[Freesurfer] Stats for HC and lobar volumes in template space
Hello, We are thinking about the hippocampal and lobar volumes in FS template space, do we have such stats? Thanks. Aize ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical thickness in the template space
Hello there, We have a bunch of files that had freesurfer run already, simply using the command recon-all -s subjid -all, in order to get the cortical thickness in fs average space, should we have to re-run all of them again using recon-all -s subjid -qcache -measure thickness, or we may apply some transformation reported already to transform the thickness from subject space to fs average space ? Does anyone have any suggestion on how to do that? Thanks. Aize Subject: Re: Cortical thickness in the template space From: ni...@nmr.mgh.harvard.edu To: caoa...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Tue, 8 Mar 2011 16:50:41 -0500 Aize, run: recon-all -s subjid -qcache -measure thickness and this will create files in the /surf dir which sample the thickness data at different smoothing levels onto the fsaverage subject space. n. On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote: Hello, We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks. Aize The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Distance between two points along cortical
Hello FS Experts, Suppose we have two points on the cortical surface (pial for example), we want to know the distance between these two point along cortical surface (not direct distance). Does FS report this kind of distance? Any suggestion will be very appreciated. Aize ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Distance between two points along cortical
It is very good to know FS has this function. It will be very helpful for us. Thanks. Aize Date: Fri, 1 Apr 2011 13:57:23 -0400 From: rudo...@nmr.mgh.harvard.edu To: caoa...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Distance between two points along cortical This question comes up sometimes -- and the short answer is 'yes', there is a tool that can allow you to do this. Although it will be available in the next version of FS (5.1), it is still a bit rough around the edges. It is called 'mris_pmake' and to use it to determine the distance between two points, do: mris_pmake --subject subject --hemi -hemi --surface0 surface --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:startArg,endVertex:endArg So, if you have a subject called 'ID1' and want to determine the shortest distance along the surface between vertex 1 and vertex 3 on the left hemisphere smoothwm, do: mris_pmake --subject ID1 --hemi lh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:1,endVertex:3 Note, that this is *not* the geodesic, but is very close. The path is constrained to run along the surface mesh, so will in general be slightly longer than the geodesic. On 4/1/11 12:28 , caoaize wrote: Hello FS Experts, Suppose we have two points on the cortical surface (pial for example), we want to know the distance between these two point along cortical surface (not direct distance). Does FS report this kind of distance? Any suggestion will be very appreciated. Aize ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Cortical thickness in the template space
Hello, We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone point me where or how I can get them? Thanks. Aize ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Whole brain gray matter image
Hello FS Experts, I am trying to generate the whole brain gray matter image, I use aparc_aseg.mgz - wm.mgz for gray matter mask, then use this mask for gray matter. Is it correct? What is the difference between aseg.mgz and ribbon.mgz? Hope your help. Thanks. Aize ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freesurfer subcortical segmentation and FSL FIRST
Hello Freesurfer Experts, I have a very basic question about the difference between Freesurfer subcortical segmentation tool and FSL FIRSTsub-cortical segmentation tool. May someone give me a point? Thanks. Aize _ MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！ http://kaba.msn.com.cn/?k=1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Question about manually editing pial surface
