Hello,
I see that after having qdec apply MonteCarlo correction to a certain contrast, the CWP cluster-wise probability is displayed. Those values, however, are not displayed when the "Find clusters and go to max" button is used, either before or after correction. WHy is that, when it seems that the CWP statistic makes sense for all 3 "stages" (max-vertex pre-correction, mean-cluster post-correction, max-vertex post-correction)?
Thank you!
--Francesco
ONe more question about this - when reporting significant clusters, should one refer to the cluster by 1) its annotation label, e.g. "sig differences were found in the precentral gyrus", 2) its max vertex as displayed after using the "Find clusters and go to max" button, e.g. "significant differences were found in a cluster whose maximum vertex was at (10,20,30)" , or 3) by its center of gravity coordinates as displayed (I think!) immediately after running the MonteCarlo correction, e.g. "significant differences were found in a cluster whose CoG was at (11,21,31)"? Thank you!
On 31 March 2014 15:05, Francesco Puccettone <francesco.puccettone@gmail.com
wrote:
Hello,
I see that after having qdec apply MonteCarlo correction to a certain contrast, the CWP cluster-wise probability is displayed. Those values, however, are not displayed when the "Find clusters and go to max" button is used, either before or after correction. WHy is that, when it seems that the CWP statistic makes sense for all 3 "stages" (max-vertex pre-correction, mean-cluster post-correction, max-vertex post-correction)?
Thank you!
--Francesco
This is just the way that the interface was programmed. It was fairly easy to add a button to run the correction, more difficult to pull that information back into the interface in a reasonable way. I agree that it makes using the interface less intuitive: once you get a button to press, you come to expect that everything else will be done for you. Unfortunately, we don't have the resources to be able to do that. You'll have to look at the text file generated by QDEC doug
On 03/31/2014 09:05 AM, Francesco Puccettone wrote:
Hello,
I see that after having qdec apply MonteCarlo correction to a certain contrast, the CWP cluster-wise probability is displayed. Those values, however, are not displayed when the "Find clusters and go to max" button is used, either before or after correction. WHy is that, when it seems that the CWP statistic makes sense for all 3 "stages" (max-vertex pre-correction, mean-cluster post-correction, max-vertex post-correction)?
Thank you!
--Francesco
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I see, makes sense! I had a second question, which I repeat below. When reporting significant clusters, should one refer to the cluster by 1) its annotation label, e.g. "sig differences were found in the precentral gyrus", 2) its max vertex as displayed after using the "Find clusters and go to max" button, e.g. "significant differences were found in a cluster whose maximum vertex was at (10,20,30)" , or 3) by its center of gravity coordinates as displayed (I think!) immediately after running the MonteCarlo correction, e.g. "significant differences were found in a cluster whose CoG was at (11,21,31)"?
On 31 March 2014 17:43, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
This is just the way that the interface was programmed. It was fairly easy to add a button to run the correction, more difficult to pull that information back into the interface in a reasonable way. I agree that it makes using the interface less intuitive: once you get a button to press, you come to expect that everything else will be done for you. Unfortunately, we don't have the resources to be able to do that. You'll have to look at the text file generated by QDEC doug
On 03/31/2014 09:05 AM, Francesco Puccettone wrote:
Hello,
I see that after having qdec apply MonteCarlo correction to a certain contrast, the CWP cluster-wise probability is displayed. Those values, however, are not displayed when the "Find clusters and go to max" button is used, either before or after correction. WHy is that, when it seems that the CWP statistic makes sense for all 3 "stages" (max-vertex pre-correction, mean-cluster post-correction, max-vertex post-correction)?
Thank you!
--Francesco
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Dear FreeSurfer list,
When reporting coordinates of significant clusters found with Qdec, should one report 1) the Talairach coordinates displayed immediately after running the MonteCarlo correction (which I imagine are the center of gravity (CoG) coordinates?!) or 2) the max vertex Talairach coordinates displayed after using the "Find clusters and go to max" button?
The two sets of coordinates are close for a given cluster, but never quite the same, and I don;t know which one to report.
