Freesurfer May 2005

freesurfer@nmr.mgh.harvard.edu

26 participants
53 discussions

RE: [Freesurfer] Manual editing tips?
by Fornito, Alexander 08 May '05

08 May '05

Hi Bruce, So then if my euler numbers for the white and pial surfaces are okay, any tips as to why I get the "Segmentation Fault" message when I run mris_anatomical_stats rh thickness? Is this a problem with the initial wm segmentation? Thanks, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 5/9/2005 10:38 AM To: Fornito, Alexander Cc: Evelina Busa; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Manual editing tips? Hi Alex, the manual editing can certainly effect the final surface placement. Mostly if a large piece of wm is missed, or sometimes we edit the brain volume directly to remove some dura that gets kept within the pial surface. The qsphere is used to guide the topology correction, but itself is not corrected, so it won't have an Euler # of 2. You can't run mris_euler_number on thickness, since it's not a surface (but a scalar field over the surface). You can run it on the ?h.white and ?h.pial surfaces if you want. There is actually a means for manual intervention in the spherical morph, but it's rarely needed. cheers, Bruce On Mon, 9 May 2005, Fornito, Alexander wrote: > Hi Evelina, > Let's see if I understand you... > The pial and white boundaries are calculated on the intensity normalized/motion/corrected/averaged image, irrespective of manual editing. > Then the manual editing is only done to obtain a surface representation that is visually accurate for display of inflated and/or flattened surfaces, but has not effect whatsoever on the surface estimation used for thickness and curvature calculations? > How about inter-subject registration? Is it affected by manual editing? > I've been having problems with my surfaces and am trying to work out what's going wrong. My euler numbers are 2 for the white and pial surfaces, but I get the following message when I comupte it for the qsphere (for one rh.qsphere case): > > euler # = v-e+f = 2g-2: 156076 - 468733 + 312496 = -161 --> 81 holes > F =2V-4: 312496 != 312152-4 (-348) > 2E=3F: 937466 != 937488 (-22) > > total defect index = 185 > > Also, I get a "segmentation fault" when I run mris_anatomical_stats rh thickness for this same person.Visually, I've noticed that the pial and wm surfaces intersects on some parts of the brain? Could this be the problem? > Than ks again for your help, > Alex > > -----Original Message----- > From: Evelina Busa [mailto:evelina@nmr.mgh.harvard.edu] > Sent: Sat 5/7/2005 6:51 AM > To: Fornito, Alexander > Cc: > Subject: RE: [Freesurfer] Manual editing tips? > > Hi Alex, > > The normalized brain volume is created quite early on in the process -- > first the raw data are converted from their native scanner format, then > motion corrected into what we call the 'orig' volume, then the > intensities are normalised to what we call the T1 volume, then the non-brain > tissues are stripped from the T1 and we have the 'brain' volume. > > The WM volume is then segmented out of the brain volume, and that's what > is edited, for the purpose of getting the surface topologically correct. > So, although it's mostly true that the brain volume is what is used to > calculate the pial/white boundary and cortical thicknesses (thus > arbitrary edits to the WM volume won't change that), if the initial > surface (which is defined by the wm edits) is far enough off, it won't > find the correct location during the final surface deformation. > > In other words, it's important that the wm edits be accurate, but rest > assured that your edits are not what Freesurfer ultimately uses to > determine the cortical surfaces. > > This should be welcomed as good news! ;) > > Good luck! > > On Thu, 5 May 2005, Fornito, Alexander wrote: > >> Hi once again, >> Just wanted to also clarify your response: >> "The surfaces are generated using the normalized brain volume and not >> strictly the segmented white matter volume, so edits on the WM volume do >> not arbitrarily affect the cortical thickness measures." >> This has me a bit confused. What exactly is the normalized brain volume (ie., created at which step/which file name?), and if edits on the WM volume don't affect thickness (and presumably therefore, surface estimation) why do we edit them at all? There's something I a missing, and I'd greatly appreciate it if you could point me in the right direction!! >> Thanks again, >> Alex >> >> >> -----Original Message----- >> From: Evelina Busa [mailto:evelina@nmr.mgh.harvard.edu] >> Sent: Thu 5/5/2005 4:23 AM >> To: Fornito, Alexander >> Cc: >> Subject: RE: [Freesurfer] Manual editing tips? >> >> Hi again, >> >> The posterior portion connects to calcarine