Re: [Freesurfer] Difficulties with segmentation
Hi, sorry, I meant the cortical parcellation, the one that is used in aparc+aseg.mgz (I believe this uses the desikan killiany atlas?), thanks,JeffOn 6/20/06, Bruce Fischl <[EMAIL PROTECTED]> wrote: I'll leave 2 for Doug. In 1. by segmentation do you mean the wm.mgzvolume? Or the cortical parcellation? If the latter, which one (as wegenerate two by default).cheers,BruceOn Tue, 20 Jun 2006, Jeffrey Spielberg wrote:> Hi, I had a couple of questions regarding cortical/subcortical segmentation->> 1. In our cortical segmentation we keep getting what look to be inaccurate> segmentation of the rostral and caudal acc. It looks some of what should be > labeled as one of those two areas is getting labelled corpus callosum or> "unlabelled subcortical" instead, sometimes fairly large chunks. Does this> indicate any problem earlier in the processing stream, and is there anything > that can be done to prevent this? If not I saw that both tksurfer and> tkmedit can be used to edit the segmentation, what would be the easiest way> to do this?>> 2. When registering a freesurfer anatomical to Feat output (using > reg-feat2anat) the registration seems to be somewhat inaccurate.> Registering brainmask.mgz to our example_func using flirt has given us a> better registration so far. Since reg-feat2anat seems to use flirt in its > registration I was wondering what the difference might be resulting from.> Does reg-feat2anat use T1.mgz as it's reference scan, and if so is there any> way to have it use brainmask instead, as that seems to give better results? >>> Thanks,> Jeff> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Difficulties with segmentation
okay, Rahul is looking into it. On Wed, 21 Jun 2006, Jeffrey Spielberg wrote: Hi, sorry, I meant the cortical parcellation, the one that is used in aparc+aseg.mgz (I believe this uses the desikan killiany atlas?), thanks, Jeff On 6/20/06, Bruce Fischl <[EMAIL PROTECTED]> wrote: I'll leave 2 for Doug. In 1. by segmentation do you mean the wm.mgz volume? Or the cortical parcellation? If the latter, which one (as we generate two by default). cheers, Bruce On Tue, 20 Jun 2006, Jeffrey Spielberg wrote: > Hi, I had a couple of questions regarding cortical/subcortical segmentation- > > 1. In our cortical segmentation we keep getting what look to be inaccurate > segmentation of the rostral and caudal acc. It looks some of what should be > labeled as one of those two areas is getting labelled corpus callosum or > "unlabelled subcortical" instead, sometimes fairly large chunks. Does this > indicate any problem earlier in the processing stream, and is there anything > that can be done to prevent this? If not I saw that both tksurfer and > tkmedit can be used to edit the segmentation, what would be the easiest way > to do this? > > 2. When registering a freesurfer anatomical to Feat output (using > reg-feat2anat) the registration seems to be somewhat inaccurate. > Registering brainmask.mgz to our example_func using flirt has given us a > better registration so far. Since reg-feat2anat seems to use flirt in its > registration I was wondering what the difference might be resulting from. > Does reg-feat2anat use T1.mgz as it's reference scan, and if so is there any > way to have it use brainmask instead, as that seems to give better results? > > > Thanks, > Jeff > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Difficulties with segmentation
Hi, thanks, would the fix for this problem be released as something that I then would use to rerun mris_ca_label (and mris_anatomical_stats and mri_aprac2aseg) and get better results, or would I have to rerun a whole bunch of earlier steps (so I would want to hold off with processing for now)? JeffOn 6/20/06, Rahul Desikan <[EMAIL PROTECTED]> wrote: Hi Jeff,With regards to the cortical parcellation and the mislabelling of theanterior cingulate cortex (rostral anterior cingulate in the parcellationatlas), we are aware of this as a problem and are in the process of fixing it as we speak. If you were interested in editing the parcellation labels,my suggestion would be to first convert the *.aparc.annot file intoindividual labels (i.e. *h.rostralanteriorcingulate.label,*h.corpuscallosum.label ) and edit the individual labels using tksurfer.You can view the parcellation labels with the curvature visible (UnderView-->Label Style-->choose Outline instead of Filled) to differentiatecortical areas from non-cortical areas ( i.e. corpus callosum, unknown).best,RahulOn Tue, 20 Jun 2006, Jeffrey Spielberg wrote:> Hi, I had a couple of questions regarding cortical/subcortical segmentation->> 1. In our cortical segmentation we keep getting what look to be inaccurate > segmentation of the rostral and caudal acc. It looks some of what should be> labeled as one of those two areas is getting labelled corpus callosum or> "unlabelled subcortical" instead, sometimes fairly large chunks. Does this > indicate any problem earlier in the processing stream, and is there anything> that can be done to prevent this? If not I saw that both tksurfer and> tkmedit can be used to edit the segmentation, what would be the easiest way > to do this?