No, there is not an easy way to work around this.
On 09/24/2014 03:01 PM, Celine Louapre wrote:
> 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
>
>
--
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/
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