Hi freesurfers,
I conducted a retinotopic analysis for one of my subjects. I was wondering if any of you knew what is represented by the values in the sig.nii file under the 'polar' directory that the process puts out.
I appreciate your help!
Cesar
It is the -log10(pvalue) where pvalue is the p-value from the F-test of the real and imaginary components doug
On 12/03/2013 05:41 PM, Cesar Echavarria wrote:
Hi freesurfers,
I conducted a retinotopic analysis for one of my subjects. I was wondering if any of you knew what is represented by the values in the sig.nii file under the 'polar' directory that the process puts out.
I appreciate your help!
Cesar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
So I want to figure out which voxels were modulated significantly by the orientation of our stimuli. Is this the right file to look at? If so what are the real and imaginary components compared against? I want to know to make sense of the negative values. On Dec 3, 2013 5:52 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It is the -log10(pvalue) where pvalue is the p-value from the F-test of the real and imaginary components doug
On 12/03/2013 05:41 PM, Cesar Echavarria wrote:
Hi freesurfers,
I conducted a retinotopic analysis for one of my subjects. I was wondering if any of you knew what is represented by the values in the sig.nii file under the 'polar' directory that the process puts out.
I appreciate your help!
Cesar
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.
They are compared against 0 (ie, no change from baseline). The negatives just mean that the real component was negative doug
On 12/03/2013 06:21 PM, Cesar Echavarria wrote:
So I want to figure out which voxels were modulated significantly by the orientation of our stimuli. Is this the right file to look at? If so what are the real and imaginary components compared against? I want to know to make sense of the negative values.
On Dec 3, 2013 5:52 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is the -log10(pvalue) where pvalue is the p-value from the F-test of the real and imaginary components doug On 12/03/2013 05:41 PM, Cesar Echavarria wrote: > Hi freesurfers, > > I conducted a retinotopic analysis for one of my subjects. I was > wondering if any of you knew what is represented by the values in the > sig.nii file under the 'polar' directory that the process puts out. > > I appreciate your help! > > Cesar > > > _______________________________________________ > 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.
To clarify, I am piggy-backing on the retinotopic analysis to map out orientation preference with the travelling-wave method. We presented subjects with a rotating grating and right now I am simply interested in finding the voxels that have significant activity in response to any orientation. Now, when I load the sig.nii file under the 'polar' folder with MATLAB I see that each voxel has 2 values. I understand that these are the p-values for the real and imaginary components of the signal. Is there a way to put these 2 values together for my purposes? Is there a file somewhere in the pipeline that will give me the values I am looking for?
Thanks you for your help
Cesar
On Wed, Dec 4, 2013 at 10:14 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
They are compared against 0 (ie, no change from baseline). The negatives just mean that the real component was negative doug
On 12/03/2013 06:21 PM, Cesar Echavarria wrote:
So I want to figure out which voxels were modulated significantly by the orientation of our stimuli. Is this the right file to look at? If so what are the real and imaginary components compared against? I want to know to make sense of the negative values.
On Dec 3, 2013 5:52 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto: greve@nmr.mgh.harvard.edu> wrote:
It is the -log10(pvalue) where pvalue is the p-value from the F-test of the real and imaginary components doug On 12/03/2013 05:41 PM, Cesar Echavarria wrote: > Hi freesurfers, > > I conducted a retinotopic analysis for one of my subjects. I was > wondering if any of you knew what is represented by the values in the > sig.nii file under the 'polar' directory that the process puts out. > > I appreciate your help! > > Cesar > > > _______________________________________________ > 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.eduhttps://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 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/
sorry, there should be an fsig.nii.gz which is the F test of the real and imaginary. That sounds like what you are asking for
On 12/04/2013 12:19 PM, Cesar Echavarria wrote:
To clarify, I am piggy-backing on the retinotopic analysis to map out orientation preference with the travelling-wave method. We presented subjects with a rotating grating and right now I am simply interested in finding the voxels that have significant activity in response to any orientation. Now, when I load the sig.nii file under the 'polar' folder with MATLAB I see that each voxel has 2 values. I understand that these are the p-values for the real and imaginary components of the signal. Is there a way to put these 2 values together for my purposes? Is there a file somewhere in the pipeline that will give me the values I am looking for?
Thanks you for your help
Cesar
On Wed, Dec 4, 2013 at 10:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
They are compared against 0 (ie, no change from baseline). The negatives just mean that the real component was negative doug On 12/03/2013 06:21 PM, Cesar Echavarria wrote: So I want to figure out which voxels were modulated significantly by the orientation of our stimuli. Is this the right file to look at? If so what are the real and imaginary components compared against? I want to know to make sense of the negative values. On Dec 3, 2013 5:52 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: It is the -log10(pvalue) where pvalue is the p-value from the F-test of the real and imaginary components doug On 12/03/2013 05:41 PM, Cesar Echavarria wrote: > Hi freesurfers, > > I conducted a retinotopic analysis for one of my subjects. I was > wondering if any of you knew what is represented by the values in the > sig.nii file under the 'polar' directory that the process puts out. > > I appreciate your help! > > Cesar > > > _______________________________________________ > 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: 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/ _______________________________________________ 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: 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/-- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012
Thanks for your help Doug. That cleared things up.
