Dear FS experts,
I just finished calculating functional connectivity maps using FreeSurfer. I just want to confirm if the following steps I used are correct:
(1). I defined configured seed regions parameters using fcseed-config command, say R01.config and R02.config and created seeds using fcseed-sess command to generate R01.dat and R02.dat files. (2). Created nuisance vaiables: wm.config and vcsf.config files using fcseed-config and -sess: this step is independent of seeds and is done only once independent of seeds (3). For mkanalysis-sess command for each seed using R0*.dat file, I used '-notask' argument because I am performing resting-state analysis. (4). For subject level analysis, I used selxavg3 for each seed (5). For 2nd level analysis: isxconcat-sess -all-contrasts -map sig.nii.gz
I can process all these steps without any error. If these steps are correct, can some one please confirm again that for RSFC, I am correctly using -notask in step (3) and -all-contrast in step (5). Also, in the instructions, it's mentioned to use -map pcc if interested in calculating partial correlation coefficient, but I am interested in using sig to get group level significant maps, would that be OK to use in this command as -map sig?
Thanks for your help.
Regards, MJ
You should not use the sig as that is the first level significance. If you pass that to the higher level, then the results will be hard to interpret. I think you'll want to use pcc or ces. Otherwise looks ok. doug
On 05/06/2016 12:03 PM, Martin Juneja wrote:
Dear FS experts,
I just finished calculating functional connectivity maps using FreeSurfer. I just want to confirm if the following steps I used are correct:
(1). I defined configured seed regions parameters using fcseed-config command, say R01.config and R02.config and created seeds using fcseed-sess command to generate R01.dat and R02.dat files. (2). Created nuisance vaiables: wm.config and vcsf.config files using fcseed-config and -sess: this step is independent of seeds and is done only once independent of seeds (3). For mkanalysis-sess command for each seed using R0*.dat file, I used '-notask' argument because I am performing resting-state analysis. (4). For subject level analysis, I used selxavg3 for each seed (5). For 2nd level analysis: isxconcat-sess -all-contrasts -map sig.nii.gz
I can process all these steps without any error. If these steps are correct, can some one please confirm again that for RSFC, I am correctly using -notask in step (3) and -all-contrast in step (5). Also, in the instructions, it's mentioned to use -map pcc if interested in calculating partial correlation coefficient, but I am interested in using sig to get group level significant maps, would that be OK to use in this command as -map sig?
Thanks for your help.
Regards, MJ
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks a lot Dr. Greve.
So as per your suggestion: I ran the command isxconcat-sess -sf sessidlist -analysis workmem.sm05.rh -contrast encode-v-base -o my-group -all-contrasts i.e.- without specifying -map argument. So this generates ces.nii.gz and vesvar.nii.gz in output folder my-group. To get the significance level from 2nd level analysis, I ran mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh --glmdir my-glm.wls --nii.gz
This generates sig.nii.gz file. Could you please confirm once again, that's how group level significant function connectivity is calculated from 1st level FC maps?
Thanks a lot for all your help.
On Fri, May 6, 2016 at 3:23 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You should not use the sig as that is the first level significance. If you pass that to the higher level, then the results will be hard to interpret. I think you'll want to use pcc or ces. Otherwise looks ok. doug
On 05/06/2016 12:03 PM, Martin Juneja wrote:
Dear FS experts,
I just finished calculating functional connectivity maps using FreeSurfer. I just want to confirm if the following steps I used are correct:
(1). I defined configured seed regions parameters using fcseed-config command, say R01.config and R02.config and created seeds using fcseed-sess command to generate R01.dat and R02.dat files. (2). Created nuisance vaiables: wm.config and vcsf.config files using fcseed-config and -sess: this step is independent of seeds and is done only once independent of seeds (3). For mkanalysis-sess command for each seed using R0*.dat file, I used '-notask' argument because I am performing resting-state analysis. (4). For subject level analysis, I used selxavg3 for each seed (5). For 2nd level analysis: isxconcat-sess -all-contrasts -map
sig.nii.gz
I can process all these steps without any error. If these steps are correct, can some one please confirm again that for RSFC, I am correctly using -notask in step (3) and -all-contrast in step (5). Also, in the instructions, it's mentioned to use -map pcc if interested in calculating partial correlation coefficient, but I am interested in using sig to get group level significant maps, would that be OK to use in this command as -map sig?
