Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

extracting single structures from aseg.mgz
by Jared Price 16 Nov '09

16 Nov '09

Anyone know how to extract a single structure from aseg.mgz? In other words I assume it is possible to use the information in aseg.mgz to extract a single structure such that there is a new.mgz file that contains just the segmentation of the putamen or just of the caudate or whatever. Thanks. Jared

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repost a mris_make_template question
by Guang Zeng 15 Nov '09

15 Nov '09

Hi, there, I am creating our own template now, and stucked at "Round 1" now (based on FreeSurfer WIKI description http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) I found a thread posted a year ago and asked the same kind of question, (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08028.html) I read the thread, but still have three questions. I pasted part of the thread here; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% "Hi everyone, We're making a template to register some monkey brain surfaces to. I've written a script based on instructions from the Surface Registration and Templates page ( http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates ) on FreeSurfer wiki. I'm stuck at "Round 1" with the "mris_make_template" command. In the first step we used: mris_make_template \ lh sphere \ bu_edited bs_edited vi_edited \ [Command. 1] lh.monk_temp_all.tif As there were no *h.sphere.reg files yes, we used the *h.phere surfaces. My question is, for the next "mris_make_template" should we use the same (*h.sphere) surface or use the newly created *h.sphere.reg surfaces to create the template? mris_make_template \ lh sphere.reg \ bu_edited bs_edited vi_edited \ [Command. 2] lh.monk_temp_all.tif" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Question. 1, >From my understanding, their template include three subjects "bu_edited", "bs_edited", "vi_edited", and their command. 1 actually is what FreeSurfer WIKI called "Prep" step. However, I think in this step, only one subject is needed to create the template "lh.monk_temp_all.tif", am I right ? Actually, Bruce also mentioned that a single subject is used in 1st round, %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Hi Jan, you should use the ?h.sphere.reg on the 2nd round. On our 1st round we use a single subject ?h.sphere to avoid blurring the folding patterns too much, then register all to that one, create the atlas from all the subjects (with the sphere.reg), then recreate all the sphere.reg by reregistering to the 2nd round atlas, then create a 3rd round atlas from the new sphere.reg files. let us know if you need more help. Bruce %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Question. 2, In round. 1, we need call mris_make_template again using all the reference subjects. I think their command. 2 is written for this. However, is this command line correct? I thought it may looks like this: [Command. 3] mris_make_template lh sphere.reg bu_edited lh.monk_temp_all.tif mris_make_template lh sphere.reg bs_edited lh.monk_temp_all.tif mris_make_template lh sphere.reg vi_edited lh.monk_temp_all.tif So which one is correct? Actually, I tried both of them, they all worked. The only difference is the file size of lh.monk_temp_all.tif from Command.2 (1.3 M) is half of the result from Command. 3. (2.7M) Question. 2, If we correctly creat our template, and load it use MATLAB, will the size of the .tif file be 512 x 256 x 9? currently, when I load my .tif files, they are all 512 x 256. Thanks a lot for your help! Guang _________________________________________________________________ Bing brings you maps, menus, and reviews organized in one place. http://www.bing.com/search?q=restaurants&form=MFESRP&publ=WLHMTAG&crea=TEXT…

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RES: qcache
by Pedro Paulo de Magalhaes Oliveira Jr 14 Nov '09

14 Nov '09

I have also done this with no visible side effect. PPJ -----Msg original----- De: Jared Price Enviado: 14/11/2009 19:26:51 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] qcache Hi all, This should be a quick question to answer. I recently ran "recon-all -s <subjectID> -qcache" on a group of subjects after they had undergone initial processing. This was done using something of the form "for subjvar in `ls`; do recon-all -s $subjvar -qcache; done" (actually this was done on a grid computing system and the syntax was a bit different but this was the basic idea). Of course "fsaverage" was in that directory as well, because it needs to be there for the -qcache recon-all option to function properly. Anyway, the point is that the -qcache option was therefore run on "fsaverage" itself. I assume this is no big deal and that it will just put some unnecessary info files into the fsaverage directory. In other words I assume I can continue to use this fsaverage directory for futre -qcache runs and that there will just be some unnecessary files in the directory. Anyway, just wanted to be extra sure. Jared _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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qcache
by Jared Price 14 Nov '09

