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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <greve@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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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> _______________________________________________ Freesurfer mailing list 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.
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 greve@nmr.mgh.harvard.eduwrote:
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 < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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>______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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> 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> _______________________________________________ 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>> 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 greve@nmr.mgh.harvard.edu <mailto:greve@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>
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 greve@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 <greve@nmr.mgh.harvard.edu< mailto:greve@nmr.mgh.harvard.edu greve@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
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu greve@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
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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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@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_statsMETHOD S2S: bbregister>> mri_vol2surf>> mri_preproc
(mri_surf2surf)>> mri_segstatsAfter 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
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