[Freesurfer] cortical thickness in the parietal lobe
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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:[EMAIL PROTECTED] Sent: Monday, May 09, 2005 10:39 AM To: Fornito, Alexander Cc: Evelina Busa; freesurfer@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:[EMAIL PROTECTED] 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
[Freesurfer] system hangs
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 sharedbuffers cached Mem: 3022 1826 1195 0 70 1399 -/+ buffers/cache:356 2665 Swap: 517 0517 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: [EMAIL PROTECTED] 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: [EMAIL PROTECTED] Minneapolis, MN 55455 Office: 160e Elliot Hall ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] system hangs
Hi Joe, we need more information than this. Do you have screen output? What process was running? Check the subject to make sure nothing is wrong with it (e.g. cerebellum attached) That said, I don't think I've ever seen a freesurfer-induced hard reboot. Sounds more like something is wrong with your machine (that's always a developers first guess :>). cheers, Bruce On Wed, 11 May 2005, Joe Berens wrote: 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 sharedbuffers cached Mem: 3022 1826 1195 0 70 1399 -/+ buffers/cache:356 2665 Swap: 517 0517 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: [EMAIL PROTECTED] 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: [EMAIL PROTECTED] Minneapolis, MN 55455 Office: 160e Elliot Hall ___ 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] system hangs
Bruce, > we need more information than this. Do you have screen output? What > process was running? Check the subject to make sure nothing is wrong with > it (e.g. cerebellum attached) There is no screen output, the screen goes blank. I am not running freesurfer myself, I am just the admin for this system, I will try to find out if there is something wrong with the subject. > That said, I don't think I've ever seen a freesurfer-induced hard reboot. > Sounds more like something is wrong with your machine (that's always a > developers first guess :>). This was my first thought also, however the system works fine in any other context. Thanks, Joe > cheers, > Bruce > > On Wed, 11 May 2005, Joe Berens wrote: > > > 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 sharedbuffers cached > > Mem: 3022 1826 1195 0 70 1399 > > -/+ buffers/cache:356 2665 > > Swap: 517 0517 > > > > > > 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: [EMAIL PROTECTED] > > 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: [EMAIL PROTECTED] > > Minneapolis, MN 55455 Office: 160e Elliot Hall > > > > > > ___ > > 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 > 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: [EMAIL PROTECTED] 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: [EMAIL PROTECTED] Minneapolis, MN 55455 Office: 160e Elliot Hall ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] occipital cuts
We find that it helps to make the calcarine cut go very far posterior, usually requiring you to rotate the brain by about 30 degrees so you can actually reach the occipital pole. Then for the cutting plane points we use the anterior point of the calcarine cut, the acsending limb of the cingulate sulcus, and on the lateral side, we use the asecding part of the slyvian fissure. Sometimes this will still result in horns or weird things on the patch. I haven't had much luck in trying to get rid of those things. Stephanie > From: "Joongnam Yang" <[EMAIL PROTECTED]> > Date: Tue, 10 May 2005 16:35:48 -0400 > To: > Subject: [Freesurfer] occipital cuts > > 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@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
답신: Re: [Freesurfer] occipital cuts
$)CThanks 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 <[EMAIL PROTECTED]> 05/05/10 [EMAIL PROTECTED] 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@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] Manual editing tips?
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:[EMAIL PROTECTED] Sent: Wed 5/11/2005 11:30 PM To: Fornito, Alexander Cc: Evelina Busa; freesurfer@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:[EMAIL PROTECTED] > Sent: Monday, May 09, 2005 10:39 AM > To: Fornito, Alexander > Cc: Evelina Busa; freesurfer@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 fa