One more question, I want to average over 2 of these scan sessions for the same subject. Is there a command or option that will let me do this and output the fsig.nii file for the average activity?
Cesar
On Wed, Dec 4, 2013 at 1:03 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
sorry, there should be an fsig.nii.gz which is the F test of the real and imaginary. That sounds like what you are asking for
On 12/04/2013 12:19 PM, Cesar Echavarria wrote:
To clarify, I am piggy-backing on the retinotopic analysis to map out orientation preference with the travelling-wave method. We presented subjects with a rotating grating and right now I am simply interested in finding the voxels that have significant activity in response to any orientation. Now, when I load the sig.nii file under the 'polar' folder with MATLAB I see that each voxel has 2 values. I understand that these are the p-values for the real and imaginary components of the signal. Is there a way to put these 2 values together for my purposes? Is there a file somewhere in the pipeline that will give me the values I am looking for?
Thanks you for your help
Cesar
On Wed, Dec 4, 2013 at 10:14 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
They are compared against 0 (ie, no change from baseline). The negatives just mean that the real component was negative doug On 12/03/2013 06:21 PM, Cesar Echavarria wrote: So I want to figure out which voxels were modulated significantly by the orientation of our stimuli. Is this the right file to look at? If so what are the real and imaginary components compared against? I want to know to make sense of the negative values. On Dec 3, 2013 5:52 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: It is the -log10(pvalue) where pvalue is the p-value from the F-test of the real and imaginary components doug On 12/03/2013 05:41 PM, Cesar Echavarria wrote: > Hi freesurfers, > > I conducted a retinotopic analysis for one of my subjects. I was > wondering if any of you knew what is represented by the values in the > sig.nii file under the 'polar' directory that the process puts out. > > I appreciate your help! > > Cesar > > > _______________________________________________ > 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: 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/ _______________________________________________ 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 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/-- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012
-- 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/
To get the F test, you will need to put the runs from both sessions in the same bold folder (and make sure to use -per-run registration) doug
On 12/5/13 4:42 PM, Cesar Echavarria wrote:
Thanks for your help Doug. That cleared things up.
One more question, I want to average over 2 of these scan sessions for the same subject. Is there a command or option that will let me do this and output the fsig.nii file for the average activity?
Cesar
On Wed, Dec 4, 2013 at 1:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
sorry, there should be an fsig.nii.gz which is the F test of the real and imaginary. That sounds like what you are asking for On 12/04/2013 12:19 PM, Cesar Echavarria wrote: To clarify, I am piggy-backing on the retinotopic analysis to map out orientation preference with the travelling-wave method. We presented subjects with a rotating grating and right now I am simply interested in finding the voxels that have significant activity in response to any orientation. Now, when I load the sig.nii file under the 'polar' folder with MATLAB I see that each voxel has 2 values. I understand that these are the p-values for the real and imaginary components of the signal. Is there a way to put these 2 values together for my purposes? Is there a file somewhere in the pipeline that will give me the values I am looking for? Thanks you for your help Cesar On Wed, Dec 4, 2013 at 10:14 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: They are compared against 0 (ie, no change from baseline). The negatives just mean that the real component was negative doug On 12/03/2013 06:21 PM, Cesar Echavarria wrote: So I want to figure out which voxels were modulated significantly by the orientation of our stimuli. Is this the right file to look at? If so what are the real and imaginary components compared against? I want to know to make sense of the negative values. On Dec 3, 2013 5:52 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>> <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: It is the -log10(pvalue) where pvalue is the p-value from the F-test of the real and imaginary components doug On 12/03/2013 05:41 PM, Cesar Echavarria wrote: > Hi freesurfers, > > I conducted a retinotopic analysis for one of my subjects. I was > wondering if any of you knew what is represented by the values in the > sig.nii file under the 'polar' directory that the process puts out. > > I appreciate your help! > > Cesar > > > _______________________________________________ > 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>>> > 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>> <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/ _______________________________________________ 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>>> 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> <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/ -- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012 -- 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/-- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012
I want to do the analysis in native space. I saw in a past thread that the native space analysis cannot make use of the -per-run flag. Does this still hold? If so, is there another way to get fsig.nii file after analyzing each session separately in native space?
Thanks for your help!
