[Freesurfer] intrinsic curvature
Hi FS Developers,I would like to know if the measures of intrinsic curvature of FS are quite reliable; I would like to launch a project with this parameter, but I've never used this.Which is your experience? Thanks,IreneResident in Neurology, Italy ___ 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] tksurfer crashes
On the off chance that you are using a Mac - I had a similar issue with X11 and tksurfer becoming unresponsive at the tkoInitWindow stage. I think this is because a recent OS X update broke X11. This update (from X11 2.5.4 to 2.6.5) fixed the problem for me: http://support.apple.com/kb/DL1605 Cheers, Johan Dear Freesurfer experts, I have a problem with Tksurfer. Whereas this worked previously fine it suddenly crashes every time I try to start it. This happens with every subject or fsaverage. A similar problem was reported before with similar terminal output but unfortunately I could not find a solution to this problem in the mailing list. Any suggestions are welcome! Ruthger Righart Hi Michelle, hmmm, no idea. Do you want to upload the the subject and we'll see if we can replicate the problem? Do you have enough memory on that machine? Bruce On Mon, 19 Mar 2012, Michelle Umali wrote: Hi Freesurfers, I've been using Freesurfer for a while, and have had no trouble with launching tksurfer. But recently I have tried to view an inflated hemisphere of a subject I have had no problem viewing before. The window no longer opens. This the case for all of my subjects, with whom I have had no previous problems. Any suggestions would be most welcome. Thanks very much. Michelle Below is the terminal output. After this it just returns to the prompt without any error message.. /usr/local/freesurfer/subjects tksurfer ld07 lh inflated subject is ld07 hemiis lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=160638, faces=321272 surfer: double buffered window surfer: tkoInitWindow(ld07) ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Johan Carlin, PhD Research Associate MRC Cognition Brain Sciences Unit 15 Chaucer Road Cambridge CB2 7EF UK johan.car...@mrc-cbu.cam.ac.uk +44 (0)1223 355294 ext 278 ___ 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] optic radiation ROI
Hi All, Is there an Optic Radiation ROI in freesurfer or some other program ? Please let me know. Thank you 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.
Re: [Freesurfer] wm vol mismatch
I understand, so i will use this images, but can you recommend me a good way to change my new volume file to a average subject space?I have tried registering the orig.mgz from the individual to the average using tkregister, mri_vol2vol, and bbregister, getting not good results at all.Any suggestions?Best Regards,Gabriel.El 21/11/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Hi Gabriel, this is normal. The volumes listed with aseg.stats have been corrected for partial volume, so it is not as simple as counting up all the voxels.dougOn 11/21/2012 12:36 PM, Gabriel Gonzalez Escamilla wrote: Dear Freesurfer, I'm trying to convert come labels from the aseg.mgz into nifti volumes I'm using: mri_extract_label aseg.mgz # and aseglabel#.nii where the # is the label as appears on the freesurferColoLUT.txt and it seems to work perfectly, but the number of voxels does not match with the number of voxels output in the aseg.stats, is this normal? they vary from i.e. 2603 in the aseg.stats to 2466 in the volume. to verify that it was't a problem from the extraction, I have tryed mris_binarize to match the same # segID as the mri_extract_label, and also use the matlab functions to open the aseg.mgz and keep those voxels which value were close to the #. With these two new options I get exactly the same number of voxels as with mri_extrac_label. So I don't know what could be the problem. Does anyone have an idea? Best Regards, Gabriel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- 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.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] optic radiation ROI
No, sorry On Nov 22, 2012, at 1:10 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: Hi All, Is there an Optic Radiation ROI in freesurfer or some other program ? Please let me know. Thank you Ri ___ 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.
[Freesurfer] How to design the contrast matrix with 12 regressors?
Dear FreeSurfers: I hope you can help me out with a problem in disgning my .mtx file. I want to examine the difference among three groups (HC group, EX group and PT group). Considing gender, I have six groups as similar as the example described inhttp://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf6G0V. But I want to correct for age. Then, I have 6 classes (two factors/three levels) and one covariate (age). How can I compare the difference among three groups (HC group, EX group, and PT group)? Could you please tall me how to design the contrast matrix with 12 regressors? Thanks a zillion times! Best wishes shiguangli ___ 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.
