Thanks, indeed we used --pvr.
The command line was:
mri_glmfit \
--y ${PATH_DIR}/{surf}.mgh \
--pvr CT_surf.mgh \
--fsgd myfsgd.fsgd \
--C cont.mat \
--surf fsaverage $hemi \
--glmdir outputdir \
--mask mask_minimum_of_subjects.mgh \
--frame-mask mask_for_0_values.mgh \
--no-prune
Would there be a way to work around, or should I just try to do it only
from non pvr glm analyses?
Celine> > 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 > > > _______________________________________________ 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 . 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