hi doug Thanks for checking my code and the hint with the smoothing rate. I appreciate your time on my issue. I’ve ran a series of different smoothing rates (from 10-30mm) and 25mm showed the best results for our data in terms of cluster size but still prominent effects in summary statistics.
vivian Am 06.11.2013 um 16:43 schrieb Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > Yes, that all looks correct. Though 25mm is a lot of smoothing. I usually use > 10-15mm. > doug > > > > On 11/06/2013 10:34 AM, Vivian R. Steiger wrote: >> Hi Doug >> >> Thanks for your answer on my issue "glmfit for paired-diff on 2 groups" in >> the mailinglist >> >> >> Commands: >> >> >> mris_preproc --target 1_average_30VPs --fsgd responder.txt --hemi lh >> --meas thickness --out respnon_lh_thickness.mgh —paired-diff-norm >> >> mri_surf2surf --hemi lh --s 1_average_30VPs --fwhm 25 --sval >> respnon_lh_thickness.mgh --cortex --tval respnon_lh_thickness.sm25.mgh >> >> mri_glmfit --y respnon_lh_thickness.sm25.mgh --fsgd >> responder_paired.txt doss --C sad_groups.txt --surf 1_average_30VPs lh >> --cortex --glmdir respnon_lh_thickness >> >> >> >> FSGD 1: (responder.txt) >> >> GroupDescriptorFile 1 >> Title Resonder_NonResponder >> Class resp >> Class nonresp >> Input 1Pre_VP02.long.VP02_Base resp >> Input 2Post_VP02.long.VP02_Base resp >> Input 1Pre_VP03.long.VP03_Base nonresp >> Input 2Post_VP03.long.VP03_Base nonresp >> Input 1Pre_VP04.long.VP04_Base resp >> Input 2Post_VP04.long.VP04_Base resp >> Input 1Pre_VP05.long.VP05_Base nonresp >> Input 2Post_VP05.long.VP05_Base nonresp >> Input 1Pre_VP06.long.VP06_Base resp >> Input 2Post_VP06.long.VP06_Base resp >> Input 1Pre_VP07.long.VP07_Base resp >> Input 2Post_VP07.long.VP07_Base resp >> Input 1Pre_VP08.long.VP08_Base resp >> Input 2Post_VP08.long.VP08_Base resp >> Input 1Pre_VP09.long.VP09_Base resp >> Input 2Post_VP09.long.VP09_Base resp >> Input 1Pre_VP10.long.VP10_Base nonresp >> Input 2Post_VP10.long.VP10_Base nonresp >> . >> . >> . >> >> >> FSGD 2: (responder_paired.txt) >> >> GroupDescriptorFile 1 >> Class resp >> Class nonresp >> Input VP02pair resp >> Input VP03pair nonresp >> Input VP04pair resp >> Input VP05pair nonresp >> Input VP06pair resp >> Input VP07pair resp >> Input VP08pair resp >> Input VP09pair resp >> Input VP10pair nonresp >> . >> . >> . >> >> >> Best, >> Vivian >> >> >> >> _____________________________________________________________ >> On 11/04/2013 03:34 PM, Douglas N Greve wrote: >>> Yes, that looks correct, though I could be more confident if you send >>> the command lines used and your fsgd file(s). >>> doug >> >> _____________________________________________________________ >> On 10/31/2013 07:32 AM, Vivian R. Steiger wrote: >>> Dear FS-Experts, >>> >>> I would like to compare 2 Groups (Responder (N=19) vs. Non-Responder (N=11)) >>> with longitudinal data. >>> Participants from both groups had only 2 scan sessions in each case 10 weeks >>> apart. >>> >>> So far is used the glmfit-variant with --paired-diff option in the first >>> place. (based on >> http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis >> ) >>> The paired-fsgd contained then 2 classes (Responder, Non-Responder) which is >>> used in glm-fit for comparison with the contrast (1 -1) for group diffs. >>> >>> This approach confirmed our hypothesized effects but I'm not sure whether I >>> used the right strategy. >>> >>> Could you might help me with this issue? >>> >>> Thank in advance >>> >>> >>> Best, >>> >>> Vivian >>> >>> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