>> 2. When registering a freesurfer anatomical to Feat output (using> reg-feat2anat) the registration seems to be somewhat inaccurate.> Registering brainmask.mgz to our example_func using flirt has given us a > better registration so far. Since reg-feat2anat seems to use flirt in its> registration I was wondering what the difference might be resulting from.> Does reg-feat2anat use T1.mgz as it's reference scan, and if so is there any > way to have it use brainmask instead, as that seems to give better results?>>> Thanks,> Jeff>-- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Difficulties with segmentation
hopefully the former, but until we understand what's going on it's hard to say. On Wed, 21 Jun 2006, Jeffrey Spielberg wrote: Hi, thanks, would the fix for this problem be released as something that I then would use to rerun mris_ca_label (and mris_anatomical_stats and mri_aprac2aseg) and get better results, or would I have to rerun a whole bunch of earlier steps (so I would want to hold off with processing for now)? Jeff On 6/20/06, Rahul Desikan <[EMAIL PROTECTED]> wrote: Hi Jeff, With regards to the cortical parcellation and the mislabelling of the anterior cingulate cortex (rostral anterior cingulate in the parcellation atlas), we are aware of this as a problem and are in the process of fixing it as we speak. If you were interested in editing the parcellation labels, my suggestion would be to first convert the *.aparc.annot file into individual labels (i.e. *h.rostralanteriorcingulate.label, *h.corpuscallosum.label) and edit the individual labels using tksurfer. You can view the parcellation labels with the curvature visible (Under View-->Label Style-->choose Outline instead of Filled) to differentiate cortical areas from non-cortical areas (i.e. corpus callosum, unknown). best, Rahul On Tue, 20 Jun 2006, Jeffrey Spielberg wrote: > Hi, I had a couple of questions regarding cortical/subcortical segmentation- > > 1. In our cortical segmentation we keep getting what look to be inaccurate > segmentation of the rostral and caudal acc. It looks some of what should be > labeled as one of those two areas is getting labelled corpus callosum or > "unlabelled subcortical" instead, sometimes fairly large chunks. Does this > indicate any problem earlier in the processing stream, and is there anything > that can be done to prevent this? If not I saw that both tksurfer and > tkmedit can be used to edit the segmentation, what would be the easiest way > to do this? > > 2. When registering a freesurfer anatomical to Feat output (using > reg-feat2anat) the registration seems to be somewhat inaccurate. > Registering brainmask.mgz to our example_func using flirt has given us a > better registration so far. Since reg-feat2anat seems to use flirt in its > registration I was wondering what the difference might be resulting from. > Does reg-feat2anat use T1.mgz as it's reference scan, and if so is there any > way to have it use brainmask instead, as that seems to give better results? > > > Thanks, > Jeff > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Basic questions
Hello all,I have a few basic questions about FreeSurfer and would appreciate any help.1) I have a number of brains in mnc format. I was wondering if these could be used in FreeSurfer because the tutorials only mention usage of the mgz format. Also, how do we convert from mnc to mgz. 2) What is the exact method of extracting the volume and cortical thickness of a particular region once the brain has been loaded into freesurfer. I can't seem to find any docs that outline how this is to be done with freesufer. If someone could point me in the right direction it would be really helpful. Thanks a lot,Anil Roy. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Basic questions
1. Yes, we support minc. 2. There is a table of structures/volumes/thicknesses in each subjects stats directory. cheers, Bruce On Wed, 21 Jun 2006, Anil Roy wrote: Hello all, I have a few basic questions about FreeSurfer and would appreciate any help. 1) I have a number of brains in mnc format. I was wondering if these could be used in FreeSurfer because the tutorials only mention usage of the mgz format. Also, how do we convert from mnc to mgz. 2) What is the exact method of extracting the volume and cortical thickness of a particular region once the brain has been loaded into freesurfer. I can't seem to find any docs that outline how this is to be done with freesufer. If someone could point me in the right direction it would be really helpful. Thanks a lot, Anil Roy. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer rendering offscreen
