Re: [Freesurfer] Head Points data files
The head points file (.hpts) is just a file of lines containing a label, an index, and an xyz coordinate: cardinal 2 0.00 0.112500 0.00 cardinal 3 0.071534 0.00 0.00 hpi 1 0.068430 0.020674 0.088621 hpi 2 0.040329 -0.083517 0.094487 hpi 3 -0.041193 -0.079972 0.100122 hpi 4 -0.054395 0.032501 0.102959 extra 1 0.72 0.111427 0.58 extra 2 0.070781 0.000371 0.000230 extra 3 -0.072046 -0.000394 -0.000207 extra 4 0.067647 0.020419 0.088373 ... The transform file (.trans) is a 4x4 float matrix: 9.999452e-01 -1.047178e-02 0.00e+00 -4.73e+00 1.044092e-02 9.969981e-01 7.671904e-02 -1.033253e+01 -8.033852e-04 -7.671483e-02 9.970528e-01 -6.399206e+01 0.00e+00 0.00e+00 0.00e+00 1.00e+00 I don't know of anybody who actively uses the head point stuff, so I'm not sure if it's up to date with how you generated the data. On Fri, Oct 27, 2006 at 11:16:04AM -0500, Juranek, Jenifer wrote: > Hi, > > What are the file format requirements for the 2 files called to load > head points - *.hpts and *.trans into tkmedit or tksurfer? > > > > We have a whole-head neuromagnetometer (4-D Neuroimaging 3600 Magnes MEG > system) with 248 sensor channels. > > I'd like to co-register my dipole locations with FreeSurfer's > aseg+aparc.mgz to efficiently localize dipoles x ROIs. I have already > co-registered index points and headshape files to each subject's aMRI > within 4D's software. > > > > Any advice is greatly appreciated! > > Jenifer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_annotation2label
Hi, I have two annotations, ?h.aparc.annot and ?h.aparc.a2005s.annot, created by recon-all with the –cortparc and –cortparc2 command options. I would like to convert each of these to a set of labels. For aparc.a2005s.annot I run (hopefully this is correct): mri_annotation2label --subject subj04_bay2 --hemi rh --annotation aparc.a2005s --labelbase $SUBJECTS_DIR/subj04_bay2/label/aparc2005-rh --table $FREESURFER_HOME/Simple_surface_labels2005.txt But for aparc.annot I don’t know what table file I should specify (there are two other files in the $FREESURFER_HOME folder that could potentially be correct: Simple_surface_labels200s.txt and surface_labels.txt). Could you tell me which table to use for aparc.annot? Thanks, Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] average T1's before correcting for inhomogeneity?
Greetings all, I'm new to freesurfer, so apologies if this has been covered. Two questions about early processing: 1) It looks like the recon-all script averages multiple T1's prior to correcting inhomogeneity. If processing T1's acquired on different days, and/or on different scanners, might it be advantageous to manually run mri_nu_correct.mni on each individually before averaging? Other than CPU time, why average first and then correct for inhomogeneity? 2) Is freesurfer's use of MNI_N3 over FSL's fast inhomogeneity correction algorithmic, empirical, historical, or other? Thanks! Stephen -- Stephen Towler [EMAIL PROTECTED] 352-294-0048 office 352-258-6409 mobile 352-392-8347 fax Leonard Lab Department of Neuroscience PO Box 100244 University of Florida HSC Gainesville, FL 32610 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_annotation2label
Which version are you using? The dev version should not require a --table option doug Dahlia Sharon wrote: Hi, I have two annotations, ?h.aparc.annot and ?h.aparc.a2005s.annot, created by recon-all with the –cortparc and –cortparc2 command options. I would like to convert each of these to a set of labels. For aparc.a2005s.annot I run (hopefully this is correct): mri_annotation2label --subject subj04_bay2 --hemi rh --annotation aparc.a2005s --labelbase $SUBJECTS_DIR/subj04_bay2/label/aparc2005-rh --table $FREESURFER_HOME/Simple_surface_labels2005.txt But for aparc.annot I don’t know what table file I should specify (there are two other files in the $FREESURFER_HOME folder that could potentially be correct: Simple_surface_labels200s.txt and surface_labels.txt). Could you tell me which table to use for aparc.annot? Thanks, Dahlia. ___ 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] average T1's before correcting for inhomogeneity?