14 Nov '09

Hi all, This should be a quick question to answer. I recently ran "recon-all -s <subjectID> -qcache" on a group of subjects after they had undergone initial processing. This was done using something of the form "for subjvar in `ls`; do recon-all -s $subjvar -qcache; done" (actually this was done on a grid computing system and the syntax was a bit different but this was the basic idea). Of course "fsaverage" was in that directory as well, because it needs to be there for the -qcache recon-all option to function properly. Anyway, the point is that the -qcache option was therefore run on "fsaverage" itself. I assume this is no big deal and that it will just put some unnecessary info files into the fsaverage directory. In other words I assume I can continue to use this fsaverage directory for futre -qcache runs and that there will just be some unnecessary files in the directory. Anyway, just wanted to be extra sure. Jared

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mris_make_template question
by Guang Zeng 13 Nov '09

13 Nov '09

Hi, there, I am going to make our own template. Based on the introduction in FreeSurfer WIKI "The Surface Registration Process; Template", the first step is "Prep". "The process starts ("Prep") by choosing one reference subject, and producing a template (Here, mytemp0.tif). No ?h.sphere is required -- this step uses the subject's own pattern as the reference." Here, I listed my script for this "Prep" step please let me if it is correct: mris_make_template lh smoothwm sample_0 my_template0.tif mris_make_template lh sulc sample_0 my_template0.tif mris_make_template lh curv sample_0 my_template0.tif mris_make_template rh smoothwm sample_0 my_template0.tif mris_make_template rh sulc sample_0 my_template0.tif mris_make_template rh curv sample_0 my_template0.tif Thanks a lot! Guang _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/

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Re: [Freesurfer] Filling Big Ventricles
by Matt Clarkson 13 Nov '09

