.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.gender_age.thickness.00.mgh mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.gender_age.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.gender_age.thickness.10B.mgh Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Surface based volumetry vs Voxel based morphometry
So the topology fix, spherical registration, etc. help the positioning for the random markov field algorithm? And in the VBM we don't have this aid. Is that correct? 2009/7/9, Bruce Fischl : > Hi PPJ > > we don't use surface-based stuff for subcortical structures, although at > some point we probably will. In general the surfaces are more accurate > cortically as they let you do subvoxel positioning. I think the advantage > for subcortical structures is that we have strong priors on both the > intensity distributions and the spatial locations of structures such as > putamen, pallidum, etc > > cheers, > Bruce > > On Thu, 9 Jul 2009, Pedro Paulo de Magalhães Oliveira > Junior wrote: > >> It's more a methodological question, and I have asked this before, but I >> think it could be better discussed in the FreeSurfer community. >> >> Several times people ask me what's the advantage of Surface based methods >> like the ones used in FreeSurfer over VBM in estimating volumetric >> parameters of subcortical structures. >> >> The plain question people ask me is: what`s the advantage of FreeSurfer >> over >> SPM in terms of volumetric measures. >> >> I have some answers for this. I have wrote something about in the FAQ of >> FreeSurfer but I was wondering if there's some comparative study or some >> better idea on this. >> >> >> --- >> Pedro Paulo de M. Oliveira Junior >> Diretor de Operações >> Netfilter & SpeedComm Telecom >> --- Novo Netfilter 3.0 www.Netfilter.com.br >> --- Em breve Netfilter Small Business >> -- Enviado do meu celular --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Surface based volumetry vs Voxel based morphometry
Hi PPJ we don't use surface-based stuff for subcortical structures, although at some point we probably will. In general the surfaces are more accurate cortically as they let you do subvoxel positioning. I think the advantage for subcortical structures is that we have strong priors on both the intensity distributions and the spatial locations of structures such as putamen, pallidum, etc cheers, Bruce On Thu, 9 Jul 2009, Pedro Paulo de Magalhães Oliveira Junior wrote: It's more a methodological question, and I have asked this before, but I think it could be better discussed in the FreeSurfer community. Several times people ask me what's the advantage of Surface based methods like the ones used in FreeSurfer over VBM in estimating volumetric parameters of subcortical structures. The plain question people ask me is: what`s the advantage of FreeSurfer over SPM in terms of volumetric measures. I have some answers for this. I have wrote something about in the FAQ of FreeSurfer but I was wondering if there's some comparative study or some better idea on this. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all taking long time
this is almost certainly a bug that is fixed in the current version. Try updating and let us know if it doesn't fix the problem On Thu, 9 Jul 2009, Barnali Basu wrote: Experts, I have been working on Freesurfer last 5 months and initially the recon processes were within normal time limits. However, I am working on a different set of subjects now and its consuming days together. For my current data,autorecon1 is fine, it stops at a particular point in autorecon2 for infinity. Any suggestions would be helpful. I am pasting the autorecon2 process here: recon-all -autorecon2 -subjid jaSubject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 barnali barnali 257784 Jul 9 10:32 /usr/local/freesurfer/subjects/ja/scripts/recon-all.log Linux barnali-work 2.6.24-16-server #1 SMP Thu Apr 10 13:58:00 UTC 2008 i686 GNU/Linux #- #...