Hi Paul, I'm not sure I understand. What does 3dcalc have to do with the LUT? doug
On 02/25/2013 05:13 PM, Paul Beach wrote: > Hi Doug. Thank you for the e-mail. > > I do, actually, have a 'next step' problem. > > I've been able to get ROIs drawn in tksurfer into an augmented > aparc+aseg file of an averaged subject. Now I need to be able to get > those ROIs, which are not part of the color LUT, into Afni space. > > For ROIs that are already in the LUT, getting them to Afni is no > problem, I simply use a 3dcalc command that utilizes their place in > the LUT. However, I have the problem of needing to export the newly > parcellated and segmented ROIs that aren't in the Freesurfer LUT to > Afni space. > > Is there a way to do this short of creating a new "spot" for them in > our LUT? If not, how does one go about adding ROIs to the LUT and/or > creating a LUT specific to my needs (since the Wiki suggests not > fussing with the original LUT)? > > > Thanks, > Paul > > > > On Mon, Feb 25, 2013 at 11:28 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Paul, do you still have a problem that needs to be solved? > doug > > > On 02/18/2013 04:39 PM, Paul Beach wrote: > > Thank you for forwarding this. > > > > I realize I need to further clarify my issue as well. > > > > With the help of Doug Greve I've taken hand made ROIs in tksurfer, > > repackaged them into a new annotation, and repackaged that into > a new > > aseg file for an average subject. Now (and this is where I'm stuck) > > I'm trying to take those newly minted ROIs, place them onto > individual > > subjects' brains and THEN send them to Afni for each of those > subjects > > (before doing seed correlation analysis). > > > > Previously I had been using mri_label2label to place the averaged > > subject ROI into single subjects' folders and then mri_label2vol to > > get them ready to send to Afni. However, this method was not > producing > > ROIs that covered the extent of a region's gray matter. Thus, Doug's > > solution of re-annotating and re-segmenting. > > > > Hopefully that makes things a bit easier. > > > > > > Thanks again for your help! > > Paul > > > > > > On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: > > > > Hi Paul > > > > we usually call those labels and have an ascii label file > format. > > Not sure how to get that into AFNI, but I'm zure Ziad (ccd) > knows. > > > > cheers > > Bruce > > > > On Mon, 18 Feb 2013, Paul Beach wrote: > > > > Hi there, > > Through the help of the Freesurfer Q&A staff I've been > able to > > get ROIs > > drawn in tksurfer into an augmented aparc+aseg file of an > > averaged subject. > > I need to be able to get those ROIs, which are not part > of the > > color LUT, > > into Afni space. > > > > For ROIs that are already in the LUT, getting them to > Afni is > > no problem, I > > simply use a 3dcalc command. However, I have the problem of > > needing to > > export newly parcellated and segmented ROIs that aren't > in the > > Freesurfer > > LUT to Afni space. > > > > Is there a way to do this short of creating a new "spot" for > > them in our > > LUT? If not, how does one go about adding ROIs to the LUT > > and/or creating a > > LUT specific to my needs (since the Wiki suggests not > fussing > > with the > > original LUT)? > > > > > > Thanks, > > Paul > > -- > > > > > > > > > > > > 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. > > > > > > > > > > -- > > Paul Beach > > DO/PhD candidate - Year V > > Michigan State University > > - College of Osteopathic Medicine - OMS V > > - Neuroscience Program > > - Bozoki Lab: Neurology/Radiology > > - President: American Physician Scientist Association, MSU COM > Chapter > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM Chapter -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