13 Nov '09

Hi Bruce, in general, the vents look good. So, just one more question, if I may. I notice that the segmentation labels have ventricles and choroid-plexus. So, in the wmparc.stats, and aseg.stats, does the volume of the left lateral ventricle include the left choroid plexus, or should I add both numbers together? Many thanks Matt ----- Original Message ----- From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> To: "Matt Clarkson" <clarkson(a)drc.ion.ucl.ac.uk> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Friday, November 13, 2009 3:09:58 PM GMT +00:00 GMT Britain, Ireland, Portugal Subject: Re: [Freesurfer] Filling Big Ventricles Hi Matt, are the ventricles labeled properly in the aseg? If so, then you probably don't need to do anything. If not, then you'll need to manually edit them, and run from there forward (-make all should do it). cheers, Bruce On Fri, 13 Nov 2009, Matt Clarkson wrote: > Hi Bruce, > > Thanks. So it sounds like FreeSurfer 4.5 should now be adequately filling ventricles in the general case, and that -bigventricles offers didn't reach a level of robustness you were happy with, so best to avoid that? What about the flag -fillven on mri_edit_wm_with_aseg? Any use? > > In terms of the fix mentioned below, the fix literally is: > > 1. recon-all -all > 2. mri_binarize --i $SUBJECTS_DIR/$PD/mri/aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 --o $SUBJECTS_DIR/$PD/mri/vents.mgz --binval 255 > 3. Add vents.mgz to wm.mgz > 4. recon-all -autorecon2-wm > > so, it could well be affecting the results more by virtue of the fact that we essentially perform a re-run? > > Thanks ever so much. > > Matt > > > > ----- Original Message ----- > From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > To: "Matt Clarkson" <clarkson(a)drc.ion.ucl.ac.uk> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Friday, November 13, 2009 2:44:03 PM GMT +00:00 GMT Britain, Ireland, Portugal > Subject: Re: [Freesurfer] Filling Big Ventricles > > Hi Matt, > > yes, the filling procedure has evolved and is better in current versions > than previous ones. > > cheers, > Bruce > > > On Fri, 13 Nov 2009, Matt Clarkson wrote: > >> Hi Bruce, >> >> I agree with your point, however this method was instigated by a previous person at our institution, so I'm looking at it afresh. Also, the addition of regions 4, 43, 5 and 44 does do "something". I agree though that when I look at wm.mgz using tkmedit on a vanilla FreeSurfer run, it appears that the white matter is a grey colour, and that the vents have been filled with white (colour 255). >> >> So, is it possible that a previous version of FreeSurfer did not by default try and fill the vents in, and now version 4.5 does by default attempt to fill the vents in? >> >> Cheers >> >> Matt >> >> >> ----- Original Message ----- >> From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> >> To: "Matt Clarkson" <clarkson(a)drc.ion.ucl.ac.uk> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Sent: Friday, November 13, 2009 2:25:16 PM GMT +00:00 GMT Britain, Ireland, Portugal >> Subject: Re: [Freesurfer] Filling Big Ventricles >> >> Hi Matt, >> >> the -bigventricles stuff is something I messed with for a while, but didn't >> get to work robustly and haven't gotten back to it. I'm not sure I >> understand your fix though. If the aseg properly labels the ventricles, >> then they should be filled in the wm.mgz, and if the aseg doesn't, then >> your fix doesn't help. Do you manually correct before doing this? >> >> cheers, >> Bruce >> >> >> On Fri, 13 Nov 2009, Matt Clarkson wrote: >> >>> Hi there, >>> >>> we have various Alzheimer cases, where the FreeSurfer pipeline can occasionally struggle to correctly segment the ventricles, which results in white matter and pial surfaces "leaking" into the ventricles. >>> >>> I have tried using -bigventricles passed into the autorecon2 stage, but I can't tell if its doing much. I checked the log files, and you can see -bigventricles passed to several binaries such as mri_ca_register and mri_ca_label, so the flag is definitely being passed from the command line. >>> >>> Is the -bigventricles meant to be used in this way, and what should it be doing? >>> >>> Also, I notice that the binary mri_edit_wm_with_aseg has a flag -fillven, but I can't find the documentation to say what it does and if I should be using it. >>> >>> So, we have previously used a technique whereby we run freesurfer once then create a vents image like: >>> mri_binarize --i aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 --o vents.mgz --binval 255 >>> >>> and then add this into the wm.mgz to fill some holes in. I have attached two .png files to illustrate the effect. In this example, I have chosen the slice where the surfaces just start to leak into the ventricles. So, on these snapshots, the problem looks quite small, but on other subsequent slices, you can get fairly large leakage into the ventricles. >>> >>> So, with these options, what would be the best way to cope with very abnormal ventricles? >>> >>> Many thanks in advance. >>> >>> Matt Clarkson >>> >>> Senior Research Associate >>> Dementia Research Centre >>> UCL >>> Institute Of Neurology >>> Queen Square >>> London WC1N 3BG >>> >>> m.clarkson(a)ucl.ac.uk >>> Tel: 08451 555 000 ext. 723653 >>> Fax: 020 7676 2066 >>> >>> >>> >> >> >> > > >

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Re: [Freesurfer] Filling Big Ventricles
by Matt Clarkson 13 Nov '09

