Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Taking a look at QDEC/glm code
by ye tian 06 Sep '13

06 Sep '13

Dear Freesurfers, I am very curious about glm's and I would like to see how it is constructed. Would anyone please direct me to freesurfer's codes so that I can get a feeling? Thank you very much! Sincerely, Ye

2 2

Otto: upgrade freesurfer to latest version?
by Otto Muzik 06 Sep '13

06 Sep '13

Dear All, I have posted this message before, but did not get any reply. Please help. I would like to upgrade my freesurfer distribution to the latest version - Is there an automated procedure to do this? My current version is linux-gnu-stable5-20110522 Many thanks! Otto

3 2

arguments to mris_curvature call in -inflate2 step of recon-all
by David Romano 06 Sep '13

06 Sep '13

Hi everyone, Since they don't appear in the documentation accessible through the --help flag, I was just wondering how the flags -n, -thresh, and -distances affect the call to mris_curvature in the inflate2 step of the -autorecon2 stage of recon-all: mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated (as described on the webpage http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) Thanks in advance for you help, David Romano

1 0

ascii list of label files
by stdp82＠virgilio.it 06 Sep '13

06 Sep '13

Hi list, After mri_binarize, I'using label2surf command to trasform labels files obtained into surface files suitable for probtrackx (FSL). I do not understand how can I provide ascii list of label files for label2surf -s <surface> -o <outputsurface> -l <labels>Thanks, Stefano

2 1

qdec_glmfit
by Yang, Daniel 06 Sep '13

06 Sep '13

Hi Freesurfer experts, Does qdec_glmfit support the option of specifying nuisance factors? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

2 1

new subcortical regions
by Luo,Yishan 06 Sep '13

06 Sep '13

Hello, I have run recon-all for my subject, if I want to get more subcortical segmentation, e.g., globus pallidus, medulla, pons and so on, how can I do?Can I manually draw these region on the bert image and transfer them to individual subject, like mri_label2label? Thanks. Lisa

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Avoid interaction term in qdec?
by Yang, Daniel 06 Sep '13

06 Sep '13

Dear FS Experts, My model has two categorical variable: Diagnosis and Sex. I am interested in the effect of Diagnosis but I want to control the Sex effect. Toward this goal, I want to model two main effects and want to avoid modeling their interaction term. Is this something feasible in FreeSurfer group analysis? Would using DOSS help with the solution? Thanks! Daniel

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tool to compare surface files (along the lines of diff)?
by David Romano 06 Sep '13

06 Sep '13

Hi everyone, I'm trying to figure out whether two surfaces which appear identical in freeview are indeed identical. Using diff shows the files are not, but since they're binary, I can't tell whether this difference is simply due to header information that might be embedded in the files, or whether the surfaces do indeed differ. Is there a FreeSurfer command that can be used to determine this? Thanks in advance for your help, David Romano

3 3

Difference between QDEC and glm results
by ye tian 05 Sep '13

05 Sep '13

Dear Freesurfers, I compared my QDEC and glm (command line) results, using the same contrast and threshold, but the size of the red cluster (barely visible on glm) is quite different. Is this a problem? Thank you very much! Sincerely, Ye

2 2

Estimated Total Intra Cranial Vol
by stdp82＠virgilio.it 05 Sep '13

05 Sep '13

Hi list. I'm looking mailing list to find responce to this question. "Estimated Total Intra Cranial Vol" obtained by asegstats2table also included ventricles volume? I'd like to assess the volumetric changes of a subcortical structures. Do you advise me to consider "Estimated Total Intra Cranial Vol" (with or without ventricles?) or, alternatively, subcortical brain volume? Thank you very much, Stefano

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