Freesurfer May 2005

freesurfer@nmr.mgh.harvard.edu

26 participants
53 discussions

RE: [Freesurfer] Manual editing tips?
by Fornito, Alexander 12 May '05

12 May '05

So generally speaking, the thickness values obtained before and after manual editing should be quite similar across the brain. How smooth should the surface be before you can move on? I tend to get slight "protrusions" here and there across the surface and it generally appears to be smooth. Is it just a matter of checking the euler numbers and being happy with the white and pial surfaces when overlaid on the T1? Also, beyond "fix topology correction", what additional processing is done when running "create final surfaces"? Sorry to labour the points, just trying to get an idea of what is/isn't acceptable. Many thanks, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 5/11/2005 11:30 PM To: Fornito, Alexander Cc: Evelina Busa; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Manual editing tips? Hi Alex, the thickness is the distance between the ?h.white and ?h.pial surfaces. These are initialized with the wm volume, so if it is too far off, they won't converge to the right answer. It's pretty robust, but if you're missing 5-6mm of wm at the crown of a gyrus for example, it probably won't recover the entire thing. cheers, Bruce On Wed, 11 May 2005, Fornito, Alexander wrote: > Hi, > Just a bit confused re: Evelina's comment: > > " 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." > > And Bruce's comment: > > " 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." > > My questions are: > - What surfaces (and at what point) is the thickness calculated from? Is > it from the edited wm and pial surfaces used when create final surfaces > is run? > - To what degree do variations in manual editing affect thickness > estimates? > - Would it be advisable to perform a reliability study to make sure the > manual editing process does not affect thickness estimates too much? > > Thanks again, > Alex > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Monday, May 09, 2005 10:39 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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답신: Re: [Freesurfer] occipital cuts
by Joongnam Yang 11 May '05

11 May '05

Thanks Bruce, but I am not sure I understand it. Would be more specific? Also, how would you make the cuts consistent across different subjects' brains? Nam. >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 05/05/10 오후 4:45 >>> Hi Nam, for occiptial 1/3 of cortex, Anders, Marty and Roger et al. typically made one planar cut to cut off the posterior 1/3, then one cut down the fundus of the calcarine all the way anterior. cheers, Bruce On Tue, 10 May 2005, Joongnam Yang wrote: > Hi all, > > The freesurfer manual on occipital cuts is clear on where to cut, but > does anyone have experience on where to cut, so that the flattening > of the cut would look reasonable and consistent? > I've tried several cuts, but whenever I tried it, the flattened surfaces > look different and it is not similar to the flattened surface that we see in > textbooks. > > If anyone has an experience on occipital cuts, please give me some > advice. > > Thanks. > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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occipital cuts
by Joongnam Yang 11 May '05

11 May '05

Hi all, The freesurfer manual on occipital cuts is clear on where to cut, but does anyone have experience on where to cut, so that the flattening of the cut would look reasonable and consistent? I've tried several cuts, but whenever I tried it, the flattened surfaces look different and it is not similar to the flattened surface that we see in textbooks. If anyone has an experience on occipital cuts, please give me some advice. Thanks. Nam.

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system hangs
by Joe Berens 11 May '05

11 May '05

Hello, I am having some trouble with freesurfer causing a system to hang. After processing a subject for several hours the system becomes unresponsive and a hard reboot is required. The system doesn't do this except when freesurfer is running. Here is some info on the system: Linux 2.4.21-15.0.4.ELsmp There are 4 processors: processor : 0 vendor_id : GenuineIntel cpu family : 15 model : 2 model name : Intel(R) Xeon(TM) CPU 2.80GHz stepping : 7 cpu MHz : 2799.707 cache size : 512 KB And lots of memory: total used free shared buffers cached Mem: 3022 1826 1195 0 70 1399 -/+ buffers/cache: 356 2665 Swap: 517 0 517 Thanks for any help or ideas, Joe ____________________________________________________________________________ Joe Berens Department of Electrical and Computer Engineering University of Minnesota - Twin Cities Phone: 612-625-4585 200 Union Street SE, Room 4-174 Email: joe(a)ece.umn.edu Minneapolis, MN 55455 Office: EE/CSsci 1-183 ____________________________________________________________________________ ____________________________________________________________________________ Joe Berens Department of Psychology University of Minnesota - Twin Cities Phone: 612-624-3601 75 East River Road Email: joe(a)umn.edu Minneapolis, MN 55455 Office: 160e Elliot Hall ____________________________________________________________________________

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RE: [Freesurfer] Manual editing tips?
by Fornito, Alexander 11 May '05

11 May '05

Hi, Just a bit confused re: Evelina's comment: " 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." And Bruce's comment: " 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." My questions are: - What surfaces (and at what point) is the thickness calculated from? Is it from the edited wm and pial surfaces used when create final surfaces is run? - To what degree do variations in manual editing affect thickness estimates? - Would it be advisable to perform a reliability study to make sure the manual editing process does not affect thickness estimates too much? Thanks again, Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, May 09, 2005 10:39 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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cortical thickness in the parietal lobe
by Marie Schaer 11 May '05

