[Freesurfer] vertex coordinates: tksurfer vs sig.cluster.summary
Dear Freesurfers, I have noticed a slight incongruity between the coordinates outputted by sig.cluster.summary and those in tksurfer. For instance, in the .summary file one of my maxima (VtxMax=92221) has the following "Tal" coordinates: -14.9, -62.2, 57.5. Now, if I open the fsaverage with tksurfer, and I enter 92221 as my Vertex Index, the Vertex Talairach coordinates are slightly different than those reported by the .summary file (-14.89, -61.61, 57.01). Is this because the Max in my significant cluster actually spans multiple adjacent vertices, and therefore the coordinates provided by the .summary file represent an average across those vertices? As for the "MNI Talairach", my understanding is that these are from the MNI305, right? If so, why the "Talairach" part of the name? Thanks, Marco _ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 ma...@nmr.mgh.harvard.edu ___ 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] Help ! Error for generating *.mgz files
Hi, Thank you for reading this email ! I am a newbie to Medical Imaging, and am learning to use FreeSurfer for surface construction. Already installed FreeSurfer in Ubuntu, and the installation has been verified to be 100% successful. I got a bunch of data (coming in pairs of *.hdr and *.img), and I am trying to convert them to *.mgz files, so that I can use recon-all then. but when I call mri_convert as follows: mri_convert Rcing.imgRcing.mgz I got the following error : mri_convert Rcing.img Rcing.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from Rcing.img... - INFO: could not find /mnt/Data/Rcing.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: -40, . INFO: if not valid, please provide the information in /mnt/Data/Rcing.mat file - Segmentation fault I have searched the freesurfer website ... no luck Would you mind to give me some advice or hints ? Thank you so much ! Best Tim ___ 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] Help ! Error for generating *.mgz files
Hi Tim, the .hdr/.img format is called Analyze, and it doesn't come with orientation informaton. This means that it is easy for example to get a left/right swap that you will never know was in your data. Can you get it in any other format, like dicom, or whatever format it came off the scanner in? If not, you can send us one of the pairs of files that gives the segfault and we'll take a look cheers Bruce On Sat, 19 Feb 2011, xiaotian yin wrote: > Hi, > > Thank you for reading this email ! > > I am a newbie to Medical Imaging, and am learning to use FreeSurfer > for surface construction. > > Already installed FreeSurfer in Ubuntu, and the installation has been > verified to be 100% successful. > > I got a bunch of data (coming in pairs of *.hdr and *.img), and I am > trying to convert them to *.mgz files, so that I can use recon-all > then. > > but when I call mri_convert as follows: > > mri_convert Rcing.imgRcing.mgz > > I got the following error : > > > mri_convert Rcing.img Rcing.mgz > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from Rcing.img... > - > INFO: could not find /mnt/Data/Rcing.mat file for direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: -40, . > INFO: if not valid, please provide the information in /mnt/Data/Rcing.mat file > - > Segmentation fault > > > I have searched the freesurfer website ... no luck > Would you mind to give me some advice or hints ? Thank you so much ! > > > Best > Tim > ___ > 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] segment lobes
Hi, This may be complicated, but ... I would like to segment various brain lobes, save them as mask files, convert them to NIFTI format, feed them to FSL for tractography. Can anyone tell me if it is possible to segment brain lobes in freesurfer and then feed them to fsl? many thanks in advance, AJ ___ 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.