@# EM Registration Thu Jul 9 10:35:21 PDT 2009 /usr/local/freesurfer/subjects/ja/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) spacing=8, using 2185 sample points, tol=1.00e-05... register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=8.0 using (107, 91, 112) as brain centroid... mean wm in atlas = 107, using box (90,77,91) --> (123, 104,132) to find MRI wm before smoothing, mri peak at 137 after smoothing, mri peak at 151, scaling input intensities by 0.709 scaling channel 0 by 0.708609 initial log_p = -92132.8 First Search limited to translation only. Found translation: (-2.8, -1.7, 1.7): log p = -39503.6 Nine parameter search. iteration 0 nscales = 0 ... Result so far: scale 1.000: max_log_p=-37619.9, old_max_log_p =-39503.6 (thresh=-39464.1) 1.062 0.000 0.000 -10.944; 0.000 1.053 0.139 -22.515; 0.000 -0.131 0.991 18.328; 0.000 0.000 0.000 1.000; Nine parameter search. iteration 1 nscales = 0 ... Result so far: scale 1.000: max_log_p=-35219.5, old_max_log_p =-37619.9 (thresh=-37582.3) 1.062 0.000 0.000 -10.944; 0.000 1.266 0.027 -29.117; 0.000 0.025 1.003 -1.688; 0.000 0.000 0.000 1.000; Nine parameter search. iteration 2 nscales = 0 ... Result so far: scale 1.000: max_log_p=-35219.5, old_max_log_p =-35219.5 (thresh=-35184.3) 1.062 0.000 0.000 -10.944; 0.000 1.266 0.027 -29.117; 0.000 0.025 1.003 -1.688; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 Nine parameter search. iteration 3 nscales = 1 ... Result so far: scale 0.250: max_log_p=-32338.2, old_max_log_p =-35219.5 (thresh=-35184.3) 1.096 0.000 0.000 -15.249; 0.000 1.208 0.026 -25.944; 0.000 0.026 1.035 -8.782; 0.000 0.000 0.000 1.000; Nine parameter search. iteration 4 nscales = 1 ... Result so far: scale 0.250: max_log_p=-31970.6, old_max_log_p =-32338.2 (thresh=-32305.8) 1.096 0.000 0.000 -17.124; 0.000 1.189 0.025 -21.806; 0.000 0.026 1.035 -6.907; 0.000 0.000 0.000 1.000; Nine parameter search. iteration 5 nscales = 1 ... Result so far: scale 0.250: max_log_p=-31970.6, old_max_log_p =-31970.6 (thresh=-31938.6) 1.096 0.000 0.000 -17.124; 0.000 1.189 0.025 -21.806; 0.000 0.026 1.035 -6.907; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 Nine parameter search. iteration 6 nscales = 2 ... Result so far: scale 0.062: max_log_p=-31028.4, old_max_log_p =-31970.6 (thresh=-31938.6) 1.083 0.000 0.000 -14.039; 0.000 1.194 0.025
[Freesurfer] recon-all taking long time
Experts, I have been working on Freesurfer last 5 months and initially the recon processes were within normal time limits. However, I am working on a different set of subjects now and its consuming days together. For my current data,autorecon1 is fine, it stops at a particular point in autorecon2 for infinity. Any suggestions would be helpful. I am pasting the autorecon2 process here: recon-all -autorecon2 -subjid jaSubject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 barnali barnali 257784 Jul 9 10:32 /usr/local/freesurfer/subjects/ja/scripts/recon-all.log Linux barnali-work 2.6.24-16-server #1 SMP Thu Apr 10 13:58:00 UTC 2008 i686 GNU/Linux #- #...@# EM Registration Thu Jul 9 10:35:21 PDT 2009 /usr/local/freesurfer/subjects/ja/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) spacing=8, using 2185 sample points, tol=1.00e-05... register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=8.0 using (107, 91, 112) as brain centroid... mean wm in atlas = 107, using box (90,77,91) --> (123, 104,132) to find MRI wm before smoothing, mri peak at 137 after smoothing, mri peak at 151, scaling input intensities by 0.709 scaling channel 0 by 0.708609 initial log_p = -92132.8 First Search limited to translation only. Found translation: (-2.8, -1.7, 1.7): log p = -39503.6 Nine parameter search. iteration 0 nscales = 0 ... Result so far: scale 1.000: max_log_p=-37619.9, old_max_log_p =-39503.6 (thresh=-39464.1) 1.062 0.000 0.000 -10.944; 0.000 1.053 0.139 -22.515; 0.000 -0.131 0.991 18.328; 0.000 0.000 0.000 1.000; Nine parameter search. iteration 1 nscales = 0 ... Result so far: scale 1.000: max_log_p=-35219.5, old_max_log_p =-37619.9 (thresh=-37582.3) 1.062 0.000 0.000 -10.944; 0.000 1.266 0.027 -29.117; 0.000 0.025 1.003 -1.688; 0.000 0.000 0.000 1.000; Nine parameter search. iteration 2 nscales = 0 ... Result so far: scale 1.000: max_log_p=-35219.5, old_max_log_p =-35219.5 (thresh=-35184.3) 1.062 0.000 0.000 -10.944; 0.000 1.266 0.027 -29.117; 0.000 0.025 1.003 -1.688; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 Nine parameter search. iteration 3 nscales = 1 ... Result so far: scale 0.250: max_log_p=-32338.2, old_max_log_p =-35219.5 (thresh=-35184.3) 1.096 0.000 0.000 -15.249; 0.000 1.208 0.026 -25.944; 0.000 0.026 1.035 -8.782; 0.000 0.000 0.000 1.000; Nine parameter search. iteration 4 nscales = 1 ... Result so far: scale 0.250: max_log_p=-31970.6, old_max_log_p =-32338.2 (thresh=-32305.8) 1.096 0.000 0.000 -17.124; 0.000 1.189 0.025 -21.806; 0.000 0.026 1.035 -6.907; 0.000 0.000 0.000 1.000; Nine parameter search. iteration 5 nscales = 1 ... Result so far: scale 0.250: max_log_p=-31970.6, old_max_log_p =-31970.6 (thresh=-31938.6) 1.096 0.000 0.000 -17.124; 0.000 1.189 0.025 -21.806; 0.000 0.026 1.035 -6.907; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 Nine parameter search. iteration 6 nscales = 2 ... Result so far: scale 0.062: max_log_p=-31028.4, old_max_log_p =-31970.6 (thresh=-31938.6) 1.083 0.000 0.000 -14.039; 0.000 1.194 0.025 -22.828; 0.000 0.026 1.039 -7.345; 0.000 0.000 0.000 1.000; Nine parameter search. iterat
