Re: [Freesurfer] inflated images
Hi Anthony, a couple of things. First, we do have a metric preservation term in the inflation, so that not too much metric distortion is incurred during the deformation. But the real answer to your question is that there is correspondene between the inflated and other (e.g. white) surfaces, so we can always transfer information like thickness, which is a propert of the white and pial surfaces, to be visualized on the inflated. cheers, Bruce On Thu, 18 May 2006, anthony gallo wrote: Hello all, Can some one edify me regarding how FreeSurfer is able to maintain the same basic brain geometry (hemisphere shape) when it creates an inflated file image. I would figure that some areas (because of deeper sulci) would blow up (produce more inflated surface) much differently than others thus not maintaining the basic shape. I was thinking that maybe the program just flattens it all period, but then I wouldn't really be able to explain how you can still view the respective cortical thickness data because that too must correspond with all the nooks and crannies. I appreciate your help, Anthony ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Installation troubleshoot (Afni won't work)
Hello everyone, I'm new here to the freesurfer community, and i've install the latest package on my Linux.64 version. I've completed the installation stages described on MGH site and it all seemed to work quite well until I've tried to run the mc-sess routine. The error message I got was that AFNI's to3d routine couldn't be found. I then realised that in Freesurfer's package there wasn't any AFNI directory to be found. I've downloaded AFNI from their official site and put the extracted file in the directory $FREESURFER_HOME/afni/$os I've also modified the FreeSurferEnv.sch to include the following lines: setenv AFNI_DIR $FREESURFER_HOME/afni setenv AFNI_BIN $AFNI_DIR/$os where $os is Linux on my computer. Still mc-sess wouldn't work on my computer. Please if somebody can tell what I'm doing wrong it would be of great help. Thanks in advance. Jeremie DREYFUSS. -- ___ Search for businesses by name, location, or phone number. -Lycos Yellow Pages http://r.lycos.com/r/yp_emailfooter/http://yellowpages.lycos.com/default.asp?SRC=lycos10 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Installation troubleshoot (Afni won't work)
Hi Jeremie, could you include the information detailed in: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting thanks, Bruce On Thu, 18 May 2006, Dreyfuss Jeremie wrote: Hello everyone, I'm new here to the freesurfer community, and i've install the latest package on my Linux.64 version. I've completed the installation stages described on MGH site and it all seemed to work quite well until I've tried to run the mc-sess routine. The error message I got was that AFNI's to3d routine couldn't be found. I then realised that in Freesurfer's package there wasn't any AFNI directory to be found. I've downloaded AFNI from their official site and put the extracted file in the directory $FREESURFER_HOME/afni/$os I've also modified the FreeSurferEnv.sch to include the following lines: setenv AFNI_DIR $FREESURFER_HOME/afni setenv AFNI_BIN $AFNI_DIR/$os where $os is Linux on my computer. Still mc-sess wouldn't work on my computer. Please if somebody can tell what I'm doing wrong it would be of great help. Thanks in advance. Jeremie DREYFUSS. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
Are you sure the volume is conformed? On Thu, May 18, 2006 at 12:14:30PM -0400, Mark Pinsk wrote: I just installed the latest release on my mac ox 10.4 Trying to set control points on a monkey volume, and something wierd keeps happening... I will middle-click to set the control point, and the green cross will appear, but when I move to another location to set another control point, the first point disappears. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FreeSurfer algorithms
Surfers,Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data...maybe there are some papers that talk about this?? Anthony ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Installation troubleshoot (Afni won't work)