Cesar
On Thu, Dec 5, 2013 at 10:16 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
To get the F test, you will need to put the runs from both sessions in the same bold folder (and make sure to use -per-run registration) doug
On 12/5/13 4:42 PM, Cesar Echavarria wrote:
Thanks for your help Doug. That cleared things up.
One more question, I want to average over 2 of these scan sessions for the same subject. Is there a command or option that will let me do this and output the fsig.nii file for the average activity?
Cesar
On Wed, Dec 4, 2013 at 1:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
sorry, there should be an fsig.nii.gz which is the F test of the real and imaginary. That sounds like what you are asking for
On 12/04/2013 12:19 PM, Cesar Echavarria wrote:
To clarify, I am piggy-backing on the retinotopic analysis to map out orientation preference with the travelling-wave method. We presented subjects with a rotating grating and right now I am simply interested in finding the voxels that have significant activity in response to any orientation. Now, when I load the sig.nii file under the 'polar' folder with MATLAB I see that each voxel has 2 values. I understand that these are the p-values for the real and imaginary components of the signal. Is there a way to put these 2 values together for my purposes? Is there a file somewhere in the pipeline that will give me the values I am looking for?
Thanks you for your help
Cesar
On Wed, Dec 4, 2013 at 10:14 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
They are compared against 0 (ie, no change from baseline). The negatives just mean that the real component was negative doug On 12/03/2013 06:21 PM, Cesar Echavarria wrote: So I want to figure out which voxels were modulated significantly by the orientation of our stimuli. Is this the right file to look at? If so what are the real and imaginary components compared against? I want to know to make sense of the negative values. On Dec 3, 2013 5:52 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: It is the -log10(pvalue) where pvalue is the p-value from the F-test of the real and imaginary components doug On 12/03/2013 05:41 PM, Cesar Echavarria wrote: > Hi freesurfers, > > I conducted a retinotopic analysis for one of my subjects. I was > wondering if any of you knew what is represented by the values in the > sig.nii file under the 'polar' directory that the process puts out. > > I appreciate your help! > > Cesar > > > _______________________________________________ > 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: 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.htmlOutgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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 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/-- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012
-- 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/
-- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012
you can try doing the same thing using the -per-session flag. The problem is that it tries to use the motion correction to correct across sessions, which may or may not work doug
On 12/06/2013 12:37 PM, Cesar Echavarria wrote:
I want to do the analysis in native space. I saw in a past thread that the native space analysis cannot make use of the -per-run flag. Does this still hold? If so, is there another way to get fsig.nii file after analyzing each session separately in native space?
Thanks for your help!
Cesar
On Thu, Dec 5, 2013 at 10:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
To get the F test, you will need to put the runs from both sessions in the same bold folder (and make sure to use -per-run registration) doug On 12/5/13 4:42 PM, Cesar Echavarria wrote:Thanks for your help Doug. That cleared things up. One more question, I want to average over 2 of these scan sessions for the same subject. Is there a command or option that will let me do this and output the fsig.nii file for the average activity? Cesar On Wed, Dec 4, 2013 at 1:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: sorry, there should be an fsig.nii.gz which is the F test of the real and imaginary. That sounds like what you are asking for On 12/04/2013 12:19 PM, Cesar Echavarria wrote: To clarify, I am piggy-backing on the retinotopic analysis to map out orientation preference with the travelling-wave method. We presented subjects with a rotating grating and right now I am simply interested in finding the voxels that have significant activity in response to any orientation. Now, when I load the sig.nii file under the 'polar' folder with MATLAB I see that each voxel has 2 values. I understand that these are the p-values for the real and imaginary components of the signal. Is there a way to put these 2 values together for my purposes? Is there a file somewhere in the pipeline that will give me the values I am looking for? Thanks you for your help Cesar On Wed, Dec 4, 2013 at 10:14 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: They are compared against 0 (ie, no change from baseline). The negatives just mean that the real component was negative doug On 12/03/2013 06:21 PM, Cesar Echavarria wrote: So I want to figure out which voxels were modulated significantly by the orientation of our stimuli. Is this the right file to look at? If so what are the real and imaginary components compared against? I want to know to make sense of the negative values. On Dec 3, 2013 5:52 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>> <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: It is the -log10(pvalue) where pvalue is the p-value from the F-test of the real and imaginary components doug On 12/03/2013 05:41 PM, Cesar Echavarria wrote: > Hi freesurfers, > > I conducted a retinotopic analysis for one of my subjects. I was > wondering if any of you knew what is represented by the values in the > sig.nii file under the 'polar' directory that the process puts out. > > I appreciate your help! > > Cesar > > > _______________________________________________ > 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>>> > 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>> <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/ _______________________________________________ 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>>> 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> <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/ -- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012 -- 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/ -- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012-- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012
freesurfer@nmr.mgh.harvard.edu
-
Cesar Echavarria -
Douglas Greve -
Douglas N Greve