Hi Stephen, 1) Yes, this is probably a better idea if you are collecting in different scan sessions. In general I think this is to be avoided as you will have other differential distortions that will add blurring (e.g. gradient nonlinearities, B0 distortions, different tongue/jaw positions, etc...). 2) Historical. We haven't really tried to compare N3 to anything else. Let us know if you think the FSL stuff works better for you. cheers, Bruce On Mon, 30 Oct 2006, Stephen Towler wrote: Greetings all, I'm new to freesurfer, so apologies if this has been covered. Two questions about early processing: 1) It looks like the recon-all script averages multiple T1's prior to correcting inhomogeneity. If processing T1's acquired on different days, and/or on different scanners, might it be advantageous to manually run mri_nu_correct.mni on each individually before averaging? Other than CPU time, why average first and then correct for inhomogeneity? 2) Is freesurfer's use of MNI_N3 over FSL's fast inhomogeneity correction algorithmic, empirical, historical, or other? Thanks! Stephen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] mri_annotation2label
I was using the std version. It works well under dev. Thanks! Dahlia. By the way, the FSwiki entry on mri_annotation2label does not mention the –annotation command option (but perhaps this is on purpose?) From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, October 30, 2006 3:24 PM To: Dahlia Sharon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_annotation2label Which version are you using? The dev version should not require a --table option doug Dahlia Sharon wrote: Hi, I have two annotations, ?h.aparc.annot and ?h.aparc.a2005s.annot, created by recon-all with the –cortparc and –cortparc2 command options. I would like to convert each of these to a set of labels. For aparc.a2005s.annot I run (hopefully this is correct): mri_annotation2label --subject subj04_bay2 --hemi rh --annotation aparc.a2005s --labelbase $SUBJECTS_DIR/subj04_bay2/label/aparc2005-rh --table $FREESURFER_HOME/Simple_surface_labels2005.txt But for aparc.annot I don’t know what table file I should specify (there are two other files in the $FREESURFER_HOME folder that could potentially be correct: Simple_surface_labels200s.txt and surface_labels.txt). Could you tell me which table to use for aparc.annot? Thanks, Dahlia. ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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] RE: regional cortical thickness
Sorry, I've been in and out. Did you try mri_annotation2label ? doug Durastanti, Valentina (NIH/NINDS) [F] wrote: Hi, I sent an e-mail few days ago asking for the direction to create a medial wall label by mapping all the labels in aparc.a2005 to label files with mri_annotation2label to mask the non cortical regions on the thickness map. Can someone help me? Thanks Valentina -- 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] ROI group analysis
Hi, I am trying to run mri_volcluster on a group ROI and am having some trouble. I was hoping someone had suggestion. I created individual ROIs and wanted to average them to obtain a group ROI. I ran isxavg-re-sess for each ROI but there is no registration file for mri_volcuster to reference. Have I hit a dead end? Does anyone know another way of creating a group ROI that I can apply the mri_volcluster command to? Thanks, Cameron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ROI group analysis
There should be a register.dat file in the bold dir of the average subject (or maybe in the bold/analysis/tal dir) doug Cameron Ellis wrote: Hi, I am trying to run mri_volcluster on a group ROI and am having some trouble. I was hoping someone had suggestion. I created individual ROIs and wanted to average them to obtain a group ROI. I ran isxavg-re-sess for each ROI but there is no registration file for mri_volcuster to reference. Have I hit a dead end? Does anyone know another way of creating a group ROI that I can apply the mri_volcluster command to? Thanks, Cameron ___ 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] Quality of Surface
Hi Paul, it looks fine, but it's hard to evaluate how good a surface is from just looking at the inflated surface. You need to overlay white/pial on the MR in tkmedit and assess it for accuracy. Bruce On Mon, 30 Oct 2006, Paul Greenberg wrote: Hello, I've attached a tif image showing the results of an inflated hemisphere viewed in Tksurfer and was wondering a) how would you rate this inflation on a scale of 1-5 with 5 being the best? and b) given that there are many brains to process, are any of the visible defects worth fixing? Thanks, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