which makes the big defect. >> The tutorial pictures and instructions for filling in the posterior >> ventricles may give the impression that *any* apparent "hole" in the >> WM volume will necessarily result in a topological defect, but that's not >> true. It depends on whether that hole when looked at in 3D will still be >> a hole. This is kind of hard to gauge when going through the slices but >> the inflated surface tells the story. >> >> Good luck and sorry for my delayed response! >> >> On Wed, 4 May 2005, Fornito, Alexander wrote: >> >>> Thanks for your comprehensive response! Very helpful! >>> Just wanted to clarify, why is it that the posterior portion of the lateral ventricles, and not the anterior portions, result in topological defects, if both appear as 'islands' inside the white matter? >>> Thanks again, >>> Alex >>> >>> -----Original Message----- >>> From: evelina(a)nmr.mgh.harvard.edu [mailto:evelina@nmr.mgh.harvard.edu] >>> Sent: Wed 5/4/2005 2:06 PM >>> To: Fornito, Alexander >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Manual editing tips? >>> >>> >>> >>> >>> Hello Alex, >>> >>> A helpful approach when editing the lateral ventricles is to view the >>> sagittal plane; usually the filling should not extend anterior to the >>> point where the posterior fornix is erased. The axial plane is also >>> useful. The tutorial focuses on the coronal plane, which isn't optimal >>> for determining when to stop the edits (moving anteriorly). >>> >>> Smoothness of the surface -- the aim of manual editing is chiefly to >>> eliminate the defects that the subsequent automated topology fixer >>> cannot likely handle, whether or not they are easily visible on the >>> surface. The large defects outlined in the manual are pretty safe bets >>> for editing in this respect, and there are other anatomical >>> idiosyncrasies that you'll find in normal or other populations which you >>> can anticipate having to edit in order to "force" a topologically >>> correct surface, e.g. brain lesions resulting in large gaps of white >>> matter voxels. >>> >>> It's hard to predict what will need to be edited without having done >>> quite a few brains, but in general your choice is to either: a) err on >>> the side of caution and edit whatever corresponds with a visible defect >>> on the inflated surface, or; b) run the topology fixer first to see >>> how/whether it could handle the remaining visible defects, with the risk >>> that you might need to edit the extra defects afterward, anyway. And of >>> course the Euler number calculation can give you precise information >>> about a hemisphere's topological defect index. I'd recommend routinely >>> editing the standard areas that lead to topological defects (as per the >>> tutorial), then running the automated topology fixer, unless it is a >>> structurally unusual brain with quite large visible defects. The >>> automated topology fixer by and large works, and it's usually a better >>> use of operator time to wait on this 5-hour process rather than spend an >>> hour or so, perhaps pointlesssly, doing extra edits first. >>> >>> The surfaces are generated using the normalized brain volume and not >>> strictly the segmented white matter volume, so edits on the WM volume do >>> not arbitrarily affect the cortical thickness measures. >>> >>> Hope this helps, if not, ask more - >>> >>>> Hi all, >>>> I've noticed that the tutorial's instructions for manual editing of >>> the ventricles stops at about slice 92 (for Bert's data). Does this mean >>> only the posterior portion of the lateral ventricles need to be filled, >>> and that there is no need to continue to fill in the ventricles up to >>> the anterior horns as well? >>>> Also, a couple more queries re: manual editing: >>>> - Sometimes I can see handles emanating from the surface that are not >>> in the areas listed in the manual. Are there any guidelines re: what >>> should be deleted as opposed to what should be filled? >>>> - Are there any guidelines for just how smooth the brain surface >>> should be before moving on to create the final surface? Some of my >>> surfaces appear quite smooth (ie., no obvious handles), although >>> somewhat bumpy, esp. around the posterior-dorsal areas. >>>> - Am I correct in assuming that what is tissue is edited or not will >>> affect surface generation and hence estimates of cortical thickness? In >>> this case, is it advisable to carry out some kind of reliability >>> analysis for morphmoteric studies? >>>> >>>> Thanks for your help, >>>> Alex >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> >>> >>> >>> >>> >>> >>> >> >> > >

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RE: [Freesurfer] Manual editing tips?
by Fornito, Alexander 08 May '05