13 Nov '09

Hi Bruce, Thanks. So it sounds like FreeSurfer 4.5 should now be adequately filling ventricles in the general case, and that -bigventricles offers didn't reach a level of robustness you were happy with, so best to avoid that? What about the flag -fillven on mri_edit_wm_with_aseg? Any use? In terms of the fix mentioned below, the fix literally is: 1. recon-all -all 2. mri_binarize --i $SUBJECTS_DIR/$PD/mri/aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 --o $SUBJECTS_DIR/$PD/mri/vents.mgz --binval 255 3. Add vents.mgz to wm.mgz 4. recon-all -autorecon2-wm so, it could well be affecting the results more by virtue of the fact that we essentially perform a re-run? Thanks ever so much. Matt ----- Original Message ----- From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> To: "Matt Clarkson" <clarkson(a)drc.ion.ucl.ac.uk> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Friday, November 13, 2009 2:44:03 PM GMT +00:00 GMT Britain, Ireland, Portugal Subject: Re: [Freesurfer] Filling Big Ventricles Hi Matt, yes, the filling procedure has evolved and is better in current versions than previous ones. cheers, Bruce On Fri, 13 Nov 2009, Matt Clarkson wrote: > Hi Bruce, > > I agree with your point, however this method was instigated by a previous person at our institution, so I'm looking at it afresh. Also, the addition of regions 4, 43, 5 and 44 does do "something". I agree though that when I look at wm.mgz using tkmedit on a vanilla FreeSurfer run, it appears that the white matter is a grey colour, and that the vents have been filled with white (colour 255). > > So, is it possible that a previous version of FreeSurfer did not by default try and fill the vents in, and now version 4.5 does by default attempt to fill the vents in? > > Cheers > > Matt > > > ----- Original Message ----- > From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > To: "Matt Clarkson" <clarkson(a)drc.ion.ucl.ac.uk> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Friday, November 13, 2009 2:25:16 PM GMT +00:00 GMT Britain, Ireland, Portugal > Subject: Re: [Freesurfer] Filling Big Ventricles > > Hi Matt, > > the -bigventricles stuff is something I messed with for a while, but didn't > get to work robustly and haven't gotten back to it. I'm not sure I > understand your fix though. If the aseg properly labels the ventricles, > then they should be filled in the wm.mgz, and if the aseg doesn't, then > your fix doesn't help. Do you manually correct before doing this? > > cheers, > Bruce > > > On Fri, 13 Nov 2009, Matt Clarkson wrote: > >> Hi there, >> >> we have various Alzheimer cases, where the FreeSurfer pipeline can occasionally struggle to correctly segment the ventricles, which results in white matter and pial surfaces "leaking" into the ventricles. >> >> I have tried using -bigventricles passed into the autorecon2 stage, but I can't tell if its doing much. I checked the log files, and you can see -bigventricles passed to several binaries such as mri_ca_register and mri_ca_label, so the flag is definitely being passed from the command line. >> >> Is the -bigventricles meant to be used in this way, and what should it be doing? >> >> Also, I notice that the binary mri_edit_wm_with_aseg has a flag -fillven, but I can't find the documentation to say what it does and if I should be using it. >> >> So, we have previously used a technique whereby we run freesurfer once then create a vents image like: >> mri_binarize --i aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 --o vents.mgz --binval 255 >> >> and then add this into the wm.mgz to fill some holes in. I have attached two .png files to illustrate the effect. In this example, I have chosen the slice where the surfaces just start to leak into the ventricles. So, on these snapshots, the problem looks quite small, but on other subsequent slices, you can get fairly large leakage into the ventricles. >> >> So, with these options, what would be the best way to cope with very abnormal ventricles? >> >> Many thanks in advance. >> >> Matt Clarkson >> >> Senior Research Associate >> Dementia Research Centre >> UCL >> Institute Of Neurology >> Queen Square >> London WC1N 3BG >> >> m.clarkson(a)ucl.ac.uk >> Tel: 08451 555 000 ext. 723653 >> Fax: 020 7676 2066 >> >> >> > > >

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Re: [Freesurfer] Filling Big Ventricles
by Matt Clarkson 13 Nov '09