In older versions of tksurfer, it was possible to set a renderoffscreen flag (in a tcl script) that would make it possible to render images in the background. I find this very valuable for rendering large batches of stats. I would like to store surface-painted timeseries data in mgh format and render each frame in order to make a movie. Since the old version of tksurfer will not read mgh files, I need to use the new one for this. But rendering onscreen is very annoying because it means you can't use your computer for hours (if rendering lots of images). The problem seems to be that tksurfer is opening a window and drawing it twice before the tcl script even begins to be interpreted. Is this something that can be fixed? Just in general, why should time be wasted drawing the surface twice upon opening? And can the tcl script be interpreted *before* any open_window or redraw commands are given? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer rendering offscreen
Sorry, that isn't supported in tksurfer. Tksurfer has a lot of inefficient redrawing as it is a very old program and has a lot of old spaghetti code that isn't being updated. I'm working on moving all the tksurfer features into scuba. On Wed, Jun 21, 2006 at 12:13:51PM -0700, Don Hagler wrote: > In older versions of tksurfer, it was possible to set a renderoffscreen > flag (in a tcl script) that would make it possible to render images in the > background. I find this very valuable for rendering large batches of stats. > > I would like to store surface-painted timeseries data in mgh format and > render each frame in order to make a movie. Since the old version of > tksurfer will not read mgh files, I need to use the new one for this. But > rendering onscreen is very annoying because it means you can't use your > computer for hours (if rendering lots of images). > > The problem seems to be that tksurfer is opening a window and drawing it > twice before the tcl script even begins to be interpreted. Is this > something that can be fixed? Just in general, why should time be wasted > drawing the surface twice upon opening? And can the tcl script be > interpreted *before* any open_window or redraw commands are given? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all without tcsh
Hi, Can recon-all run even if tcsh is not installed on the system. When I try running it, I get the message: -bash: /home/aju/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory Thanks, Aju. ** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. Ph: +91 821 2514449 Ext 186 (O) +91 821 2514449 Ext 224 (R) Fax: +91 821 2510515 Email: [EMAIL PROTECTED] ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] nu_correct problem
>Hi Bruce: >> >> I installed the new version of freesurfer. I found that nu_correct does >> not work properly, the error message is >> spawn: exec of nu_estimate_np_and_em failed: No such file or directory >> nu_correct: crashed while running nu_estimate_np_and_em (termination >> status=65280) >> >> so I try to execute nu_estimate_np_and_em, and get following message: >> nu_estimate_np_and_em: data directory for package "N3" not found in >> /usr/pubsw/packages/freesurfer/RH3-x86_32/lib/mni/data >> >> Any idea? Thanks in advance. BTW, the GUI can pass that, but there is no >> intensity correction, of course. >> Tao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all without tcsh
Aju, tcsh will need to be installed in order for recon-all to work. it should be possible to get tcsh for most any system, and can be built from source also. Nick > Hi, > > Can recon-all run even if tcsh is not installed on the system. When I try > running it, I get the message: > > -bash: /home/aju/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No > such file or directory > > Thanks, > > Aju. > > ** > Mr.Ajith Kumar U > Junior Research Fellow, > Department of Audiology, > All India Institute of Speech and Hearing, Naimisham Camppus, > Manasagangothri, > Mysore,570006 > INDIA. > Ph:+91 821 2514449 Ext 186 (O) >+91 821 2514449 Ext 224 (R) > Fax: +91 821 2510515 > Email: [EMAIL PROTECTED] > **___ > 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] FS-FAST: mkcontrast-sess -setwdelay
Hi, I have a large (~100) number of FIR analyses where I need to set the weights for each post-stimulus delay (and then collapse them with -sumdelays). The weights are the same for all analyses. However the -setwdelay weights can only be entered manually upon prompt. This means that I would have to sit by the computer for a few days just to copy-paste a short series of numbers every 25 min. This makes no sense of course. Is there a way to make feeding the -setwdelay numbers part of the analysis script so I could just let it run without human intervention? I would be very happy if I could just set in the analysis script, for example, mkcontrast-sess -analysis XXX -setwdelay 0 0 0 0 1 1 1 0 0 0 0 0 -sumdelays -contrast A-REST -a 1 -c 0 Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Basic questions