08 May '05

Hi Evelina, Let's see if I understand you... The pial and white boundaries are calculated on the intensity normalized/motion/corrected/averaged image, irrespective of manual editing. Then the manual editing is only done to obtain a surface representation that is visually accurate for display of inflated and/or flattened surfaces, but has not effect whatsoever on the surface estimation used for thickness and curvature calculations? How about inter-subject registration? Is it affected by manual editing? I've been having problems with my surfaces and am trying to work out what's going wrong. My euler numbers are 2 for the white and pial surfaces, but I get the following message when I comupte it for the qsphere (for one rh.qsphere case): euler # = v-e+f = 2g-2: 156076 - 468733 + 312496 = -161 --> 81 holes F =2V-4: 312496 != 312152-4 (-348) 2E=3F: 937466 != 937488 (-22) total defect index = 185 Also, I get a "segmentation fault" when I run mris_anatomical_stats rh thickness for this same person.Visually, I've noticed that the pial and wm surfaces intersects on some parts of the brain? Could this be the problem? Than ks again for your help, Alex -----Original Message----- From: Evelina Busa [mailto:evelina@nmr.mgh.harvard.edu] Sent: Sat 5/7/2005 6:51 AM To: Fornito, Alexander Cc: Subject: RE: [Freesurfer] Manual editing tips? Hi Alex, The normalized brain volume is created quite early on in the process -- first the raw data are converted from their native scanner format, then motion corrected into what we call the 'orig' volume, then the intensities are normalised to what we call the T1 volume, then the non-brain tissues are stripped from the T1 and we have the 'brain' volume. The WM volume is then segmented out of the brain volume, and that's what is edited, for the purpose of getting the surface topologically correct. So, although it's mostly true that the brain volume is what is used to calculate the pial/white boundary and cortical thicknesses (thus arbitrary edits to the WM volume won't change that), if the initial surface (which is defined by the wm edits) is far enough off, it won't find the correct location during the final surface deformation. In other words, it's important that the wm edits be accurate, but rest assured that your edits are not what Freesurfer ultimately uses to determine the cortical surfaces. This should be welcomed as good news! ;) Good luck! On Thu, 5 May 2005, Fornito, Alexander wrote: > Hi once again, > Just wanted to also clarify your response: > "The surfaces are generated using the normalized brain volume and not > strictly the segmented white matter volume, so edits on the WM volume do > not arbitrarily affect the cortical thickness measures." > This has me a bit confused. What exactly is the normalized brain volume (ie., created at which step/which file name?), and if edits on the WM volume don't affect thickness (and presumably therefore, surface estimation) why do we edit them at all? There's something I a missing, and I'd greatly appreciate it if you could point me in the right direction!! > Thanks again, > Alex > > > -----Original Message----- > From: Evelina Busa [mailto:evelina@nmr.mgh.harvard.edu] > Sent: Thu 5/5/2005 4:23 AM > To: Fornito, Alexander > Cc: > Subject: RE: [Freesurfer] Manual editing tips? > > Hi again, > > The posterior portion connects to calcarine which makes the big defect. > The tutorial pictures and instructions for filling in the posterior > ventricles may give the impression that *any* apparent "hole" in the > WM volume will necessarily result in a topological defect, but that's not > true. It depends on whether that hole when looked at in 3D will still be > a hole. This is kind of hard to gauge when going through the slices but > the inflated surface tells the story. > > Good luck and sorry for my delayed response! > > On Wed, 4 May 2005, Fornito, Alexander wrote: > >> Thanks for your comprehensive response! Very helpful! >> Just wanted to clarify, why is it that the posterior portion of the lateral ventricles, and not the anterior portions, result in topological defects, if both appear as 'islands' inside the white matter? >> Thanks again, >> Alex >> >> -----Original Message----- >> From: evelina(a)nmr.mgh.harvard.edu [mailto:evelina@nmr.mgh.harvard.edu] >> Sent: Wed 5/4/2005 2:06 PM >> To: Fornito, Alexander >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Manual editing tips? >> >> >> >> >> Hello Alex, >> >> A helpful approach when editing the lateral ventricles is to view the >> sagittal plane; usually the filling should not extend anterior to the >> point where the posterior fornix is erased. The axial plane is also >> useful. The tutorial focuses on the coronal plane, which isn't optimal >> for determining when to stop the edits (moving anteriorly). >> >> Smoothness of the surface -- the aim of manual editing is chiefly to >> eliminate the defects that the subsequent automated topology fixer >> cannot likely handle, whether or not they are easily visible on the >> surface. The large defects outlined in the manual are pretty safe bets >> for editing in this respect, and there are other anatomical >> idiosyncrasies that you'll find in normal or other populations which you >> can anticipate having to edit in order to "force" a topologically >> correct surface, e.g. brain lesions resulting in large gaps of white >> matter voxels. >> >> It's hard to predict what will need to be edited without having done >> quite a few brains, but in general your choice is to either: a) err on >> the side of caution and edit whatever corresponds with a visible defect >> on the inflated surface, or; b) run the topology fixer first to see >> how/whether it could handle the remaining visible defects, with the risk >> that you might need to edit the extra defects afterward, anyway. And of >> course the Euler number calculation can give you precise information >> about a hemisphere's topological defect index. I'd recommend routinely >> editing the standard areas that lead to topological defects (as per the >> tutorial), then running the automated topology fixer, unless it is a >> structurally unusual brain with quite large visible defects. The >> automated topology fixer by and large works, and it's usually a better >> use of operator time to wait on this 5-hour process rather than spend an >> hour or so, perhaps pointlesssly, doing extra edits first. >> >> The surfaces are generated using the normalized brain volume and not >> strictly the segmented white matter volume, so edits on the WM volume do >> not arbitrarily affect the cortical thickness measures. >> >> Hope this helps, if not, ask more - >> >> > Hi all, >> > I've noticed that the tutorial's instructions for manual editing of >> the ventricles stops at about slice 92 (for Bert's data). Does this mean >> only the posterior portion of the lateral ventricles need to be filled, >> and that there is no need to continue to fill in the ventricles up to >> the anterior horns as well? >> > Also, a couple more queries re: manual editing: >> > - Sometimes I can see handles emanating from the surface that are not >> in the areas listed in the manual. Are there any guidelines re: what >> should be deleted as opposed to what should be filled? >> > - Are there any guidelines for just how smooth the brain surface >> should be before moving on to create the final surface? Some of my >> surfaces appear quite smooth (ie., no obvious handles), although >> somewhat bumpy, esp. around the posterior-dorsal areas. >> > - Am I correct in assuming that what is tissue is edited or not will >> affect surface generation and hence estimates of cortical thickness? In >> this case, is it advisable to carry out some kind of reliability >> analysis for morphmoteric studies? >> > >> > Thanks for your help, >> > Alex >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> >> >> >> >> >> >> > > --

