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
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-- 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/
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