13 Nov '09

Hi Bruce, I agree with your point, however this method was instigated by a previous person at our institution, so I'm looking at it afresh. Also, the addition of regions 4, 43, 5 and 44 does do "something". I agree though that when I look at wm.mgz using tkmedit on a vanilla FreeSurfer run, it appears that the white matter is a grey colour, and that the vents have been filled with white (colour 255). So, is it possible that a previous version of FreeSurfer did not by default try and fill the vents in, and now version 4.5 does by default attempt to fill the vents in? Cheers Matt ----- Original Message ----- From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> To: "Matt Clarkson" <clarkson(a)drc.ion.ucl.ac.uk> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Friday, November 13, 2009 2:25:16 PM GMT +00:00 GMT Britain, Ireland, Portugal Subject: Re: [Freesurfer] Filling Big Ventricles Hi Matt, the -bigventricles stuff is something I messed with for a while, but didn't get to work robustly and haven't gotten back to it. I'm not sure I understand your fix though. If the aseg properly labels the ventricles, then they should be filled in the wm.mgz, and if the aseg doesn't, then your fix doesn't help. Do you manually correct before doing this? cheers, Bruce On Fri, 13 Nov 2009, Matt Clarkson wrote: > Hi there, > > we have various Alzheimer cases, where the FreeSurfer pipeline can occasionally struggle to correctly segment the ventricles, which results in white matter and pial surfaces "leaking" into the ventricles. > > I have tried using -bigventricles passed into the autorecon2 stage, but I can't tell if its doing much. I checked the log files, and you can see -bigventricles passed to several binaries such as mri_ca_register and mri_ca_label, so the flag is definitely being passed from the command line. > > Is the -bigventricles meant to be used in this way, and what should it be doing? > > Also, I notice that the binary mri_edit_wm_with_aseg has a flag -fillven, but I can't find the documentation to say what it does and if I should be using it. > > So, we have previously used a technique whereby we run freesurfer once then create a vents image like: > mri_binarize --i aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 --o vents.mgz --binval 255 > > and then add this into the wm.mgz to fill some holes in. I have attached two .png files to illustrate the effect. In this example, I have chosen the slice where the surfaces just start to leak into the ventricles. So, on these snapshots, the problem looks quite small, but on other subsequent slices, you can get fairly large leakage into the ventricles. > > So, with these options, what would be the best way to cope with very abnormal ventricles? > > Many thanks in advance. > > Matt Clarkson > > Senior Research Associate > Dementia Research Centre > UCL > Institute Of Neurology > Queen Square > London WC1N 3BG > > m.clarkson(a)ucl.ac.uk > Tel: 08451 555 000 ext. 723653 > Fax: 020 7676 2066 > > >

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Filling Big Ventricles
by Matt Clarkson 13 Nov '09

13 Nov '09

Hi there, we have various Alzheimer cases, where the FreeSurfer pipeline can occasionally struggle to correctly segment the ventricles, which results in white matter and pial surfaces "leaking" into the ventricles. I have tried using -bigventricles passed into the autorecon2 stage, but I can't tell if its doing much. I checked the log files, and you can see -bigventricles passed to several binaries such as mri_ca_register and mri_ca_label, so the flag is definitely being passed from the command line. Is the -bigventricles meant to be used in this way, and what should it be doing? Also, I notice that the binary mri_edit_wm_with_aseg has a flag -fillven, but I can't find the documentation to say what it does and if I should be using it. So, we have previously used a technique whereby we run freesurfer once then create a vents image like: mri_binarize --i aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 --o vents.mgz --binval 255 and then add this into the wm.mgz to fill some holes in. I have attached two .png files to illustrate the effect. In this example, I have chosen the slice where the surfaces just start to leak into the ventricles. So, on these snapshots, the problem looks quite small, but on other subsequent slices, you can get fairly large leakage into the ventricles. So, with these options, what would be the best way to cope with very abnormal ventricles? Many thanks in advance. Matt Clarkson Senior Research Associate Dementia Research Centre UCL Institute Of Neurology Queen Square London WC1N 3BG m.clarkson(a)ucl.ac.uk Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066

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nu_correct problem.
by Mr k hanimireddy 13 Nov '09

13 Nov '09

Hi Bruce, I got a problem with mri_nu_correct in recon-all process. After mri_nu_corret step, nu.mgz looks oversmoothed. Could you please let me know why this is happening and how can I get rid of this? This is happening with few images only. I attached original (001.mgz), nu corrected (nu.mgz) images and mri_nu_correct.mni.log file for your reference. Thanks in advance! Reddy. The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/

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Freesurfer November 2009