Hello Freesurfer expert, I have a question on how to manually edit the pial surface. My structure data are fully processed using recon-all -all. Then I go back to look at the white/pial surface and sub-cortical boundaries. In some data, I found the gray matter is not included in the pial surface. I looked at the freesurfer archive, got some idea of how to edit the pial surface by removing and painting the brainmask.mgz and T1.mgz, but it does not tell me how to change the pial surface to include the gray matter that should be inside pial surface. May someone please give me a help? Thanks. Aize _ 想知道明天天气如何？必应告诉你！ http://cn.bing.com/search?q=%E5%A4%A9%E6%B0%94%E9%A2%84%E6%8A%A5form=MICHJ2___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Symmetry on four major cortex lobes on left and right hemisphere
Hello Bruce, Based on Freesurfer segmentation, we calculated the volumes of four major cortex lobes on left and right hemisphere seperately. Now I hope to find some reports illustrate the symmetry stuff using Freesurfer. Do you know where I can find it ? Thanks. Aize _ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TLswm=1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Volumes of four major cortical lobes
Hi, Bruce, We want calculate the four major cortical lobe volumes, i.e. frontal, parietal, temporal, and occipital, to see the relationship between them and some ROIs. I did fully run recon-all, but not clear which file should be used and what cortical areas should be included in these four lobes seperatively. May you please give me some instruction? Thanks. Aize _ MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！ http://kaba.msn.com.cn/?k=1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] (no subject)
Hi, Bruce, I have two quick question, 1. After auto-segmentation, we are using 3D slicer to edit hippocampus. Are there any other researchers who did the same way, auto + manual editing? 2. Since we have a lot of data for related studies that needs hippocampus volume, we still prefer to use auto one (without editing). What can we do if I provide you one original data with edited hippocampus label map? What kind of other information is required? Please let me know then, thanks. Aize Date: Tue, 18 Aug 2009 09:33:49 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject) Hi Aize, I think hippocampus will probably be the hardest since it shares so much of a border with dark things that will be low contrast in your images. I didn't really look at other structures - did they appear accurate? One thing you can try is to manually correct a single image, then there are some switches I can dig up that will take the intensity distribution parameters from it instead of from the atlas, that should help. cheers Bruce On Tue, 18 Aug 2009, caoaize wrote: Hi, Bruce, Do you mean that we can not use freesurfer for hippocampus volume segmentation, if my data are with the same scanning parameters? We did statitical analysis for volumes of other sub-cortical areas from freesurfer, found some interesting results. If you said that the gray matter is too dark in our image, can we still use it for other sub-cortical areas volume segmentation? I will be appreciated for your answer. With my best regards, Aize Date: Mon, 17 Aug 2009 17:01:40 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject) Hi Aize, I think the hippocampal gray matter is so dark in your images that it is very difficult to distinguish from CSF. Do you have a lot of data collected with these parameters? If not, we probably could suggest some better ones. cheers, Bruce On Tue, 18 Aug 2009, caoaize wrote: Hello Bruce, The sequence we used is called Turbo field Echo, I need to check it again. I checked our scanning protocol, found that we did have marker on the subjects' forehead. I generate the right hippocampus from freesurfer, overlay with orig.nii (from orig.mgz), the overlay shows that the subject's right side is the right side in freesurfer's statistical report. It means that our left side is bigger than the right side. This result consitently appears on our other subjects data. I extract the hippocampus left side mask in this way: mri_binarize --i aseg.mgz --match 17 --o hippo_left.nii The label for right side is 53. Anything wrong for what I used? Also, I used asegstats2table --subject s1 s2... --meas volume --tablefile stats.txt to get the statistical report. If we accept the low corelation between manual and auto segmentation, how can we explain that the left side is bigger than the right side? I hope your help. Thanks a lot. Best Regards, Aize Date: Mon, 17 Aug 2009 13:51:26 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com Subject: RE: [Freesurfer] (no subject) wow, I don't think I've ever seen a T1-weighted MR with gray matter this dark. The gray/csf contrast is very low. What kind of sequence is it? On Tue, 18 Aug 2009, caoaize wrote: Hi, Bruce, Here is the aseg.mgz and norm.mgz files. Thanks. Aize Date: Mon, 17 Aug 2009 13:27:07 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com