[Freesurfer] Label boundary
Hi, Is there any freesurfer utility to isolate/plot the vertices that form the boundary of any label ? If no, how can one go about doing this ? Thank you. Shriks Forgot the famous last words? Access your message archive online at http://in.messenger.yahoo.com/webmessengerpromo.php___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Label boundary
Hi Shriks, tksurfer can do this by clicking the label outline button. Is that what you mean? The boundary is just the set of points that are in the label that nbr points not in the label. cheers, Bruce On Fri, 28 Mar 2008, SHRIKANTH KULASHEKHAR wrote: Hi, Is there any freesurfer utility to isolate/plot the vertices that form the boundary of any label ? If no, how can one go about doing this ? Thank you. Shriks Forgot the famous last words? Access your message archive online at http://in.messenger.yahoo.com/webmessengerpromo.php ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] purpose of creating own "average subject"
Good points! I (partly) see the light :) Still (please correct me if I'm wrong), creating a study specific average subject for visualizing the "average" anatomy doesn't address the issue of whether the method by which those subjects were brought into register (i.e., via sphere.reg using a term in the energy functional based on the buckner40 sulcal patterns) is indeed "appropriate" for the subjects under study. Which leads me to inquire: Do you know if anyone has looked at the "robustness" of the buckner40 registration target relative to other study populations and demographics? (I imagine that this would have to be an empirical question). Anyone out there that has created their own registration target? If yes, and you're willing to share, I think this (or any other alternative atlases such as customized volume gca, or surface gcs classifiers) would be a great contribution to the FS community. I know users have queried about the possibility of creating their own targets and/or classifiers, but has anyone actually created one or is in the process of doing so?? cheers, Mike H. On Thu, 2008-03-27 at 14:21 -0400, Bruce Fischl wrote: > Hi Mike, > > imagine you had only on subject your study. Then using the buckner > atlas as an overlay (or fsaverage, which is kind of equivalent) would not > be representative at all. If the registration works perfectly and you have > a fair number of subjects then there probably isn't much difference, but > there's really no reason *not* to visualize on the average anatomy of your > subjects, except to make cross-study comparisons easier. > > cheers, > Bruce > > > On Thu, 27 Mar 2008, Michael Harms wrote: > > > > > Hi Bruce, > > > > Re your 2nd point: My assumption was that very few FS users are actually > > creating their own atlases. To do that you need to do (much) more than > > just run make_average_subject, right? (Namely, create your own .gcs > > file for annotations, and .tif for registration, correct? And isn't > > that quite an involved process?) > > > > Re your 1st point: As for a truer anatomical visualization (without > > deriving your own atlas), it seems that is predicated on the assumption > > that the buckner40 based registration is representative of the > > population under study in the first place (so that the subsequent > > averaging to the buckner40 target is indeed appropriate for the > > population under study). And, if you're making this assumption, > > shouldn't the average white, pial, curv, sulc, etc. files derived from > > buckner40 by extension already be "representative" as well? In which > > case, I'm still left wondering why bother with making your own average > > subject? It seems that unless you go all-out and create your own > > atlases, you'll always be left wondering if the registration was truly > > appropriate for the population under study, and thus by extension > > whether the "average" surfaces are truly "representative" as well. > > > > (I guess that technically, the key assumption is that the sulcal > > pattern, and its variance, are consistent across populations in order > > for the buckner40 based registration to be appropriate as the basis for > > creating your own average subject. But again, without ever actually > > computing your registration atlas, how would you ever know if this was > > in fact true?) > > > > thanks for helping me understand this, > > Mike H. > > > > On Thu, 2008-03-27 at 13:16 -0400, Bruce Fischl wrote: > >> Hi Mike, > >> > >> a couple of things. One is that creating your own average will give you a > >> better ability to see what the true anatomical localization of your effects > >> are. Another is that you can re-register your subjects to your own atlas, > >> and possibly obtain better registration, particularly if your population is > >> substantially different from the ones in our atlas (e.g. young kids maybe). > >> > >> cheers, > >> Bruce > >> > >> > >> On Thu, 27 Mar 2008, Michael Harms wrote: > >> > >>> > >>> Hello, > >>> There have been numerous posts recently related to the creation of a > >>> study specific "average subject". I have a question about the > >>> purpose/motivation of this for surface-stream analysis/visualization > >>> that I was hoping someone could clarify. > >>> > >>> Specifically, my understanding is that the annotation/labels for any > >>> derived study specific average subject are determined by the "buckner40" > >>> gcs file (for the case of the desikan atlas). And similarly, the > >>> average surface (e.g., white, pial) and curvature-format files (e.g., > >>> curv, sulc, thickness) are registered across subjects via sphere.reg, > >>> which is determined by ?h.curvature.filled.buckner40.tif? > >>> > >>> So, since the annotation and registration for any study specific > >>> "average subject" is going to be determined by the "buckner40" set of > >>> subjects regardless of the specific subjects in a particular study, what > >>> is the purpose, advanta
