Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way?
Best regards, Amirhossein Manzouri
you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug
On 03/14/2014 11:15 AM, amirhossein manzouri wrote:
Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way?
Best regards, Amirhossein Manzouri
Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results?
Best regards, Amirhossein Manzouri
On Fri, Mar 14, 2014 at 4:49 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug
On 03/14/2014 11:15 AM, amirhossein manzouri wrote:
Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way?
Best regards, Amirhossein Manzouri
-- 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/
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 don't know what you mean. Can you elaborate? doug On 03/17/2014 01:19 PM, amirhossein manzouri wrote:
Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results?
Best regards, Amirhossein Manzouri
On Fri, Mar 14, 2014 at 4:49 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug On 03/14/2014 11:15 AM, amirhossein manzouri wrote: Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri -- 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/ 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.
Yes. Basically I want to see the effect of restricting the brain area on the group comparison clusters from Monte Carlo Simulation (threshold 1.3). As you mentioned before from mdi_glmfit I just get a masked version of whole brain analysis. How can I do the correction for multiple comparison with Monte Carlo (threshold 1.3) command based?
Best regards, Amirhossein Manzouri
On Mon, Mar 17, 2014 at 6:52 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
I don't know what you mean. Can you elaborate? doug
On 03/17/2014 01:19 PM, amirhossein manzouri wrote:
Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results?
Best regards, Amirhossein Manzouri
On Fri, Mar 14, 2014 at 4:49 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug On 03/14/2014 11:15 AM, amirhossein manzouri wrote: Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri -- 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/ 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 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/
you will have to run the correction for multiple comparisons with mri_glmfit-sim (ie, you can't do it in qdec). doug
On 03/17/2014 02:03 PM, amirhossein manzouri wrote:
Yes. Basically I want to see the effect of restricting the brain area on the group comparison clusters from Monte Carlo Simulation (threshold 1.3). As you mentioned before from mdi_glmfit I just get a masked version of whole brain analysis. How can I do the correction for multiple comparison with Monte Carlo (threshold 1.3) command based?
Best regards, Amirhossein Manzouri
On Mon, Mar 17, 2014 at 6:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I don't know what you mean. Can you elaborate? doug On 03/17/2014 01:19 PM, amirhossein manzouri wrote: Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results? Best regards, Amirhossein Manzouri On Fri, Mar 14, 2014 at 4:49 PM, 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: you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug On 03/14/2014 11:15 AM, amirhossein manzouri wrote: Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri -- 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: 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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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: 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/
Tanks doug, Is it ok like this: mri_glmfit-sim --glmdir qdec/Untitled --cache 1.3 neg ?
Best regards, Amirhossein Manzouri
On Mon, Mar 17, 2014 at 8:25 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
you will have to run the correction for multiple comparisons with mri_glmfit-sim (ie, you can't do it in qdec). doug
On 03/17/2014 02:03 PM, amirhossein manzouri wrote:
Yes. Basically I want to see the effect of restricting the brain area on the group comparison clusters from Monte Carlo Simulation (threshold 1.3). As you mentioned before from mdi_glmfit I just get a masked version of whole brain analysis. How can I do the correction for multiple comparison with Monte Carlo (threshold 1.3) command based?
Best regards, Amirhossein Manzouri
On Mon, Mar 17, 2014 at 6:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I don't know what you mean. Can you elaborate? doug On 03/17/2014 01:19 PM, amirhossein manzouri wrote: Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results? Best regards, Amirhossein Manzouri On Fri, Mar 14, 2014 at 4:49 PM, 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: you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug On 03/14/2014 11:15 AM, amirhossein manzouri wrote: Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri -- 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: 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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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 sentto
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: 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/-- 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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yes
On 3/18/14 9:14 AM, amirhossein manzouri wrote:
Tanks doug, Is it ok like this: mri_glmfit-sim --glmdir qdec/Untitled --cache 1.3 neg ?
Best regards, Amirhossein Manzouri
On Mon, Mar 17, 2014 at 8:25 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
you will have to run the correction for multiple comparisons with mri_glmfit-sim (ie, you can't do it in qdec). doug On 03/17/2014 02:03 PM, amirhossein manzouri wrote: > Yes. Basically I want to see the effect of restricting the brain area > on the group comparison clusters from Monte Carlo Simulation > (threshold 1.3). As you mentioned before from mdi_glmfit I just get a > masked version of whole brain analysis. How can I do the correction > for multiple comparison with Monte Carlo (threshold 1.3) command based? > > Best regards, > Amirhossein Manzouri > > > > > On Mon, Mar 17, 2014 at 6:52 PM, 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: > > I don't know what you mean. Can you elaborate? > doug > > On 03/17/2014 01:19 PM, amirhossein manzouri wrote: > > Can I also use mri_surfcluster as it is in qdec since I want > to compare the whole brain and masked brain results? > > Best regards, > Amirhossein Manzouri > > > > > On Fri, Mar 14, 2014 at 4:49 PM, 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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > you are doing it the right way. There is no difference in the > uncorrected analysis. There will be a difference when you > correct > for multiple comparisons > doug > > > > On 03/14/2014 11:15 AM, amirhossein manzouri wrote: > > Dear Experts, > I have read the previous posts in the list regarding > restricted ROI analysis. So I generated my label from > tksurfer > and used that for group difference analysis by adding > --label > to mri_glmfit, but the result (sig.mgh) seems just a > masked > version of the analysis including whole brain ( no > difference > in significance! ). I expected to see a different > pattern of > significance by limiting the region. Would you please > advise > if I am doing this in a right way? > > Best regards, > Amirhossein Manzouri > > > > -- 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>> > <mailto: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>> > <tel: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>> <tel: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> > 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> > <http://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/ > > > > 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> <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: 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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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: 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
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