Re: [Freesurfer] Total cerebral volume.
Hi Doug, I sum all structures except ventricle, CSF, cerebellum and brainstem in order to compare with SubCortGrayVol. Even the former includes some white matter structures and all subcortical structures, it is smaller compared to SubCortGrayVol.My original question is about calculating the total cerebral volumes, when I foundCortexVol CorticalWhiteMatterVol SubCortGrayVol is much bigger thanCortexVol CorticalWhiteMatterVol Sum(all structures (after ICV inthe list) except ventricle, CSF, cerebellum and brainstem).Hope I explained it better this time.Cheers,Zheng HuiOn 11/6/12 2:14 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:Hi Zheng, there is something wrong with your math. When I sum up all the columns in your table from Left-Lateral-Ventricle to CC_Anterior, I get 215952 for the first row (you get only 67548). Can you double check your calculations?dougOn 10/28/2012 11:53 PM, Zheng Hui wrote: Forgot to attach the excel file. Sorry for that. From: zhenghui zheng@duke-nus.edu.sg mailto:zheng@duke-nus.edu.sg Date: Monday, October 29, 2012 11:52 AM To: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: [Freesurfer] Total cerebral volume. Hi Doug, Thanks for replying. But our datasets do showed that Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) is much smaller SubCortGrayVol. The former is only about 30-40% of the later. We are using FS 5.1.0 without the SupraTentorialVol fix.I attached the aseg file for your reference (the last three columns in the sheet). Thanks, Zheng Hui On 10/24/2012 09:01 AM, Zheng Hui wrote: Hi freesurfer, We are trying to calculate the total cerebral volume which excludes cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use CortexVol CorticalWhiteMatterVol SubCortGrayVol Or CortexVol CorticalWhiteMatterVol Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) This should give very close to the same value. I don't think it makes a difference.Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run the segstats for longitudinal subjects, any extra step other than recon-all –long tpN baseID –segstats and does it affect any other structure or just SupraTentorialVol? It should not affect other structures. doug-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose 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] Total cerebral volume.
Hi freesurfer, We are trying to calculate the total cerebral volume which excludes cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use CortexVol + CorticalWhiteMatterVol + SubCortGrayVol Or CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run the segstats for longitudinal subjects, any extra step other than recon-all –long tpN baseID –segstats and does it affect any other structure or just SupraTentorialVol? Thank you, Zheng Hui ___ 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] New data point for longitudinal processing.
Hi freesurfer,We have processed two time point using freesurfer 5.1.0. I would like to know if we have a third point data, do I need to recreate the base and use this new base to re-process tp1,tp2?Thank you,Zheng Hui ___ 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] MEMPRAGE sequence.
Hi all,We did a scanner software upgrade to BV17 (Siemens) and lost the multi-echo MPRAGE sequence. Does anyone have any idea where to get the sequence? The scanner we have is a Siemens Tim Trio.Any help will be appreciated!Thank you,Zheng Hui ___ 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] mpr2mni305 failed for 2 subjects.
Hi Freesurfers,We are using version 5.1.0, and have two subjects failed at the talairach_avi step. I have attached the talairach_avi.log for your reference.Thanks,Zheng Hui talairach_avi.log Description: talairach_avi.log talairach_avi.log Description: talairach_avi.log ___ 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] freesurfer and VBM
Hi Ri, We have a paper comparing results from freesurfer and VBM. Chee MW, Zheng H, Goh JO, Park D, Sutton BP. Brain Structure in Young and Old East Asians and Westerners: Comparisons of Structural Volume and Cortical Thickness. J Cogn Neurosci. 2010 Apr 30. Cheers, Zheng Hui On 1/25/11 12:14 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: Hello All, Are there any papers comparing freesurfer to VBM ? Can anyone point me to them ? Thanks Ri ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Segmentation of pallidum.
Hi all, We are doing a test-retest study of FreeSurfer segmentation on our dataset. We found reliable estimations for most of the subcortical structures (1% difference) except palladum(3% to 4% difference) while in Fisch's 2002 Neuron paper, pallidum is one of the best segmented structure using manual tracing as gold standard. Any comment? By looking at the aseg, there is no intensity change from pallidum voxels and neighborhood white matter voxels. Is the definition of boundary purely based on the probabilistic atlas? Thanks, Zheng Hui ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem launching qdec.
Hi, I have two questions: 1) I just upgrade our intel Mac OS from Tiger to Leopard, and now are having problem using qdec. I am using version 4.0.0. When I type qdec in xterm, it outputs the following error msg: dyld: Library not loaded: /usr/X11R6/lib/libexpat.0.dylib Referenced from: /Applications/freesurfer/lib/KWWidgets/lib/KWWidgets/libKWWidgets.dylib Reason: image not found Trace/BPT trap Any idea how to fix this? 2) We have done the editing on 300 subjects (pial, wm and control point) and re-generated all the surfaces. One thing I realized is that the aseg.mgz does not follow the surfaces as it is processed before the surface reconstruction. Is there any way to re-generate the aseg.mgz using ?h.pial, ?h.white? Thanks, Zheng Hui ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