[Freesurfer] Surface based volumetry vs Voxel based morphometry
It's more a methodological question, and I have asked this before, but I think it could be better discussed in the FreeSurfer community. Several times people ask me what's the advantage of Surface based methods like the ones used in FreeSurfer over VBM in estimating volumetric parameters of subcortical structures. The plain question people ask me is: what`s the advantage of FreeSurfer over SPM in terms of volumetric measures. I have some answers for this. I have wrote something about in the FAQ of FreeSurfer but I was wondering if there's some comparative study or some better idea on this. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] pial surface
Hi Barnali, what do you mean you "don't get to see the pial surface"? If you type: tksurfer lh pial does it not show the pial? If it finished autorecon3 it should have a pial surface for both hemis. cheers Bruce On Thu, 9 Jul 2009, Barnali Basu wrote: Experts, I have successfully run recon-all (all the 3 processes autorecon1,2 and 3) on a subject. When I see the surfaces on tksurfer, I dont get to see the pial surface. I gather I could construct Pial surface by running autorecon2-pial. Would this affect in any way, since I have already finished autorecon3. Do I have to run autorecon3 again ? Any help would be appreciated Thanks Barnali ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] pial surface
Experts, I have successfully run recon-all (all the 3 processes autorecon1,2 and 3) on a subject. When I see the surfaces on tksurfer, I dont get to see the pial surface. I gather I could construct Pial surface by running autorecon2-pial. Would this affect in any way, since I have already finished autorecon3. Do I have to run autorecon3 again ? Any help would be appreciated Thanks Barnali ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec question
The newest version of FreeSurfer does not contain any changes to qdec I believe. Allison -- On Thu, 9 Jul 2009, Prapti Gautam wrote: Dear Freesurfers, I just have some quick questions regarding qdec: 1. How many covariates does the latest version of qdec allow you to select? I am using FS version 4.3.0 and I cannot select more than 2 continuous variables. I am just wondering if a newer version allows you to select more covariates. 2. Does qdec allow you to choose between study designs DOSS and DODS? I currently do not see this option and I think my current version of qdec defaults to the DODS option. Thank you for your time, Prapti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
it means that an autorecon? was started for that subject and never finished. You should be able to do recon-all -make all -s and it will redo what it needs to On Thu, 9 Jul 2009, Kirk Gregory R. wrote: hi q. from a collaborator, someone got a comment for 1 subject the # of vertices of sphere file different from the length of thickness data for the same subject. thanks Greg. -Original Message- From: Deepti Pachauri [mailto:deepti.pacha...@gmail.com] Sent: Wed 6/24/2009 1:02 AM To: Kirk Gregory R. Subject: Re: Help Deepti with some questions Dear Greg I have been looking at FreeSurfer data provided by you for 21 subjects(AD/Control). For P1_AD subject I found the # of vertices of sphere file different from the length of thickness data for the same subject. # of vertices for P1.AD subject are 131364 and length of thickness data for the same subject is 131215. However for rest 20 subjects # of vertices and length of thickness data are same. I am using MATLAB to read thickness.asc data and last column is thickness (mm) at given x,y,z. For vertices and faces I am using the standard freesurfer_read_surf.m form http://eeg.sourceforge.net/doc_m2html/bioelectromagnetism/freesurfer_read_surf.html I am just wondering how to fix this discrepancy of freesurfer output? Also thickness data P10 is missing in asc folder. Sphere and pial files are present in surf folder for P10 subject. Thanks On Tue, Jun 23, 2009 at 3:55 PM, Vikas Singh wrote: Hi Greg, Deepti, a new CS grad student (copied on this email) is studying the cortical surface characterization problem, and using the output you generated. Is is possible that you can answer some of her questions regarding FreeSurfer? I am copying her on this email. I am out of town until July 16th, and we wanted to get on top of this over the summers. Please let us know, possibly with a phone number she can reach you at. regards, Vikas. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