11 May '05

Hello all Freesurfer users! I am planning to do some cortical thickness analysis in children affected by psychiatric disorders, and after a few months of reflection, I still have some trouble to obtain a correct segmentation in the parietal region with my images. Actually, I am especially interested in the parietal lobe where we already observed a decrease in the gray matter volume in this sample of patients, but I have some trouble with the segmentation of the gray-white matter in this region. In fact, my orig and smoothwm surfaces look pretty good, except in about 10 slices in the parietal lobe where parietal cortex is so bright that it is classified as white matter. I first thought that it was either due to the quality of the scan (1.5 Tesla, slices 1.5mm) or related to a bias in the magnetic field. So first I tried to apply different bias correctors, but it has no effect on the segmentation. Finally, I found that forcing the high gray and white low values during the segmentation (in the Wm Filter Expert Preferences) was really interesting to obtain a better orig surface on my images. What I did is I applied a Gaussian Fitting algorithm of segmentation on the normalized and skull stripped image (brain), and took the limit values of the partial volume intensity for the high gray and low white value, so that the segmentation included the tissue classified as partial volume (about 97 for white low and 104 for high gray, depending on the subjects). This had a quite benefic effect on the parietal cortex, but as you can probably imagine, it excluded the subcortical structure of my wm images, and increase drastically the time spent for manual editing. Further, most of the time I have to delineate the insular cortex manually, so I just displaced the segmentation problem from the upper to the medial structures. I am quite perturbed by this failure to obtain a correct cortical ribbon in the parietal region with my images, any advice or idea will be greatly appreciated… Are my images not enough good for what I want to do? Did someone already notice that parietal cortical thickness was sometimes difficult to assess? (I checked the bert’s one, which also show a really thin parietal cortex?) How can I solve this problem? Is there any way to apply differentially the rules for the segmentation according to the region in Freesurfer? For example, based on a reference atlas that specifies that partial volume have to be included in the parietal region, and excluded in the subcortical region? Or referring to the talairach boxes, that means specify the high gray and low white value for all the regions that correspond to the coordinates of the parietal talairach boxes? Thank you very much for your help, Best regards, Marie Schaer Neuroimaging Laboratory Child Psychiatry Department Geneva Faculty of Medicine Switzerland PS: I attached the images with my first message, but it was refused because too big for the mailing list, but I can easily provide you the images again.

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multiple comparision on cortex
by Moo K. Chung 10 May '05

10 May '05

In case anyone wish to perform a multiple comparison on the cortex, I have written a MATLAB function that gives the threshold for t statistic: http://www.stat.wisc.edu/~mchung/softwares/pvalue/pvalue.html You need to compute the area of all triangles by yourself to be put into the MATLAB function and requires some sort of surface-based smoothing that controls the amount of FWHM. The detail can be found in http://www.stat.wisc.edu/~mchung/papers/ni_heatkernel.pdf Moo. -- Moo Chung http://www.stat.wisc.edu/~mchung Assistant Professor Department of Statistics University of Wisconsin-Madison

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Re: [Freesurfer] mri_convert
by Nick Schmansky 09 May '05

09 May '05

Wan, The problem is that the DICOM files are JPEG compressed, and currently Freesurfer only supports raw data format. A work-around is to use a converter, such as MRIcro to load the files and convert to a supported format, such as that output by the MRIcro's Import->Conversion wizard tool. Then run mri_convert with that file (a .img extension is produced). I've done this, and mri_convert produces the desired COR files. I can post either the .img file or the COR files for ftp download if you like. Better DICOM file validation will appear in a future version of Freesurfer. Nick > On Thu, 5 May 2005, Wan Park wrote: > > > 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 09 May '05

09 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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FW: [Freesurfer] Manual editing tips?
by Fornito, Alexander 09 May '05

09 May '05

-----Original Message----- From: Fornito, Alexander Sent: Mon 5/9/2005 1:14 PM To: Bruce Fischl Cc: Subject: RE: [Freesurfer] Manual editing tips? That did the trick. So then the ?.thickness file contains data needed to calculate thickness stats (and I assume the same is true for the ?.sulc and ?.curv, and ?.area files). Is it possible to visualize them? I've noticed that you display thickess in fig 2 of you PNAS paper. I was wandering if there is an output surface that can be overlaid onto the inflated surface that displays thickness variations across the cortex. Thanks for your quick responses!!! Alex -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 5/9/2005 11:52 AM To: Fornito, Alexander Cc: Evelina Busa; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Manual editing tips? because thickness isn't a surface - it's a scalar field (it has no geometry information, just a list of vertex indices and thickness values). You can only run mris_euler_number on a surface On Mon, 9 May 2005, Fornito, Alexander wrote: > 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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Freesurfer May 2005