Hi Gari, you can use the data from the surf2surf in qdec/mri_glmfit. If you are using qdec, you might want to let qdec generate the file for you to make sure they are consistent. It is just running mris_preproc and should give an identical file, but just to make sure.
doug On 09/29/2012 05:17 PM, Garikoitz Lerma-Usabiaga wrote: > Hi Doug, > you are right, we are very happy with the results, we were just trying > to be as conservative as possible and testing different methods and > regions before making any decision. We are going to introduce one of > the methods in a stream for several studies and we wanted to know if > you have any recommendation. As the results are not exactly the same > maybe you think one of those is better than the other for any reason. > > For example, considering that the accuracy between methods is > similar, could we use the data in Qdec (with Colin27) with the > surf2surf method? I understand that we couldn't do that with the > label2label method. > > Many thanks again for your help! > Gari > > > > > > On Fri, Sep 28, 2012 at 4:18 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > hi Gari, looking at this I don't really see a problem. Yes, the > t-test is very significant, but I would expect that from a paired > t looking across different methods. the size of the effect is very > small, about 1.5%. Do you see this as a problem? > doug > > > > > On 09/28/2012 05:14 AM, Garikoitz Lerma-Usabiaga wrote: > > Hi Doug, > > I think that the differences are significant enough, but just > in case please find attached an excel file with the data and > the t-test. > > Some of the ROI-s are small (Triangularis, Operculum, > Orbitalis and then all together in the IFG). I attached images > for each of them for reference. > > > If in any case you assume that there are going to be > differences, which method would you recommend and why? > > Thanks! > Gari > > PS after mri_preproc I didn't smooth the surface as in the > qdec example, żshould I do that? > > > > > > > On Fri, Sep 28, 2012 at 4:24 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > OK, got it (finally). I would not expect the answers to be > identical, but I would expect them to be "close". How > close are > they? If the ROI is very small, there might be appreciable > differences between the two. > > doug > > > > On 9/27/12 6:26 PM, Garikoitz Lerma-Usabiaga wrote: > > Hi, > You are right, this was one of the methods. The second > one is as > follows (I copy the repeated steps): > > For a given ROI, you have a nifti file (roi.nii) > in 2mm space > defined on colin27. This ROI volume has a voxel > value == 1 if it > is in the ROI or 0 if it is out. > > You have a registration between roi.nii and orig.mgz > > You run mri_vol2surf on roi.nii to get lh.roi.mgh > > > I run mris_preproc for every subject to Colin27: > mris_preproc > --out /subject/surf/ROI_toColin27.mgh --target Colin27 > --hemi lh > --meas thickness --s subject > > mri_segstats --seg /Colin27/surf/lh.roi.mgh --in > /subject/surf/ROI_to_Colin127.mgh --sum > subject/stats/target_lh.ROI.stats > > > Thanks for your help, > Gari > > > Note: > You said: You run mri_cor2label (with --surf option) > to convert > lh.roi.mgh into lh.roi.label > Just in case, this is how I run it: > > * mri_cor2label --i /subjects/Colin27/lh.ROI.mgh > --surf Colin27 > > lh --id 1 --l /subjects/Colin27/lh.ROI.label > * mri_label2label --srclabel > > /subjects/Colin27/lh.ROI.label --srcsubject Colin27 > --trgsubject subject --trglabel lh.ROI_Colin27_to_bert > --regmethod surface --hemi lh > > > > > On 26/09/2012, at 23:56, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > Sorry, I'm still a little lost. Let me see if I > have it right: > > For a given ROI, you have a nifti file (roi.nii) > in 2mm space > defined on colin27. This ROI volume has a voxel > value == 1 if it > is in the ROI or 0 if it is out. > > You have a registration between roi.nii and orig.mgz > > You run mri_vol2surf on roi.nii to get lh.roi.mgh > > You run mri_cor2label (with --surf option) to > convert lh.roi.mgh > into lh.roi.label > > You run mri_label2label on lh.roi.label to map it > into an > individual subject > > You run mris_anatomical_stats on the individual > lh.roi.label file > > Does this describe one of your processing streams > correctly? If > so, what is the other processing stream (given in > this kind of > detail)? > > doug > > > > On 09/25/2012 04:43 PM, Garikoitz Lerma-Usabiaga > wrote: > > I have both. In origin, the ROI-s are 2mm > volume based .nii > that I convert to FS .mgh with register.dat I > obtained with > bbregister. > -- In the case of label2label method I create > the surface > version with mri_vol2surf (and the > correspondence is perfect), > and then use mri_label2label in order to get > the CT averages. > -- In the case of surf2surf, I use the volume > based .mgh with > mri_preproc (mri_surf2surf) > > thanks! > Gari > > On Tue, Sep 25, 2012 at 5:57 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > So you have ROIs in Colin27 space and you > want to map them into > your CT space and compute average CT > intensities over them? Are > the ROIs volume-based or surface-based? > doug > > > On 09/25/2012 05:09 AM, Garikoitz > Lerma-Usabiaga wrote: > > Hi Doug, > many thanks for your answer, I try to > detail it more: > > 1.- bbregister is registering two > Colin27 brains. First > one is > a 2mm found in > spm/canonical/single_subject_T1.nii, and > second > one is the FS_spm_Canonical found in > SurfRend > distribution. It > was in .COR format and I run recon-all > to have a modern > version of it. As they are almost the > same brain the > registration matrix is quite simple and > the registration was > perfect. This way I had exactly the same > ROI-s for Colin27 in > SPM and in FS (it did not work that well > for fsaverage, > that's > why I took this approach). > > 2.- In any case, I have several ROI-s in > Colin27 space in FS, > and then when I try to obtain average CT > values from my > subjects I use these 2 different > approaches: label2label and > surf2surf. > mri_anatomical_stats is run on the > labels created by > mri_label2label. > > > If you think it will be of help I can > send the detailed > command line calls, > thanks! > Gari > > > > > > > > > > > > On Sat, Sep 22, 2012 at 12:47 AM, > Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: > > Hi Gari, I'll need more information. > I can't tell > what you > are doing. > Eg, what is being registered with > BBR? what is > mris_anatomical_stats run > on? Where does Colin27 come into it > and why? > doug > > On 09/19/2012 06:15 PM, Garikoitz > Lerma-Usabiaga > (Gari) wrote: > > Dear Freesurfers, > We've been comparing 2 different methods > to obtain CT averages > > for 4 Volume ROI-s (volume ROI-s > were in Colin27 space). > > We've used the 40 buckner subjects for the > comparisons. > > METHOD L2L: bbregister>> > mri_vol2surf (mgh)>> > > mri_binarize (mgh)>> mri_cor2label > (label)>> > mri_label2label>> > mris_anatomical_stats > > METHOD S2S: bbregister>> > mri_vol2surf>> mri_preproc > > (mri_surf2surf)>> mri_segstats > > > > After performing t-test-s over the > results, we can observe that > > the results are in many cases different. > > > -- Is there a way to choose the "best" > method? Which one should > > we use for our work and why? > > > Many thanks again for your help, > Gari > > PD We've tabulated a third method as well: > METHOD SurfRend: Surfrend (.w)>> > mri_surf2surf(.mgh)>> > > mri_binarize(.mgh)>> mri_cor2label > (.label)>> > mris_anatomical_stats > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto: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> > <http://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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 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> > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