[Freesurfer] Error
Hi, We are getting an error where our preprocessing step seems to be failing, any help would be greatly appreciated, thank you! *running from the following directory /autofs/homes/014/jake/AnalysisPrograms *using the following command (which sources /usr/local/freesurfer/nmr-stable3-env) striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh *error: --- Parsing Config File: /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg -gammafit 2.25 1.25 -timewindow 25. -prestim 0 -polyfit 1 -TER 2.5000 -nskip 0 -fwhm 0 -rescale 1000 ERROR: 022/fmcsm4 does not have a .meanval file, run inorm ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): selxavg failed ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat -- stxgrinder-sess logfile is /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log -- ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 **The logfile for preprocessing can be found in: /autofs/space/meso_018/users/ablood/cerv/log striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log ***Here is the error from the logfile: to3d WARNING: Significant outliers detected in these sub-bricks: 60 103 104 105 106 107 108 120 122 You should inspect the dataset for possible corruption. [Outliers are defined as in program 3dToutcount. ] [Outliers early in an EPI time series may be due to ] [the longitudinal magnetization equilibration effect.] [Other causes are subject movement, scanner problems,] [or anything that makes a time series look irregular.] [ 3dToutcount -save outnam dataset | 1dplot -stdin ] [can be used to make a dataset 'outnam' that marks ] [outlier voxels; see 3dToutcount -help for details. ] ++ 3D dataset written to disk -- Motion Correcting --- /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp set VR = 3dvolreg 3dvolreg -verbose -dfile /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] 6776+orig ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] ++ Authored by: RW Cox ++ Reading in base dataset ./targ-6776+orig.BRIK ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same dimensi ons! Input: nx=64 ny=64 nz=30 Base: nx=64 ny=64 nz=16 ** FATAL ERROR: perhaps you could make your datasets match? set st = 1 if ( 1 ) then echo ERROR: 3dvolreg existed with status 1 ERROR: 3dvolreg existed with status 1 exit 1 ERROR: mc-sess failed Thanks, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Fwd: Re: [Freesurfer] Error]
Hi, Thanks for the bugr command. Here is my information, Thank you! Please include the following additional information in your report: 1) subject name: CD_aftbotox_ctrl5 2) the entire command-line executed csh CD_aftbotox_ctrl5_ContrastAnalysis.csh 3) the error message generated (please see below, our preprocessing step is built into our csh file.) 4) optionally include the subject's /script/recon-all.log **The logfile for preprocessing can be found in: > /autofs/space/meso_018/users/ablood/cerv/log > striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log - FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects ***(this is set to be /space/meso/18/users/ablood/cerv by the .csh script) PWD: /homes/14/jake/AnalysisPrograms - Original Message Subject: Re: [Freesurfer] Error From:"Pratap Kunwar" <[EMAIL PROTECTED]> Date:Fri, March 28, 2008 12:00 pm To: [EMAIL PROTECTED] -- Jake, Are you doing preprocessing or stxgrinder, and are you running from > *running from the following directory > /autofs/homes/014/jake/AnalysisPrograms or /autofs/space/meso_018/users/ablood/cerv/ ? it will be nice if you provide more info. use "bugr" to get report and send to freesurfer. about bugreporting, https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?action=highlight&value=bugr pratap > Hi, > > We are getting an error where our preprocessing step seems to be failing, > any help would be greatly appreciated, thank you! > > > > *using the following command (which sources > /usr/local/freesurfer/nmr-stable3-env) > striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh > > *error: > --- Parsing Config File: > /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg > > -gammafit 2.25 1.25 -timewindow 25. -prestim 0 -polyfit 1 -TER 2.5000 > -nskip 0 -fwhm 0 -rescale 1000 > ERROR: 022/fmcsm4 does not have a .meanval file, run inorm > ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): > selxavg failed > ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat > -- > stxgrinder-sess logfile is > /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log > -- > ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 > > > > > > > > **The logfile for preprocessing can be found in: > /autofs/space/meso_018/users/ablood/cerv/log > striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log > > ***Here is the error from the logfile: > to3d WARNING: > Significant outliers detected in these sub-bricks: > 60 103 104 105 106 107 108 120 122 > You should inspect the dataset for possible corruption. > [Outliers are defined as in program 3dToutcount. ] > [Outliers early in an EPI time series may be due to ] > [the longitudinal magnetization equilibration