Re: [Freesurfer] problem feeding design matrix to mri_glmfit

1/18/2013 12:09 PM, Laura M. Tully wrote: > > Hello freesurfers, > > > > I'm trying to run mri_glmfit between groups analysis (patients vs. > > controls) with gender, age, medication (continuous), and duration of > > illness as covariates. Because the control group ha

[Freesurfer] problem feeding design matrix to mri_glmfit

00 ---p 00:00 0 [vsyscall] Aborted -- -- Laura M. Tully, PhD Post-Doctoral Fellow in Psychiatry UC Davis Imaging Research Center 4701 X Street, Sacramento, CA 95817 Phone: (916) 734-7927 Fax: (916) 734-8750 Alumnus of Social Neuroscience & Psychopathology Lab, Harvard Universi

[Freesurfer] problem feeding design matrix to mri_glmfit

00 ---p 00:00 0 [vsyscall] Aborted -- -- Laura M. Tully, PhD Post-Doctoral Fellow in Psychiatry UC Davis Imaging Research Center 4701 X Street, Sacramento, CA 95817 Phone: (916) 734-7927 Fax: (916) 734-8750 Alumnus of Social Neuroscience & Psychopathology Lab, Harvard Universi

Re: [Freesurfer] ill conditioned matrix with covariates that are unequal between groups

I am interested in is detecting group differences in thickness whilst controlling for confounds such as age, medication, and duration of illness... if I recoded the HC group wouldn't this change the analysis from between group to within? > > doug > > On 10/21/2013 11:01 PM, La

[Freesurfer] ill conditioned matrix with covariates that are unequal between groups

itioned or badly scaled, condno = 1e+08 -- -- Laura M. Tully, PhD Post-Doctoral Fellow in Psychiatry UC Davis Imaging Research Center 4701 X Street, Sacramento, CA 95817 Phone: (916) 734-7927 Fax: (916) 734-8750 Alumnus of Social Neuroscience & Psychopathology Lab, Harvard

Re: [Freesurfer] Merging PArcellation labels

> Thank you so much. > It worked well. > Do you know how to make cuts on the merged label, for eg. if I need to > seperate DLPFC from premotor cortex. > > >---------- > *From:* Laura M. Tully > *To:* Anupa AV > *Cc:* "freesurfer@nmr.mg

Re: [Freesurfer] Merging PArcellation labels

nceline . 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. > > -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment

Re: [Freesurfer] help with contrasts

information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773) > 406-2464 or email. > > > On Fri, Mar 22, 2013 at 11:38 AM, Laura M. Tully < > tully.la...@goog

Re: [Freesurfer] help with contrasts

d run separate GLMs within each group, as you suggested - I just want to make sure I am understanding the weights correctly first... LT On Fri, Mar 22, 2013 at 8:23 AM, MCLAREN, Donald wrote: > > On Thu, Mar 21, 2013 at 8:59 PM, Laura M. Tully < > tully.la...@googlemail.com&g

Re: [Freesurfer] help with contrasts

information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773)

[Freesurfer] help with contrasts

.5 .5 -.5 -.5 Does this look right? Thanks! Laura. -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0

Re: [Freesurfer] Stat doubts

to recompute rvarmat (don't load rvar or beta) > > [betamat rvarmat] = fast_glmfit(y,X); > > Make sure you have $FREESURFER_HOME/fsfast/**toolbox in your matlab path > > doug > > > > On 03/21/2013 05:04 PM, Laura M. Tully wrote: > >> Hi Doug, >> >

Re: [Freesurfer] Stat doubts

ontrasts that you specify. You can run the same commands > on the cluster averaged data (xxx.y.ocn...). To do this, don't load in the > beta file. Instead > > y = load('xxx.y.ocn...'); > beta = inv(X'*X)*X'*y; > then proceed with the rest of the code > >

Re: [Freesurfer] y values from glmfit-sim

Thank you! On Thu, Mar 21, 2013 at 10:56 AM, Douglas N Greve wrote: > Yes, the average thickness over the cluster for each subject. > doug > > On 03/21/2013 01:54 PM, Laura M. Tully wrote: > >> Thanks - one last clarification: just to confirm - the values of >&g