hi q. from a collaborator, someone got a comment for 1 subject the # of vertices of sphere file different from the length of thickness data for the same subject. thanks Greg. -Original Message- From: Deepti Pachauri [mailto:deepti.pacha...@gmail.com] Sent: Wed 6/24/2009 1:02 AM To: Kirk Gregory R. Subject: Re: Help Deepti with some questions Dear Greg I have been looking at FreeSurfer data provided by you for 21 subjects(AD/Control). For P1_AD subject I found the # of vertices of sphere file different from the length of thickness data for the same subject. # of vertices for P1.AD subject are 131364 and length of thickness data for the same subject is 131215. However for rest 20 subjects # of vertices and length of thickness data are same. I am using MATLAB to read thickness.asc data and last column is thickness (mm) at given x,y,z. For vertices and faces I am using the standard freesurfer_read_surf.m form http://eeg.sourceforge.net/doc_m2html/bioelectromagnetism/freesurfer_read_surf.html I am just wondering how to fix this discrepancy of freesurfer output? Also thickness data P10 is missing in asc folder. Sphere and pial files are present in surf folder for P10 subject. Thanks On Tue, Jun 23, 2009 at 3:55 PM, Vikas Singh wrote: > Hi Greg, > > Deepti, a new CS grad student (copied on this email) is studying the > cortical surface characterization problem, and using the output you > generated. Is is possible that you can answer some of her questions > regarding FreeSurfer? I am copying her on this email. I am out of town > until July 16th, and we wanted to get on top of this over the summers. > Please let us know, possibly with a phone number she can reach you at. > > regards, > > Vikas. > -- Deepti Pachauri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation
Hi Gregory, it's hard to tell accuracy looking at one slice, but that one looks fine. Note that we do not generally use the cortical segmentation in the aseg - for that we use the surfaces. So if you want to assess accuracy you should overlay the ?h.white and ?h.pial surfaces and see if cortical gray matter is accurately contained between them. cheers, Bruce On Thu, 9 Jul 2009 si...@cyceron.fr wrote: Hi. I'm a new user of freesurfer. The default settings of recon-all performed a good white segmentation of my data but I find that grey matter (see attached picture) could be optimized when I look at aseg.mgz results. Indeed the surface cortical grey matter was not extend as expected. What were the different parameters that I can optimize to have a better grey matter segmentation without manual correction? Thank a lot for your answers. Gregory SIMON ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] contrast matrix
Hi, I think that I know what you mean. So, if I want to get the result with A > B > C, I should get A > B and B > C, respectively. And then, to combine these two results. Would you tell me detail with step by step and what command I should type and how to type ? Or, have some reference to follow or to consult? Thank you in advance!! Feng-Xian On Wed, 08 Jul 2009 15:28:44 -0400, Douglas N Greve wrote > You can't do that with a contrast matrix. In general, you can't test > "ANDs" with a contrast, you have to test "ORs". For AND, you have to > use a conjunction in which you make two contrasts A > B and B > C, > threshold both (mri_binarize), then do a logical AND. > > doug > > Feng-Xian wrote: > > Hi, > > I want to analysis three independence groups. And, I want to display a > > result of A group > B group > C group with positive(red) and A group < B > > group < C group with negative(blue). To show that, how do I write the number > > of columns in the contrast matrix? > > > > Thank you in advance! > > > > Feng-Xian > > > > > > > > - > > Chang Gung University Mail Server Web Mail system > > By Chang-Gung University Information Center > > (http://www.cgu.edu.tw/ic/) > > > > ___ > > 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 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
