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.