Re: [Freesurfer] Stat doubts

ressed. 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 info

Re: [Freesurfer] y values from glmfit-sim

y.dat by the number of vertices in the cluster. > > doug > > ps. What version of FS are you using? If not 5.2, do you have the patch to > fix the area and volume analysis? > > > > On 03/21/2013 12:52 PM, Laura M. Tully wrote: > >> hi Doug, >> A follow up question

Re: [Freesurfer] y values from glmfit-sim

the clusters. > They are raw input, no detrending. > doug > On 03/20/2013 05:16 PM, Laura M. Tully wrote: > > Hello experts, > > > > could someone clarify for me what the y values in the xxx.ocn.y.dat > > files represent following glmfit-sim? are they the residualized y

[Freesurfer] y values from glmfit-sim

. -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist:

Re: [Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions

.abs.sig.ocn.annot.annot No such file or directory Thanks! LT On Wed, Mar 20, 2013 at 9:54 AM, Douglas N Greve wrote: > > On 03/20/2013 12:09 PM, Laura M. Tully wrote: > >> Sorry - meant to respond to list. >> >> Thanks for the response Doug - I have a few follow up question

Re: [Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions

overall model) but >I could not find the .m scripts for the functions (MRIread >or fast_glm_pcc?) - would these functions be appropriate and if so where >might I find them? > > Thanks in advance for your help! > > Laura. > > > On Wed, Mar 20, 2013 at 8:2

[Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions

, Mar 18, 2013 at 5:05 PM, Laura M. Tully wrote: > Hi Freesurfer experts, > > I'm hoping you can help me understand how to interpret interactions in > clusters identified in whole brain analysis using glmfit and glmfit-sim. > Below I describe what I've done and what I

[Freesurfer] interpreting clusters from 2 and 3 way interactions

nking is that I do something similar in fMRI analysis in spm where I can plot the contrasts in a significant cluster and then extract both the average contrast estimates for each group and the contrast estimates for each individual subject. Thanks in advance! Laura. -- -- Laura M. Tully, M

Re: [Freesurfer] running mris_preproc for each glm?

times if the > subjects changed between analyses. If it is the same subjects in the same > order, then you only need to run it once. > doug > > > > On 3/15/13 4:42 PM, Laura M. Tully wrote: > > Hi freesurfer experts, > > I'm planning to run a few different glms

[Freesurfer] running mris_preproc for each glm?

ached, and it seems that there may be an option (-cache--in?) that I can use on just one mris_preproc but I'm not sure if this is correct, or what the -cache--in option does. Thanks! Laura. -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

mit this is a rather weak justification and if the images >> are good, perhaps the pial could be just as good, despite the fact that it >> somewhat depends on the white for its construction. >> >> >> >>> >>>1. Is there a way to run mri_anatomical_

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

ical_stats on multiple subjects at >>once and write to a tablefile (similar to asegstats2table output)? >> >> > I think you can use aparcstats2table, then add up all regions in a > spreadsheet (or even with awk/gawk). Alternatively, you can use "grep" to > pick the White

[Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

? mri_anatomical_stats can produce both pial and white matter mean surface area stats. 3. Is there a way to run mri_anatomical_stats on multiple subjects at once and write to a tablefile (similar to asegstats2table output)? Thanks! Laura. -- -- Laura M. Tully, MA Social Neuroscience

Re: [Freesurfer] qdec table

@nmr.mgh.harvard.edu Message-ID: <4fccd21d.4040...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed OK, I've replicated that this is happening, but Nick will have to take a look. doug On 06/04/2012 11:05 AM, Laura M. Tully wrote: > > > > Hi Do

[Freesurfer] qdec table file

Hi Doug, Attached is the qdec table file and associated levels files. It's strange that qdec won't let me select more than one continuous variable. What's even more strange is that I have been able to do that last month when I originally looked at these data before doing manual edits and quality c

[Freesurfer] qdec: selecting multiple continuous variables

Hi, I am using freesurfer 5.1.0 and qdec 1.4. I'm interested in looking at between group differences in thickness in relation to two other continuous measures whilst controlling for ICV. However, qdec doesn't seem to let me select more that one continuous variable even though I only have group sel