[Freesurfer] Skipping time consuming FS parts.
Dear FS experts, I have a large data set which I want to recon-all, in order to obtain the cortical, sub-cortical parcellations and the corresponding volumes and thicknesses. As the reconstruction is very time-consuming I was wondering which steps I might skip without significant decrease in quality of the cortical segmentation. I noticed for instance that the automated topology fix takes quite long - if I skip this part, how does that change my results? Thanks in advance. Mohammed. ___ 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] Skipping time consuming FS parts.
Hi Mohammed, sorry, you can't really skip any of it if you want those results. cheers, Bruce On Fri, 26 Mar 2010, Mohammed el Morabit wrote: > > > Dear FS experts, > > I have a large data set which I want to recon-all, in order to obtain the > cortical, sub-cortical parcellations and the corresponding volumes and > thicknesses. As the reconstruction is very time-consuming I was wondering > which steps I might skip without significant decrease in quality of the > cortical segmentation. I noticed for instance that the automated topology fix > takes quite long - if I skip this part, how does that change my results? > > Thanks in advance. > > Mohammed. > > > ___ 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] Poor Talairach registration and effect on ICV
Hi, in our population of MCI patients, unfortunately parts of the cerebellum were not completely scanned. I ran the data throught the whole FS-4.5.0 pipeline and I see that the eTIV normalized volumes of the segmented structues have very large variance compared to the eTIV normalized group of independent age matched subjects with the full brain coveage. I assume that this is possibly due to the suboptimal registration to the template, which is used to compute eTIV. In fact, all the subjects with incomplete cerebellum failed to pass the quality check of the registration to Talairach, but on the first glance the registration seemed fine to me so I just used -notal-check flag to complete recon-all -all. I know I could go back, check more carefully and correct the Talairach transform manually, but I hesitate to go this way. Rather I thougt if it would be possible/feasible to remove the cerebellum from each subject AND the template and possibly achieve better registration from these images. Thanks in advance for opinions, Martin ___ 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] Poor Talairach registration and effect on ICV
Hi Martin, I guess that might work. It's hard for us to speculate as we've never tried anything like it Bruce On Fri, 26 Mar 2010, Martin Kavec wrote: > Hi, > > in our population of MCI patients, unfortunately parts of the cerebellum were > not completely scanned. I ran the data throught the whole FS-4.5.0 pipeline > and I see that the eTIV normalized volumes of the segmented structues have > very large variance compared to the eTIV normalized group of independent age > matched subjects with the full brain coveage. I assume that this is possibly > due to the suboptimal registration to the template, which is used to compute > eTIV. In fact, all the subjects with incomplete cerebellum failed to pass the > quality check of the registration to Talairach, but on the first glance the > registration seemed fine to me so I just used -notal-check flag to complete > recon-all -all. > > I know I could go back, check more carefully and correct the Talairach > transform manually, but I hesitate to go this way. Rather I thougt if it would > be possible/feasible to remove the cerebellum from each subject AND the > template and possibly achieve better registration from these images. > > Thanks in advance for opinions, > > Martin > ___ > 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 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] changing watershed threshold has no effect
Something like that I would say you usually have to manually edit. Allison -- On Fri, 26 Mar 2010, Andreas Berger wrote: > hello freesurfers, > > we are having a problem with insufficient skull stripping, in 66 out > of 200 subjects this affects the pial surface, as can be seen in the > attached screenshot1. since the problem is somewhat generalized in > location, i tried to change the watershed threshold as suggested by > the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean > -wsthresh n), but even 0 seems to have no effect (it looks different, > but not less skull), see screenshot2. am i doing it wrong? > ___ 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] Poor Talairach registration and effect on ICV
Thanks a lot for the opinion, Bruce! >From practical point of view, removing the cerebellum from each subjuct should be rather easy since I have its segmentation. Howabout the template? Is there any segmentation of the cerebellum for the template, or I would have to do it manually? I suppose I should edit the template, which is used for talairach registration during autorecon1. If so, could you please point me to the image file name? Thanks again, Martin On Friday 26 March 2010 13:32:26 you wrote: > Hi Martin, > > I guess that might work. It's hard for us to speculate as we've never > tried anything like it > Bruce > ___ 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 Digest, Vol 73, Issue 64
Hi Andreas: As far as I know, the complete command is: recon-all -s subjid -skullstrip -no-wsgcaatlas -wsthresh 35 -clean-bm Sincerely, Gonzalo Rojas Costa Laboratory of Medical Imaging Processing Department of Radiology Clínica Las Condes Santiago Chile > Date: Fri, 26 Mar 2010 11:07:01 +0100 > From: Andreas Berger > Subject: [Freesurfer] changing watershed threshold has no effect > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <68f948a91003260307g4fee4b69s9c04624544df2...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hello freesurfers, > > we are having a problem with insufficient skull stripping, in 66 out > of 200 subjects this affects the pial surface, as can be seen in the > attached screenshot1. since the problem is somewhat generalized in > location, i tried to change the watershed threshold as suggested by > the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean > -wsthresh n), but even 0 seems to have no effect (it looks different, > but not less skull), see screenshot2. am i doing it wrong? ___ 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] calculate the average thickness of a ROI around PCC
Hi, there, I'd like to measure the average thickness of a ROI around PCC (posterior cingulate cortex). I only have its MNI152 coordinate (-2, -45, 34). How can I calculate its corresponding RAS and Talaraich coordinate, is there an equation? Thanks! Guang _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_3___ 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.