Anil, In freesurfer, the utility mri_convert will convert minc files to mgz. This would be the first step in the reconstruction process. You might want to have a look at the tutorial that is available: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Nick > Hello all, > > I have a few basic questions about FreeSurfer and would appreciate any > help. > > 1) I have a number of brains in mnc format. I was wondering if these could > be used in FreeSurfer because the tutorials only mention usage of the mgz > format. Also, how do we convert from mnc to mgz. > > 2) What is the exact method of extracting the volume and cortical > thickness > of a particular region once the brain has been loaded into freesurfer. I > can't seem to find any docs that outline how this is to be done with > freesufer. If someone could point me in the right direction it would be > really helpful. > > Thanks a lot, > > Anil Roy. > ___ > 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
Re: [Freesurfer] Basic questions
Anil, In freesurfer, the utility mri_convert will convert minc files to mgz. This would be the first step in the reconstruction process. You might want to have a look at the tutorial that is available: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Nick > Hello all, > > I have a few basic questions about FreeSurfer and would appreciate any > help. > > 1) I have a number of brains in mnc format. I was wondering if these could > be used in FreeSurfer because the tutorials only mention usage of the mgz > format. Also, how do we convert from mnc to mgz. > > 2) What is the exact method of extracting the volume and cortical > thickness > of a particular region once the brain has been loaded into freesurfer. I > can't seem to find any docs that outline how this is to be done with > freesufer. If someone could point me in the right direction it would be > really helpful. > > Thanks a lot, > > Anil Roy. > ___ > 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] viewing group analysis results in tkmedit (3D) while using spherical space intersubject morphing
Hi FreeSurfers, A small group analysis question of fMRI data (fixed effects). The target brain is "fsaverage". I have resampled and averaged the stat maps across subjects in _spherical_ space using func2sph-sess / sphsmooth-sess / isxavg-fe-sess / stxgrinder-sess. Viewing the results on a "fsaverage" surface with tksurfer works fine, thanks. Now I would like to also view the mean functional maps in 3D space (tkmedit) on the "fsaverage" brain. This does not seem to work - obviously because the results were calculated in spherical space and were never resampled back to 3D space. Is there a way to resample the group average from sperical space to 3D space so that it could be viewed in tkmedit? Or is the only way to achieve something like this to recalculate the analyses entirely in Talairach space without using the spherical space? To make the results actually comparable between 3D (tkmedit) and surface-based (tksurfer) viewing, I think I should use the same type of space for intersubject averaging - preferably spherical in both cases. Hence, if a tool such as sph2func-sess exists (could not find it in the wiki), or there is a workaround, any suggestions would be very much welcome. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] viewing group analysis results in tkmedit (3D) whileusing spherical space intersubject morphing
This is Doug's response to my question. It might be also relevant to your question. Reza ** Not directly. tkmedit is a volume viewer, and the spherical maps are of course on the surface. You can take your .w files and stuff them back into the volume with mri_surf2vol. doug Reza Rajimehr wrote: > Hi, > > Is there any way to visualize spherically-averaged maps in tkmedit-sess? > Currently, it seems that tkmedit-sess only accepts -space native or tal. > > Thanks, > Reza ** > Hi FreeSurfers, > > A small group analysis question of fMRI data (fixed effects). The target > brain is "fsaverage". > > I have resampled and averaged the stat maps across subjects in _spherical_ > space using func2sph-sess / sphsmooth-sess / isxavg-fe-sess / > stxgrinder-sess. Viewing the results on a "fsaverage" surface with > tksurfer works fine, thanks. > > Now I would like to also view the mean functional maps in 3D space > (tkmedit) on the "fsaverage" brain. This does not seem to work - obviously > because the results were calculated in spherical space and were never > resampled back to 3D space. > > Is there a way to resample the group average from sperical space to 3D > space so that it could be viewed in tkmedit? Or is the only way to achieve > something like this to recalculate the analyses entirely in Talairach > space without using the spherical space? > > To make the results actually comparable between 3D (tkmedit) and > surface-based (tksurfer) viewing, I think I should use the same type of > space for intersubject averaging - preferably spherical in both cases. > > Hence, if a tool such as sph2func-sess exists (could not find it in the > wiki), or there is a workaround, any suggestions would be very much > welcome. > > Thanks, > > Tommi > > --- > Tommi Raij, M.D., Ph.D. > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > Bldg 149, 13th St > Charlestown, MA 02129 > U.S.A. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