Thanks for your help.
Regards, MJ
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.
Yes, those are the right commands. That will give you the ces (the regression coefficient). Typically, people use the pearson correlation coefficient (pcc), but I have not seen many differences between the two.
On 05/06/2016 05:13 PM, Martin Juneja wrote:
Thanks a lot Dr. Greve.
So as per your suggestion: I ran the command isxconcat-sess -sf sessidlist -analysis workmem.sm05.rh -contrast encode-v-base -o my-group -all-contrasts i.e.- without specifying -map argument. So this generates ces.nii.gz and vesvar.nii.gz in output folder my-group. To get the significance level from 2nd level analysis, I ran mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm--surface fsaverage lh--glmdir my-glm.wls --nii.gz This generates sig.nii.gz file. Could you please confirm once again, that's how group level significant function connectivity is calculated from 1st level FC maps? Thanks a lot for all your help.
On Fri, May 6, 2016 at 3:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You should not use the sig as that is the first level significance. If you pass that to the higher level, then the results will be hard to interpret. I think you'll want to use pcc or ces. Otherwise looks ok. doug On 05/06/2016 12:03 PM, Martin Juneja wrote: > Dear FS experts, > > I just finished calculating functional connectivity maps using > FreeSurfer. I just want to confirm if the following steps I used are > correct: > > (1). I defined configured seed regions parameters using fcseed-config > command, say R01.config and R02.config and created seeds using > fcseed-sess command to generate R01.dat and R02.dat files. > (2). Created nuisance vaiables: wm.config and vcsf.config files using > fcseed-config and -sess: this step is independent of seeds and is done > only once independent of seeds > (3). For mkanalysis-sess command for each seed using R0*.dat file, I > used '-notask' argument because I am performing resting-state analysis. > (4). For subject level analysis, I used selxavg3 for each seed > (5). For 2nd level analysis: isxconcat-sess -all-contrasts -map sig.nii.gz > > I can process all these steps without any error. If these steps are > correct, can some one please confirm again that for RSFC, I am > correctly using -notask in step (3) and -all-contrast in step (5). > Also, in the instructions, it's mentioned to use -map pcc if > interested in calculating partial correlation coefficient, but I am > interested in using sig to get group level significant maps, would > that be OK to use in this command as -map sig? > > Thanks for your help. > > Regards, > MJ > > > _______________________________________________ > 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Dr. Greve,
Thanks for all your help. After displaying second level functional connectivity maps (actually when I display subject-wise FC maps also), I tried to match the seed region location on FC maps using tksurfer, I found that that at the seed-region partial correlation coefficient (pcc) value is not 1 and when I display sig.nii, at seed region, FC value is not signifiant. I was wondering if that's normal and freesurfer ignores self connectivity i.e. connectivity of seed region with itself or I did something wrong.
Thanks much !
On Fri, May 6, 2016 at 4:37 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Yes, those are the right commands. That will give you the ces (the regression coefficient). Typically, people use the pearson correlation coefficient (pcc), but I have not seen many differences between the two.
On 05/06/2016 05:13 PM, Martin Juneja wrote:
Thanks a lot Dr. Greve.
So as per your suggestion: I ran the command isxconcat-sess -sf sessidlist -analysis workmem.sm05.rh -contrast encode-v-base -o my-group -all-contrasts i.e.- without specifying -map argument. So this generates ces.nii.gz and vesvar.nii.gz in output folder my-group. To get the significance level from 2nd level analysis, I ran mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm--surface fsaverage lh--glmdir my-glm.wls --nii.gz This generates sig.nii.gz file. Could you please confirm once again, that's how group level significant function connectivity is calculated from 1st level FC maps? Thanks a lot for all your help.
