X and C have different numbers of columns. What was your mri_glmfit command line? If you used a --pvr, then the pcc script will not work. doug
On 09/22/2014 01:21 PM, Celine Louapre wrote: > Thanks for pointing me to the file and the help. I found the info I needed > there fro the cache.th13.abs.y.ocn.dat file. > > For the partial correlation coefficient script fast_glm_pcc.m I could not > make it run however. I got this error: > Error using * > Inner matrix dimensions must agree. > > Error in fast_glm_pcc (line 28) > Xc = X*C'; > > And also I found this info in the script WARNING: X must have a column of > 1s or both X and y must have been demeaned before the glm. > But I am not sure about what it means. Attached are Xg.dat and C.dat files. > Thanks again for your help > Celine > >> >> should be something like cache.th13.abs.y.ocn.dat >> also, you can look in mri_glmfit-sim --help to get info about each >> output file >> >> On 09/19/2014 04:47 PM, Celine Louapre wrote: >>> Indeed I ran mri_glmfit-sim. What file is the output of mri_segstat? >>> The cache.th13.abs.sig.ocn.annot contains the significant clusters it >>> that >>> correct? So to get individual mean values from cluster 1 for example >>> where >>> should I look? >>> Thanks! >>> Celine >>> >>> >>>> Have you run mri_glmfit-sim? It will create labels (ie, annotations) of >>>> the clusters as well as run mri_segstats to get means in each cluster >>>> for each subject. Try that link now >>>> doug >>>> >>>> On 09/18/2014 12:15 PM, Celine Louapre wrote: >>>>> Hi Doug and FS team >>>>> >>>>> I did glm analyses using mri_glmfit, and I was trying to plot the >>>>> individual values in the population for a specific significant >>>>> cluster. >>>>> However I am not sure how to extract individual values from the entire >>>>> cluster. (note that the concatenated surface used as input for the glm >>>>> contains some 0 values that I want to exclude from the mean value of >>>>> the >>>>> cluster). >>>>> Is there a way to build a label from a specific significant cluster? >>>>> >>>>> Then, I was thinking about using mri_segstats --avgwf on the 4D >>>>> concatenated file to get the average of the region but is there a way >>>>> to >>>>> not include 0 values? >>>>> >>>>> And then I was also interested in getting the correlation coefficient >>>>> from >>>>> that same cluster, so maybe the script below would be helpful for that >>>>> but >>>>> I could not open it. >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m >>>>> >>>>> Thanks so much for your help >>>>> Best >>>>> Celine >>>>> >>>>> On 05/31/2012 06:09 AM, Knut J Bjuland wrote: >>>>>> Hi >>>>>> >>>>>> I am trying to calculate correlation coefficient using freesurfer GLM >>>>>> for associations between volumes and IQ. I found this ealier answar, >>>>>> but the matlab script but the link appear to be dead. >>>>>> >>>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html >>>>>> >>>>>> Best regards >>>>>> >>>>>> Knut J >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> 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/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> 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 >> 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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> 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 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/ _______________________________________________ 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.