Subject: RE: [Freesurfer] (no subject) Hi Aize, I need the aseg.mgz as well (and probably the norm.mgz). Differences in the definitions of what is hippocampus and what isn't will reduce the correlation coefficient. They should still be somewhat correlated, but even a perfect pair of segmentations under each protocol for each subject will not have a perfect correlation, so it's hard to assess what it means, since the protocols are different. Bruce On Tue, 18 Aug 2009, caoaize wrote: Our data is 3T, the manual segmentation follow the McConnell protocol described in Volumetry of hippocampus and amygdala with high-resolution MRI and three-dimensional analysis software: minimizing the discrpancies between laboratories. I do not know what is the difference between yours and theirs. But, if both method are consistant, then the correlation coeffienct should be high. Here is one image that has bad segmention on happocampus. I am appreciate for your help. Aize Date: Mon, 17 Aug 2009 11:52:19 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com CC: ni
Re: [Freesurfer] (no subject)
Hi, Bruce, I am not clear what manual segmentation protocol we are using, it was done by a trained RA. Currently we just calculate the volumes correlation between manual segmentation and the auto one, but not your DICE method. Our aquisitions are: Philips 3D sense, T1TFE, TR 7.9ms. In 27 subjects, we have two hippocampus volumes from Freesurfer auto segmentation around 1700, it keeps the edge, but lost lots of inside voxels. I am thinking to manual edit these two volumes, but do not know what happened. Aize Date: Sat, 15 Aug 2009 09:14:30 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject) Hi Aize, you are using the CMA manual segmentation protocol? We have not found a bias in volumes, and our DICE is usually close to .9 for hippocampus. What acquisitions are you using? cheers, Bruce On Sat, 15 Aug 2009, caoaize wrote: Hi, Bruce, Our segmentation protocol is the same one as Freesurfer's auto segmentation, I used recon-all -s subject -all, command. I do not know in this protocol, whether fimbria and alveus are included. We do not have skin fiducial to tell right or left side. The interesting thing the mean volume for auto is less than manual segmentation. Aize Subject: Re: [Freesurfer] (no subject) From: ni...@nmr.mgh.harvard.edu To: fis...@nmr.mgh.harvard.edu CC: caoa...@hotmail.com; freesurfer@nmr.mgh.harvard.edu Date: Fri, 14 Aug 2009 18:53:41 -0400 just to add a factoid, from the ADNI data set, 793 subjects processed by freesurfer: Volume Mean: StdDev: --- - --- Left-Hippocampus 3184.335 604.930 Right-Hippocampus 3233.753 621.896 seems pretty symmetric, with the right being slightly larger (but within std). this subject set is a mix of controls, MCI and AD patients. n. On Fri, 2009-08-14 at 17:53 -0400, Bruce Fischl wrote: is your segmentation protocol the same as the one we base our automated segmentation on? For example, are fimbria and alveus considered part of the hippocampus? As far as left/right switches go, do you have any fiducial markers (e.g. vitamin E tablets) in the images? cheers Bruce On Sat, 15 Aug 2009, caoaize wrote: Hi, there, I have some problem for the hippocampus segmentation results. 1. My structural data are originally in par-rec file. I used r2agui to convert them into .nii format, then use recon-all -i to convert the .nii data into freesurfer .mgz format. Based on these operations, I run recon-all -all on all my data, the statistical report show that the mean left hippocampus volume is bigger than the right one, while literature shows that the right one should be bigger. This problem continuously appeared in our different studies. I am not sure whether it is r2agui's problem, which changed the oritation of the structural data. Do you have any idea? 2. After autosegmentation, we did a statistical comparison analysis between automatic segmentation and manual segmentation, and the correlation is quite low, less than 80%, which is not acceptable for us. 3. Can I edit the auto segmentation results in Freesurfer if we think the auto segmentation is not good enough in some area? I will be really appreciated for your help. Aize _ Messenger°²È«±£»¤ÖÐÐÄ£¬Ãâ·ÑÐÞ¸´ÏµÍ³Â©¶´£¬±£»¤Messenger°²È«£¡ http://im.live.cn/safe/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ ÿÿWindows Live Messengerÿÿ http://www.windowslive.cn _ 与任何您希望的人分享您的回忆。 http://www.microsoft.com/china/windows/windowslive/products/photos-share.aspx?tab=1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
