Hi Maria, these files are described in the help for mri_glmfit-sim (ie, mri_glmfit-sim --help) doug

On 7/29/13 11:45 AM, Maria Kharitonova wrote:

Hi Doug,

Thanks. Per your advice, I'm trying to visualize output in tksurfer but it would help me to do what the different overlays refer to. Could you clarify what the differences are between: mc-z.abs.tho20.sig.cluster.mgh vs mc-z.abs.tho20.sig.ocn.mgh vs mc-z.abs.tho20.sig.vertex.mgh

I think .ocn.mgh draws the regions that I see output in the terminal when I run qdec, but am not 100% sure. I searched the archives/tutorials and couldn't find the explanation of these different files.

Thanks! Maria

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Message: 14 Date: Fri, 26 Jul 2013 13:47:41 -0400 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec question: discrepancy in sig. clusters To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51F2B63D.6020706@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Maria, can you tar up the qdec output folder and send it to our file drop? I'm traveling now, so it might be the 1st week of august before I can take a look. You can also go into the qdec output folder and run tksurfer to show you the results.

doug

On 7/26/13 1:37 PM, Maria Kharitonova wrote:

...

Hello,

I have another newbie question. I'm running qdec, trying to compare cortical thickness in children with and without ADHD. However, I'm seeing a discrepancy between the clusters that are significant according to the terminal (after applying the Monte-Carlo simulation with default parameters; output below) and the ones that pop up when I hit "Find clusters and goto Max". For example, I'm seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. However, when I hit "Find clusters and goto Max", I only see the Frontalpole.

Using mri_surfcluster to extrat thickness measures only extracts it for the frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be able to extract stats on those 4 that are listed in the terminal, if possible.

Can you please help me reconcile the 2 types of output? Thanks!

*** terminal output:

# Input /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.75828 at vertex 134555 # Overall min -2.56762 at vertex 93241 # NClusters 4 # Total Cortical Surface Area 65020.8 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 4.758 134555 1015.59 8.7 58.2 -5.8 0.00010 0.00000 0.00020 1292 medialorbitofrontal 2 3.968 135840 466.91 40.0 -66.8 25.9 0.01790 0.01620 0.01960 750 inferiorparietal 3 3.954 115431 497.60 29.3 21.4 39.9 0.01150 0.01010 0.01290 900 caudalmiddlefrontal 4 3.242 133890 439.44 49.4 -5.1 22.0 0.02520 0.02320 0.02720 932 precentral

Simulation complete.

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Message: 15 Date: Fri, 26 Jul 2013 13:56:13 -0400 From: Satrajit Ghosh satra@mit.edu Subject: Re: [Freesurfer] Freesurfer surface circle of pre-defined size To: sarahp@nmr.mgh.harvard.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: CA+A4wO=cfM+7MnCVi-GvadUT5s4NFNGASU_+DS4nUStUoQ4frQ@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"

hi sarah,

you'll get a much quicker response posting PySurfer related questions to:

nipy-devel@neuroimaging.scipy.org

cheers,

satra

On Fri, Jul 26, 2013 at 12:57 PM, sarahp@nmr.mgh.harvard.edu wrote:

...

Hello Freesurfer Experts,

We would like to use PySurfer's function plot_label_foci.py to automatically create circular labels of a pre-defined radius (eg. 14mm) on the fsaverage surface of freesurfer.

What are the specified units of "n_steps" in the command line argument "utils.coord_to_label(subject_id, coord, label='coord', hemi='lh', n_steps=50"?

Thank you, Sarah _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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