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parcellation help
by peggy christidis 06 May '05

06 May '05

Hi there, Is there any documentation available on how to use the parcellation tool in FreeSurfer? Thanks, Peggy

2 1

mri_convert
by Wan Park 05 May '05

05 May '05

hi, i am trying to convert 124 slices of .dcm files COR, but when i put mri_convert E9042_S002_A0001_anon.dcm . (E9042_S002_A0001_anon.dcm is the first slice). i receive this message: %mri_convert E9042_S002_A0001_anon.dcm . mri_convert E9042_S002_A0001_anon.dcm . reading from E9042_S002_A0001_anon.dcm... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... Segmentation fault % could you please help me with this? thanks, wan

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some atlas questions
by Nguyen, Thang Q 05 May '05

05 May '05

Hello all, I have a few questions that bassically address atlas maps in freesurfer. I understand that the freesurfer average atlas uses a customized manually traced atlas. 1. Are the subjects aligned to any canonical map when running an mri_glm analysis? 2. If we have an fmri analysis through SPM, how can we ensure that the fmri atlas and the freesurfer atlas are aligned properly? 3. Can we align the parcellation map to the MNI map and reparcellate the subject? Thanks for all of your help, Thang

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wm volume
by Lars Tjelta Westlye 05 May '05

05 May '05

Hi all, is there a way I can attain the total wm volume for each of the hemispheres? And is it possible to estimate the wm volume of certain gross anatomical areas, like the different lobes? Thanks! Best wishes, Lars Tjelta Westlye

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Aligning in the command line
by Fornito, Alexander 05 May '05

