[Freesurfer] tkmedit question
Aloha FreeSurfers, I have a small question regarding tkmedit and the line tool. Is it possible to specify start and end point for a line on the tcl prompt? My goal is to create a line in a volume that is not parallel to one of the main axes. ATM I resort to turning the volume in question into a plane parallel to the line, but my overlays are not rotated accordingly so that is not as comfortable as I want it to be, and since it is somewhat exploratory pre-rotating volume and overlay is a bit unwieldy ;). For completeness, I am using 3.0.5 centos4-x86_64 under suse linux 10.1, but I guess that does not really matter. ahoi thanks for supplying these nice powerful tools Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] label ID in tksurfer
Hi, I've created a script for my MEG data which uses surfcluster and tksurfer to output functionally defined labels. It also makes an image of the labels overlaid on the cortical surface. I was wondering if there is any way to have it automatically identify the labels in the image, say by printing the label-id next to the actual label outline. Thanks, Szymon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] label ID in tksurfer
I was wondering if there is any way to have it automatically identify the labels in the image, say by printing the label-id next to the actual label outline. Sorry, no. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit question
On Tue, 2007-04-17 at 12:36 +0200, Sebastian Moeller wrote: Aloha FreeSurfers, I have a small question regarding tkmedit and the line tool. Is it possible to specify start and end point for a line on the tcl prompt? Sorry, no. My goal is to create a line in a volume that is not parallel to one of the main axes. ATM I resort to turning the volume in question into a plane parallel to the line, but my overlays are not rotated accordingly so that is not as comfortable as I want it to be, and since it is somewhat exploratory pre-rotating volume and overlay is a bit unwieldy ;). For completeness, I am using 3.0.5 centos4-x86_64 under suse linux 10.1, but I guess that does not really matter. I'm sorry but I don't understand what you're trying to do here. Why do you need to create a line parallel to the main axes? What does this have to do with specifying a line on the shell? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] label ID in tksurfer
that's too bad. instead, i assigned the label outline color based on a preset color map, so i can now id the labels that way. szymon On Tue, 2007-04-17 at 11:50 -0400, Kevin Teich wrote: I was wondering if there is any way to have it automatically identify the labels in the image, say by printing the label-id next to the actual label outline. Sorry, no. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert, primary slice direction and resampling
What happened to the .mat file? mri_convert should work with all orientations. Julia Hamstra wrote: To more fully explain the road block, this is the output of 'mri_info analyzefile --slicedirection' MatlabRead: readHeader returned NULL WARNING: analyzeRead(): matfile analyzefile.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. - INFO: could not find analyzefile.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in analyzefile.mat file I am running on a Mac. Does this have anything to do with it? I don't have matlab on the mac, but on a windows virtual machine. thanks ~julia On 4/16/07, Julia Hamstra [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected from right to left), but when I create files from mri_convert the header reads axial. This is particularly problematic when converting to analyze format from dicoms or another file type because the dimensions of the sagittal slices are applied the transverse plane. Using in_orientation and out_orientation options, the images will display correctly, but the header still reads axial. Can mri_convert subsample an image by retaining every other voxel without interpolating between voxels? Thank you, ~julia -- UC Davis Neuroscience Graduate Group The M.I.N.D. Institute - Amaral Lab (916) 703-0376 ___ 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
Re: [Freesurfer] Total brain volume, correlation coefficient after GLM
[EMAIL PROTECTED] wrote: Hello all, I have two questions here: 1. The summation of all the structure volumes listed in the aseg.stats seems to exceed the Brain Segmentation Volume given in the same file. With the exclusion of CSF and ventricles, the number becomes smaller than the Brain Segmentation Volume. If I am to study the total brain volume changes with age or other structure volumes (hippocampus), which number would be a better representation of the TBV volume? There is a discrepancy between the BrainSeg measure and the sum of the seg volumes in that the BrainSeg does not account for partial voluming. This was an oversite on my part, which I will fix. The BrainSeg also includes ventricles, which you probably don't want. I'll add another field for BrainSeg without ventricles. 2. We are interested in studying the correlation coefficient after mris_glmfit at every voxel. Is there any output file contains this information? We don't output the correlation coeff, but the gamma.mgh is the regression coefficient. Thanks, Zheng Hui ___ 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] 3T sequence
Hi, we just got our 3T Siemens scanner and I was lookinging for the recomendations on sequence and protocoll parameters that are sugested for data acquisitions to give best results with freesurfer segmntation/cortical recon etc. It seems there was a web page that had the suggested best for this but I can't seem to find it. Is there something still around ? thanks Greg. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 3T sequence
Greg, From the Data Requirements section of the beginners page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide there is a link to Andre Van der Kouwe's page on the scanner protocols used at the NMR Center: http://www.nmr.mgh.harvard.edu/~andre/ Nick On Tue, 2007-04-17 at 17:09 -0400, Kirk, Gregory wrote: Hi, we just got our 3T Siemens scanner and I was lookinging for the recomendations on sequence and protocoll parameters that are sugested for data acquisitions to give best results with freesurfer segmntation/cortical recon etc. It seems there was a web page that had the suggested best for this but I can't seem to find it. Is there something still around ? thanks Greg. ___ 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