Hello Bruce, The sequence we used is called Turbo field Echo, I need to check it again. I checked our scanning protocol, found that we did have marker on the subjects' forehead. I generate the right hippocampus from freesurfer, overlay with orig.nii (from orig.mgz), the overlay shows that the subject's right side is the right side in freesurfer's statistical report. It means that our left side is bigger than the right side. This result consitently appears on our other subjects data. I extract the hippocampus left side mask in this way: mri_binarize --i aseg.mgz --match 17 --o hippo_left.nii The label for right side is 53. Anything wrong for what I used? Also, I used asegstats2table --subject s1 s2... --meas volume --tablefile stats.txt to get the statistical report. If we accept the low corelation between manual and auto segmentation, how can we explain that the left side is bigger than the right side? I hope your help. Thanks a lot. Best Regards, Aize Date: Mon, 17 Aug 2009 13:51:26 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com Subject: RE: [Freesurfer] (no subject) wow, I don't think I've ever seen a T1-weighted MR with gray matter this dark. The gray/csf contrast is very low. What kind of sequence is it? On Tue, 18 Aug 2009, caoaize wrote: Hi, Bruce, Here is the aseg.mgz and norm.mgz files. Thanks. Aize Date: Mon, 17 Aug 2009 13:27:07 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com Subject: RE: [Freesurfer] (no subject) Hi Aize, I need the aseg.mgz as well (and probably the norm.mgz). Differences in the definitions of what is hippocampus and what isn't will reduce the correlation coefficient. They should still be somewhat correlated, but even a perfect pair of segmentations under each protocol for each subject will not have a perfect correlation, so it's hard to assess what it means, since the protocols are different. Bruce On Tue, 18 Aug 2009, caoaize wrote: Our data is 3T, the manual segmentation follow the McConnell protocol described in Volumetry of hippocampus and amygdala with high-resolution MRI and three-dimensional analysis software: minimizing the discrpancies between laboratories. I do not know what is the difference between yours and theirs. But, if both method are consistant, then the correlation coeffienct should be high. Here is one image that has bad segmention on happocampus. I am appreciate for your help. Aize Date: Mon, 17 Aug 2009 11:52:19 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject) it lost interior voxels? That doesn't sound right. Can you send us an image? If your manual protocol is different than the one we used then the DICE overlap is somewhat irrelevant. cheers, Bruce On Mon, 17 Aug 2009, caoaize wrote: Hi, Bruce, I am not clear what manual segmentation protocol we are using, it was done by a trained RA. Currently we just calculate the volumes correlation between manual segmentation and the auto one, but not your DICE method. Our aquisitions are: Philips 3D sense, T1TFE, TR 7.9ms. In 27 subjects, we have two hippocampus volumes from Freesurfer auto segmentation around 1700, it keeps the edge, but lost lots of inside voxels. I am thinking to manual edit these two volumes, but do not know what happened. Aize Date: Sat, 15 Aug 2009 09:14:30 -0400 From: fis...@nmr.mgh.harvard.edu To: caoa...@hotmail.com CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject) Hi Aize, you are using the CMA manual segmentation protocol? We have not found a bias in volumes, and our DICE is usually close to .9 for hippocampus. What acquisitions are you using? cheers, Bruce On Sat, 15 Aug 2009, caoaize wrote: Hi, Bruce, Our segmentation protocol is the same one as Freesurfer's auto segmentation, I used recon-all -s subject -all, command. I do not know in this protocol, whether fimbria and alveus are included. We do not have skin fiducial to tell right or left side. The interesting thing the mean volume for auto is less than manual segmentation. Aize Subject: Re: [Freesurfer] (no subject) From: ni...@nmr.mgh.harvard.edu To: fis...@nmr.mgh.harvard.edu CC: caoa...@hotmail.com; freesurfer@nmr.mgh.harvard.edu Date: Fri, 14 Aug 2009 18:53:41 -0400 just to add a factoid, from the ADNI data set, 793 subjects processed by freesurfer: Volume Mean: StdDev: --- - --- Left-Hippocampus 3184.335 604.930 Right-Hippocampus 3233.753 621.896 seems pretty symmetric, with the right being slightly larger (but within std). this subject set is a mix of controls
Re: [Freesurfer] (no subject)