05 May '05

Hi all, I've noticed you can set expert preferences to align before averaging in the GUI, but how do you do it from the command line? My understanding of the following from the usage is that it assumes that the transform already exists in the /transforms dir, but how do I create this? "The volume can be resampled into another space by supplying a transform using the --apply_transform flag. This reads the transform file and applies the transform (when --apply_inverse_transform is used, the transform is inverted and then applied). An example of a transform file is talairach.xfm as found in subjectid/mri/transforms." Do you create it separately through the MNI tools before proceeding with freesurfer, or is there some way to do it through Fressurfer? Thanks, Alex

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Re: [Freesurfer] Manual editing tips?
by evelina＠nmr.mgh.harvard.edu 04 May '05

04 May '05

Hello Alex, A helpful approach when editing the lateral ventricles is to view the sagittal plane; usually the filling should not extend anterior to the point where the posterior fornix is erased. The axial plane is also useful. The tutorial focuses on the coronal plane, which isn't optimal for determining when to stop the edits (moving anteriorly). Smoothness of the surface -- the aim of manual editing is chiefly to eliminate the defects that the subsequent automated topology fixer cannot likely handle, whether or not they are easily visible on the surface. The large defects outlined in the manual are pretty safe bets for editing in this respect, and there are other anatomical idiosyncrasies that you'll find in normal or other populations which you can anticipate having to edit in order to "force" a topologically correct surface, e.g. brain lesions resulting in large gaps of white matter voxels. It's hard to predict what will need to be edited without having done quite a few brains, but in general your choice is to either: a) err on the side of caution and edit whatever corresponds with a visible defect on the inflated surface, or; b) run the topology fixer first to see how/whether it could handle the remaining visible defects, with the risk that you might need to edit the extra defects afterward, anyway. And of course the Euler number calculation can give you precise information about a hemisphere's topological defect index. I'd recommend routinely editing the standard areas that lead to topological defects (as per the tutorial), then running the automated topology fixer, unless it is a structurally unusual brain with quite large visible defects. The automated topology fixer by and large works, and it's usually a better use of operator time to wait on this 5-hour process rather than spend an hour or so, perhaps pointlesssly, doing extra edits first. The surfaces are generated using the normalized brain volume and not strictly the segmented white matter volume, so edits on the WM volume do not arbitrarily affect the cortical thickness measures. Hope this helps, if not, ask more - > Hi all, > I've noticed that the tutorial's instructions for manual editing of the ventricles stops at about slice 92 (for Bert's data). Does this mean only the posterior portion of the lateral ventricles need to be filled, and that there is no need to continue to fill in the ventricles up to the anterior horns as well? > Also, a couple more queries re: manual editing: > - Sometimes I can see handles emanating from the surface that are not in the areas listed in the manual. Are there any guidelines re: what should be deleted as opposed to what should be filled? > - Are there any guidelines for just how smooth the brain surface should be before moving on to create the final surface? Some of my surfaces appear quite smooth (ie., no obvious handles), although somewhat bumpy, esp. around the posterior-dorsal areas. > - Am I correct in assuming that what is tissue is edited or not will affect surface generation and hence estimates of cortical thickness? In this case, is it advisable to carry out some kind of reliability analysis for morphmoteric studies? > > Thanks for your help, > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

Manual editing tips?
by Fornito, Alexander 03 May '05

03 May '05

Hi all, I've noticed that the tutorial's instructions for manual editing of the ventricles stops at about slice 92 (for Bert's data). Does this mean only the posterior portion of the lateral ventricles need to be filled, and that there is no need to continue to fill in the ventricles up to the anterior horns as well? Also, a couple more queries re: manual editing: - Sometimes I can see handles emanating from the surface that are not in the areas listed in the manual. Are there any guidelines re: what should be deleted as opposed to what should be filled? - Are there any guidelines for just how smooth the brain surface should be before moving on to create the final surface? Some of my surfaces appear quite smooth (ie., no obvious handles), although somewhat bumpy, esp. around the posterior-dorsal areas. - Am I correct in assuming that what is tissue is edited or not will affect surface generation and hence estimates of cortical thickness? In this case, is it advisable to carry out some kind of reliability analysis for morphmoteric studies? Thanks for your help, Alex

1 0

mask to label
by Stephanie McMains 03 May '05

03 May '05

I was wondering if there was a script that allowed me to convert a mask back into a label. I was looking at mri_vol2roi, but it seems to want the input in bshort format. Thanks for any help, Stephanie McMains

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Freesurfer May 2005