[Freesurfer] Motion correction
Dear all, we are currently processing a dataset using FreeSurfer 5.0 and in a (very) few subjects (3 of 450) the output is distorted. However, when rerunning the 3 subjects adding the -flirt-motioncor flag to the recon-all -all command, the output is fine (please see http://folk.uio.no/haakongr/files/inflated444.jpg for an example, left side is the -flirt-motioncor version). Any ideas as how to solve this problem without mixing procedures (or rerunning all subjects) would be highly appreciated! Thanks, Håkon Grydeland --- FREESURFER_HOME: /psyklab/local/freesurfer.5.0.0 Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 RedHat release: Red Hat Enterprise Linux Client release 5.5 (Tikanga) Kernel info: Linux 2.6.18-194.11.4.el5.usit_CVE_2010_3081 x86_64 ___ 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] squashed ascii coordinates of flattened patch
Hi, I'm trying to get the coordinates of vertices on a flattened patch that I've cut out of an inflated surface using tksurfer in fs 4.5.0. I save the patch, use mris_flatten, and then mris_convert -p. However, the coordinates I'm getting render the patch somewhat distorted and I'm wondering how I can recover the original geometry. Loading the ascii file back into tksurfer results in the correct geometry, so is there some distortion that tksurfer accounts for when loading up a patch. At the link below I've put a screen shot of the ascii coordinates plotted (ignore the black line) and the flat patch as it looks in tksurfer. I've also put the patch files I'm using. Note how the patch seems squashed. http://web.mit.edu/~edechter/Public/ After saving the patch I run: mris_flatten -w 10 patch_file patch_file.flat mris_convert -p patch_file.flat patch_file.flat.asc Also, there are a number of extraneous random vertices that show up in the ascii files. They are speckled around the patch in the left hand plot. What are these? And how do I get rid of them? Thanks, Eyal Dechter -- edech...@mit.edu Kanwisher Lab MIT ___ 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] Making a surface from the skull?
Hi all, I know this is slightly outside the normal bounds, but I am wondering if there is a way to create a surface from the skull? One of our folks is looking to create some custom-fitted recording chambers for nonhuman primates based on the individual skull. I seem to recall that FS has a way of generating STL files, which would be perfect for submitting to a rapid prototyping machine. Here's what the user says: In brief, I would like to shape the bottom-side of my recording chambers (elliptical/circular cylinder) so that they form-fit to the curvature of the primate skull. Ideally, this will involve segmenting and extracting a 3D portion of the skull and converting it into an STL file to use for machining the implant. Best, mjp ___ 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] Making a surface from the skull?
Hi Mark, you might check Matti Hamalainen's MNE website. He uses the watershed code to generate boundary models, including skull. Or just try out mri_watershed with -surf I think (it's covered in the help, at least a bit) cheers Bruce On Fri, 1 Oct 2010, Mark J. Pearrow wrote: Hi all, I know this is slightly outside the normal bounds, but I am wondering if there is a way to create a surface from the skull? One of our folks is looking to create some custom-fitted recording chambers for nonhuman primates based on the individual skull. I seem to recall that FS has a way of generating STL files, which would be perfect for submitting to a rapid prototyping machine. Here's what the user says: In brief, I would like to shape the bottom-side of my recording chambers (elliptical/circular cylinder) so that they form-fit to the curvature of the primate skull. Ideally, this will involve segmenting and extracting a 3D portion of the skull and converting it into an STL file to use for machining the implant. Best, mjp ___ 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] Making a surface from the skull?
also, once you get a surface file, then mris_convert will convert to .stl format, which we've used in 3d printer applications. if you can get a skull from mri_watershed, then mri_tessellate will make a surface. mris_smooth and mris_keep_main_component are two other useful utility to clean things up. n. On Fri, 2010-10-01 at 16:24 -0400, Bruce Fischl wrote: Hi Mark, you might check Matti Hamalainen's MNE website. He uses the watershed code to generate boundary models, including skull. Or just try out mri_watershed with -surf I think (it's covered in the help, at least a bit) cheers Bruce On Fri, 1 Oct 2010, Mark J. Pearrow wrote: Hi all, I know this is slightly outside the normal bounds, but I am wondering if there is a way to create a surface from the skull? One of our folks is looking to create some custom-fitted recording chambers for nonhuman primates based on the individual skull. I seem to recall that FS has a way of generating STL files, which would be perfect for submitting to a rapid prototyping machine. Here's what the user says: In brief, I would like to shape the bottom-side of my recording chambers (elliptical/circular cylinder) so that they form-fit to the curvature of the primate skull. Ideally, this will involve segmenting and extracting a 3D portion of the skull and converting it into an STL file to use for machining the implant. Best, mjp ___ 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 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] correcting segmentation errors near the cerebellum
Hi Mehul, it's hard for me to evaluate this kind of pseudo color image. If you want to upload the dataset we'll take a look Bruce On Fri, 1 Oct 2010, Mehul Sampat wrote: Hi Folks, One of my colleagues has a case which has a strange artifcfact near the cerebellum; it seems like it recognizes the tentorium as part of brain This bright artifact (?) throws off the segmentation and also the main surface. To correct this artifact should he just make manual edits to the wm.mgz ? Thanks Mehul ___ 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] problem with tksurfer display
Dear Freesurfers： When I display and edit surfaces with tksurfer, the image can be loaded correctly, but whenever i rotate it, load curvatures, or load patches, it always freezes after my first operation and can't continue with the next operations. The freesurfer version i use is FS 4.5.0 under Fedora core 12, and the woking momory of computer is 4 Gigabytes with 4 processors, also enough hard disk space is available. can someone tell my what the problem is, and how i can fix it? thank you very much! changming___ 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.