Hi, Bruce, Our segmentation protocol is the same one as Freesurfer's auto segmentation, I used recon-all -s subject -all, command. I do not know in this protocol, whether fimbria and alveus are included. We do not have skin fiducial to tell right or left side. The interesting thing the mean volume for auto is less than manual segmentation. Aize Subject: Re: [Freesurfer] (no subject) From: ni...@nmr.mgh.harvard.edu To: fis...@nmr.mgh.harvard.edu CC: caoa...@hotmail.com; freesurfer@nmr.mgh.harvard.edu Date: Fri, 14 Aug 2009 18:53:41 -0400 just to add a factoid, from the ADNI data set, 793 subjects processed by freesurfer: Volume Mean: StdDev: --- - --- Left-Hippocampus 3184.335 604.930 Right-Hippocampus 3233.753 621.896 seems pretty symmetric, with the right being slightly larger (but within std). this subject set is a mix of controls, MCI and AD patients. n. On Fri, 2009-08-14 at 17:53 -0400, Bruce Fischl wrote: is your segmentation protocol the same as the one we base our automated segmentation on? For example, are fimbria and alveus considered part of the hippocampus? As far as left/right switches go, do you have any fiducial markers (e.g. vitamin E tablets) in the images? cheers Bruce On Sat, 15 Aug 2009, caoaize wrote: Hi, there, I have some problem for the hippocampus segmentation results. 1. My structural data are originally in par-rec file. I used r2agui to convert them into .nii format, then use recon-all -i to convert the .nii data into freesurfer .mgz format. Based on these operations, I run recon-all -all on all my data, the statistical report show that the mean left hippocampus volume is bigger than the right one, while literature shows that the right one should be bigger. This problem continuously appeared in our different studies. I am not sure whether it is r2agui's problem, which changed the oritation of the structural data. Do you have any idea? 2. After autosegmentation, we did a statistical comparison analysis between automatic segmentation and manual segmentation, and the correlation is quite low, less than 80%, which is not acceptable for us. 3. Can I edit the auto segmentation results in Freesurfer if we think the auto segmentation is not good enough in some area? I will be really appreciated for your help. Aize _ Messenger°²È«±£»¤ÖÐÐÄ£¬Ãâ·ÑÐÞ¸´ÏµÍ³Â©¶´£¬±£»¤Messenger°²È«£¡ http://im.live.cn/safe/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ 上Windows Live 中国首页，下载最新版Messenger！ http://www.windowslive.cn___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
Hi, there, I have some problem for the hippocampus segmentation results. 1. My structural data are originally in par-rec file. I used r2agui to convert them into .nii format, then use recon-all -i to convert the .nii data into freesurfer .mgz format. Based on these operations, I run recon-all -all on all my data, the statistical report show that the mean left hippocampus volume is bigger than the right one, while literature shows that the right one should be bigger. This problem continuously appeared in our different studies. I am not sure whether it is r2agui's problem, which changed the oritation of the structural data. Do you have any idea? 2. After autosegmentation, we did a statistical comparison analysis between automatic segmentation and manual segmentation, and the correlation is quite low, less than 80%, which is not acceptable for us. 3. Can I edit the auto segmentation results in Freesurfer if we think the auto segmentation is not good enough in some area? I will be really appreciated for your help. Aize _ Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！ http://im.live.cn/safe/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampus segmentation problem
Hi, there, I have some problem for the hippocampus segmentation results. 1. My structural data are originally in par-rec file. I used r2agui to convert them into .nii format, then use recon-all -i to convert the .nii data into freesurfer .mgz format. Based on these operations, I run recon-all -all on all my data, the statistical report show that the mean left hippocampus volume is bigger than the right one, while literature shows that the right one should be bigger. This problem continuously appeared in our different studies. I am not sure whether it is r2agui's problem, which changed the oritation of the structural data. Do you have any idea? 2. After autosegmentation, we did a statistical comparison analysis between automatic segmentation and manual segmentation, and the correlation is quite low, less than 80%, which is not acceptable for us. 3. Can I edit the auto segmentation results in Freesurfer if we think the auto segmen! tation is not good enough in some area? I will be really appreciated for your help. Aize _ 上Windows Live 中国首页，下载最新版Messenger！ http://www.windowslive.cn___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