On Fri, May 6, 2016 at 3:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You should not use the sig as that is the first level significance.If
you pass that to the higher level, then the results will be hard to interpret. I think you'll want to use pcc or ces. Otherwise looks ok. doug On 05/06/2016 12:03 PM, Martin Juneja wrote: > Dear FS experts, > > I just finished calculating functional connectivity maps using > FreeSurfer. I just want to confirm if the following steps I usedare
> correct: > > (1). I defined configured seed regions parameters using fcseed-config > command, say R01.config and R02.config and created seeds using > fcseed-sess command to generate R01.dat and R02.dat files. > (2). Created nuisance vaiables: wm.config and vcsf.config files using > fcseed-config and -sess: this step is independent of seeds and is done > only once independent of seeds > (3). For mkanalysis-sess command for each seed using R0*.dat file,I
> used '-notask' argument because I am performing resting-state analysis. > (4). For subject level analysis, I used selxavg3 for each seed > (5). For 2nd level analysis: isxconcat-sess -all-contrasts -map sig.nii.gz > > I can process all these steps without any error. If these steps are > correct, can some one please confirm again that for RSFC, I am > correctly using -notask in step (3) and -all-contrast in step (5). > Also, in the instructions, it's mentioned to use -map pcc if > interested in calculating partial correlation coefficient, but I am > interested in using sig to get group level significant maps, would > that be OK to use in this command as -map sig? > > Thanks for your help. > > Regards, > MJ > > > _______________________________________________ > 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.
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
no, that is not normal, you must have done something wrong :(
On 05/09/2016 12:09 PM, Martin Juneja wrote:
Hi Dr. Greve,
Thanks for all your help. After displaying second level functional connectivity maps (actually when I display subject-wise FC maps also), I tried to match the seed region location on FC maps using tksurfer, I found that that at the seed-region partial correlation coefficient (pcc) value is not 1 and when I display sig.nii, at seed region, FC value is not signifiant. I was wondering if that's normal and freesurfer ignores self connectivity i.e. connectivity of seed region with itself or I did something wrong.
Thanks much !
On Fri, May 6, 2016 at 4:37 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes, those are the right commands. That will give you the ces (the regression coefficient). Typically, people use the pearson correlation coefficient (pcc), but I have not seen many differences between the two. On 05/06/2016 05:13 PM, Martin Juneja wrote: > Thanks a lot Dr. Greve. > > So as per your suggestion: I ran the command isxconcat-sess -sf > sessidlist -analysis workmem.sm05.rh -contrast encode-v-base -o > my-group -all-contrasts i.e.- without specifying -map argument. So > this generates ces.nii.gz and vesvar.nii.gz in output folder my-group. > To get the significance level from 2nd level analysis, I ran > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm--surface > fsaverage lh--glmdir my-glm.wls --nii.gz > This generates sig.nii.gz file. Could you please confirm once again, > that's how group level significant function connectivity is calculated > from 1st level FC maps? > Thanks a lot for all your help. > > On Fri, May 6, 2016 at 3:23 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 should not use the sig as that is the first level significance. If > you pass that to the higher level, then the results will be hard to > interpret. I think you'll want to use pcc or ces. Otherwise looks ok. > doug > > On 05/06/2016 12:03 PM, Martin Juneja wrote: > > Dear FS experts, > > > > I just finished calculating functional connectivity maps using > > FreeSurfer. I just want to confirm if the following steps I used are > > correct: > > > > (1). I defined configured seed regions parameters using > fcseed-config > > command, say R01.config and R02.config and created seeds using > > fcseed-sess command to generate R01.dat and R02.dat files. > > (2). Created nuisance vaiables: wm.config and vcsf.config files > using > > fcseed-config and -sess: this step is independent of seeds and > is done > > only once independent of seeds > > (3). For mkanalysis-sess command for each seed using R0*.dat file, I > > used '-notask' argument because I am performing resting-state > analysis. > > (4). For subject level analysis, I used selxavg3 for each seed > > (5). For 2nd level analysis: isxconcat-sess -all-contrasts -map > sig.nii.gz > > > > I can process all these steps without any error. If these steps are > > correct, can some one please confirm again that for RSFC, I am > > correctly using -notask in step (3) and -all-contrast in step (5). > > Also, in the instructions, it's mentioned to use -map pcc if > > interested in calculating partial correlation coefficient, but I am > > interested in using sig to get group level significant maps, would > > that be OK to use in this command as -map sig? > > > > Thanks for your help. > > > > Regards, > > MJ > > > > > > _______________________________________________ > > 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. > > > > > _______________________________________________ > 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
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Martin Juneja