Jeremie, The AFNI package must be installed and setup independently from Freesurfer. Since you have it installed, it sounds like you just need to add the AFNI bin path to the search path. Something like this: setenv PATH $PATH:$AFNI_BIN rehash Then test if it finds to3d by running it. Nick On Thu, 2006-05-18 at 09:21 -0500, Dreyfuss Jeremie wrote: Hello everyone, I'm new here to the freesurfer community, and i've install the latest package on my Linux.64 version. I've completed the installation stages described on MGH site and it all seemed to work quite well until I've tried to run the mc-sess routine. The error message I got was that AFNI's to3d routine couldn't be found. I then realised that in Freesurfer's package there wasn't any AFNI directory to be found. I've downloaded AFNI from their official site and put the extracted file in the directory $FREESURFER_HOME/afni/$os I've also modified the FreeSurferEnv.sch to include the following lines: setenv AFNI_DIR $FREESURFER_HOME/afni setenv AFNI_BIN $AFNI_DIR/$os where $os is Linux on my computer. Still mc-sess wouldn't work on my computer. Please if somebody can tell what I'm doing wrong it would be of great help. Thanks in advance. Jeremie DREYFUSS. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FreeSurfer algorithms
Anthony, See the references section at the bottom of the main wiki page, where most of the papers themselves can be downloaded: https://surfer.nmr.mgh.harvard.edu/fswiki On Thu, 2006-05-18 at 17:02 -0400, Doug Greve wrote: btw, most of these are also listed at the end of: recon-all -help Bruce Fischl wrote: Be careful what you ask for :) -- if you use surface recons Dale, A.M. and M.I. Sereno (1993) Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach. Journal of Cognitive Neuroscience 5:162-176. Segonne F, Dale, AM, Busa E, Glessner M, Salvolini U, Hahn HK, Fischl B, A Hybrid Approach to the Skull-Stripping Problem in MRI. NeuroImage, 22, pp. 1160-1075, 2004 Dale, A.M., Fischl, Bruce, Sereno, M.I., (1999). Cortical Surface- Based Analysis I: Segmentation and Surface Reconstruction. NeuroImage 9(2):179-194 Fischl, Bruce, Sereno, M.I., Dale, A.M., (1999). Cortical Surface- Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System. NeuroImage 9(2):195-207 Fischl, Bruce, Liu, Arthur, and Dale, A.M., (2001). Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex. IEEE Transactions on Medical Imaging, 20(1):70-80 if you do inter-subject spherical averaging Fischl, Bruce, Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). High-resolution inter-subject averaging and a coordinate system for the cortical surface. Human Brain Mapping, 8:272-284 if you do a thickness study Fischl, Bruce, and Dale, A.M., (2000). Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images. Proceedings of the National Academy of Sciences, 97:11044-11049. if you use cortical parcellations Fischl B, van der Kouwe A, Destrieux C, Halgren E, Ségonne F, Salat DH, Busa E, Seidman LJ, Goldstein J, Kennedy D, Caviness V, Makris N, Rosen B, Dale, AM Automatically Parcellating the Human Cerebral Cortex. Cerebral Cortex, 2004; 14:11-22. there should be another one here by Desikan and Killiany - I'll have to add it. if you do subcortical segmentation Fischl B, Salat DH, van der Kouwe AJW, Makris N, Ségonne F, Dale AM. Sequence-Independent Segmentation of Magnetic Resonance Images. NeuroImage 23 Suppl 1, S69-84. Fischl B, Salat D, Busa E, Albert M, Dieterich M, Haselgrove C, van der Kouwe A, Killiany R, Kennedy D, Klaveness S, Montillo A, Makris N, Rosen B, Dale A.M.. Whole brain segmentation. Automated labeling of neuroanatomical structures in the human brain. Neuron. 2002; 33(3): 341-355. misc other ones F. Segonne, E. Grimson and B. Fischl (2003). Topology Correction of Subcortical Segmentation, MICCAI 2003. Salat DH, Buckner RL, Snyder AZ, Greve DN, Desikan RSR, Busa E, Morris JC, Dale AM, Fischl B. Thinning of the cerebral cortex in aging. Cerebral Cortex. Accepted with revision. On Thu, 18 May 2006, anthony gallo wrote: Surfers, Can someone please point me towards some detailed description of the algorithms that freesurfer uses to process the data...maybe there are some papers that talk about this?? Anthony ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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
[Freesurfer] retinotopy starting with blanks
Hi, I'm analyzing a retinotopy data-set in which each scan started with 2 TRs of a blank screen, and then proceeded to 8 cycles as usual. Is there any possibility to tell a retinotopy analysis to ignore these 2 TRs? Thanks! Dahlia. PS - I can't answer as to why these 2 blank TRs were put there. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