Thank you! --Francesco
On 31 March 2014 20:20, Francesco Puccettone <francesco.puccettone@gmail.com
wrote:
I see, makes sense! I had a second question, which I repeat below.
When reporting significant clusters, should one refer to the cluster by
- its annotation label, e.g. "sig differences were found in the
precentral gyrus", 2) its max vertex as displayed after using the "Find clusters and go to max" button, e.g. "significant differences were found in a cluster whose maximum vertex was at (10,20,30)" , or 3) by its center of gravity coordinates as displayed (I think!) immediately after running the MonteCarlo correction, e.g. "significant differences were found in a cluster whose CoG was at (11,21,31)"?
On 31 March 2014 17:43, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
This is just the way that the interface was programmed. It was fairly easy to add a button to run the correction, more difficult to pull that information back into the interface in a reasonable way. I agree that it makes using the interface less intuitive: once you get a button to press, you come to expect that everything else will be done for you. Unfortunately, we don't have the resources to be able to do that. You'll have to look at the text file generated by QDEC doug
On 03/31/2014 09:05 AM, Francesco Puccettone wrote:
Hello,
I see that after having qdec apply MonteCarlo correction to a certain contrast, the CWP cluster-wise probability is displayed. Those values, however, are not displayed when the "Find clusters and go to max" button is used, either before or after correction. WHy is that, when it seems that the CWP statistic makes sense for all 3 "stages" (max-vertex pre-correction, mean-cluster post-correction, max-vertex post-correction)?
Thank you!
--Francesco
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: https://gate.nmr.mgh.harvard.edu/filedrop2 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
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.
The QDEC output does not quite report what you want to report. I would run mri_glmfit-sim using --glmdir /path/to/qdec/folder and the same parameters as you used for the monte carlo simulation. this will produce several files including a summary/table file with the MNI305 coordinates of most significant voxel in the cluster. If you want the centroid, add --centroid to the cmd line.
doug
On 04/03/2014 07:17 AM, Francesco Puccettone wrote:
Dear FreeSurfer list,
When reporting coordinates of significant clusters found with Qdec, should one report
- the Talairach coordinates displayed immediately after running the
MonteCarlo correction (which I imagine are the center of gravity (CoG) coordinates?!) or 2) the max vertex Talairachcoordinates displayed after using the "Find clusters and go to max" button?
The two sets of coordinates are close for a given cluster, but never quite the same, and I don;t know which one to report.
Thank you! --Francesco
On 31 March 2014 20:20, Francesco Puccettone <francesco.puccettone@gmail.com mailto:francesco.puccettone@gmail.com> wrote:
I see, makes sense! I had a second question, which I repeat below. When reporting significant clusters, should one refer to the cluster by 1) its annotation label, e.g. "sig differences were found in the precentral gyrus", 2) its max vertex as displayed after using the "Find clusters and go to max" button, e.g. "significant differences were found in a cluster whose maximum vertex was at (10,20,30)" , or 3) by its center of gravity coordinates as displayed (I think!) immediately after running the MonteCarlo correction, e.g. "significant differences were found in a cluster whose CoG was at (11,21,31)"? On 31 March 2014 17:43, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: This is just the way that the interface was programmed. It was fairly easy to add a button to run the correction, more difficult to pull that information back into the interface in a reasonable way. I agree that it makes using the interface less intuitive: once you get a button to press, you come to expect that everything else will be done for you. Unfortunately, we don't have the resources to be able to do that. You'll have to look at the text file generated by QDEC doug On 03/31/2014 09:05 AM, Francesco Puccettone wrote: > Hello, > > I see that after having qdec apply MonteCarlo correction to a certain > contrast, the CWP cluster-wise probability is displayed. Those values, > however, are not displayed when the "Find clusters and go to max" > button is used, either before or after correction. WHy is that, when > it seems that the CWP statistic makes sense for all 3 "stages" > (max-vertex pre-correction, mean-cluster post-correction, max-vertex > post-correction)? > > Thank you! > > --Francesco > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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.
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Francesco Puccettone