effect.] > [Other causes are subject movement, scanner problems,] > [or anything that makes a time series look irregular.] > [ 3dToutcount -save outnam dataset | 1dplot -stdin ] > [can be used to make a dataset 'outnam' that marks ] > [outlier voxels; see 3dToutcount -help for details. ] > > ++ 3D dataset written to disk > -- Motion Correcting --- > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp > set VR = 3dvolreg > 3dvolreg -verbose -dfile > /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct > rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] > 6776+orig > ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] > ++ Authored by: RW Cox > ++ Reading in base dataset ./targ-6776+orig.BRIK > ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same > dimensi > ons! >Input: nx=64 ny=64 nz=30 >Base: nx=64 ny=64 nz=16 > ** FATAL ERROR: perhaps you could make your datasets match? > set st = 1 > if ( 1 ) then > echo ERROR: 3dvolreg existed with status 1 > ERROR: 3dvolreg existed with status 1 > exit 1 > ERROR: mc-sess failed > > > > > Thanks, > > Jake > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr
Re: [Fwd: Re: [Freesurfer] Error]
I apologize, the csh file is located in the home directory, /homes/14/jake/AnalysisPrograms Thanks > Hi, > > Thanks for the bugr command. Here is my information, Thank you! > > > Please include the following additional information in your report: > > 1) subject name: > > CD_aftbotox_ctrl5 > > 2) the entire command-line executed > > csh CD_aftbotox_ctrl5_ContrastAnalysis.csh > > 3) the error message generated (please see below, our preprocessing > step is built into our csh file.) > > 4) optionally include the subject's /script/recon-all.log > **The logfile for preprocessing can be found in: >> /autofs/space/meso_018/users/ablood/cerv/log >> striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log > > > - > > FREESURFER_HOME: /usr/local/freesurfer/stable3 > > Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 > > RedHat release: CentOS release 5 (Final) > > Kernel info: Linux 2.6.18-8.1.15.el5 i686 > > NMR Center info (/space/freesurfer exists): > > machine: striatum > > SUBJECTS_DIR: /space/sake/3/users/inverse/subjects > > ***(this is set to be /space/meso/18/users/ablood/cerv by the .csh script) > > PWD: /homes/14/jake/AnalysisPrograms > > - > > > > > > > Original Message > Subject: Re: [Freesurfer] Error > From:"Pratap Kunwar" <[EMAIL PROTECTED]> > Date:Fri, March 28, 2008 12:00 pm > To: [EMAIL PROTECTED] > -- > > Jake, > > Are you doing preprocessing or stxgrinder, and are you running from >> *running from the following directory >> /autofs/homes/014/jake/AnalysisPrograms > > or > /autofs/space/meso_018/users/ablood/cerv/ ? > > it will be nice if you provide more info. use "bugr" to get report and > send to freesurfer. > about bugreporting, > https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?action=highlight&value=bugr > > pratap > >> Hi, >> >> We are getting an error where our preprocessing step seems to be >> failing, >> any help would be greatly appreciated, thank you! >> >> > >> >> *using the following command (which sources >> /usr/local/freesurfer/nmr-stable3-env) >> striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh >> >> *error: >> --- Parsing Config File: >> /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg >> >> -gammafit 2.25 1.25 -timewindow 25. -prestim 0 -polyfit 1 -TER >> 2.5000 >> -nskip 0 -fwhm 0 -rescale 1000 >> ERROR: 022/fmcsm4 does not have a .meanval file, run inorm >> ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): >> selxavg failed >> ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat >> -- >> stxgrinder-sess logfile is >> /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log >> -- >> ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for >> /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5 >> >> >> >> >> >> >> >> **The logfile for preprocessing can be found in: >> /autofs/space/meso_018/users/ablood/cerv/log >> striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log >> >> ***Here is the error from the logfile: >> to3d WARNING: >> Significant outliers detected in these sub-bricks: >> 60 103 104 105 106 107 108 120 122 >> You should inspect the dataset for possible corruption. >> [Outliers are defined as in program 3dToutcount. ] >> [Outliers early in an EPI time series may be due to ] >> [the longitudinal magnetization equilibration effect.] >> [Other causes are subject movement, scanner problems,] >> [or anything that makes a time series look irregular.] >> [ 3dToutcount -save outnam dataset | 1dplot -stdin ] >> [can be used to make a dataset 'outnam' that marks ] >> [outlier voxels; see 3dToutcount -help for details. ] >> >> ++ 3D dataset written to disk >> -- Motion Correcting --- >> /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp >> set VR = 3dvolreg >> 3dvolreg -verbose -dfile >> /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct >> rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] >> 6776+orig >> ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] >> ++ Authored by: RW Cox >> ++ Reading in base dataset ./targ-6776+orig.BRIK >> ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same >> dimensi >> ons! >>Input: nx=64 ny=64 nz=30 >>Base: nx=64 ny=64 nz=16 >> ** FATAL ERROR: perhaps you could make your datasets match? >> set st = 1 >> if ( 1 ) then >> echo ERROR: 3dvolreg existed with status 1 >> ERROR: 3dvolreg existed with status 1 >> exit 1 >> ERROR: mc-sess failed >>
