Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Douglas N Greve
gh.harvard.edu > Gesendet: Dienstag, 21. Februar 2017 18:56:17 > Betreff: Re: [Freesurfer] cluster as ROI > > That will be the average value over the vertices in the ROI, which is > not what you want for surface area. Add --accumulate to the mri_segstats > command line to get th

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Clara Kühn
that doesn't change the values. I've attached the file for you. - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 21. Februar 2017 18:56:17 Betreff: Re: [Freesurfer] cluster as ROI That will be the average value over

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Douglas N Greve
kuehn" > An: "Freesurfer support list" > Gesendet: Dienstag, 21. Februar 2017 18:28:25 > Betreff: Re: [Freesurfer] cluster as ROI > > ah! Perfect, thank you! I'll give that a try. > > - Ursprüngliche Mail - > Von: "Douglas N Greve" &g

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Clara Kühn
Mail - Von: "ckuehn" An: "Freesurfer support list" Gesendet: Dienstag, 21. Februar 2017 18:28:25 Betreff: Re: [Freesurfer] cluster as ROI ah! Perfect, thank you! I'll give that a try. - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Clara Kühn
ah! Perfect, thank you! I'll give that a try. - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 21. Februar 2017 18:23:48 Betreff: Re: [Freesurfer] cluster as ROI then that is the "ocn" file to use with mri_se

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Douglas N Greve
then that is the "ocn" file to use with mri_segstats On 02/21/2017 12:18 PM, Clara Kühn wrote: > yes! > > - Ursprüngliche Mail - > Von: "Douglas N Greve" > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 21. Februar 2017 17:58:37 >

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Clara Kühn
yes! - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 21. Februar 2017 17:58:37 Betreff: Re: [Freesurfer] cluster as ROI Does this file exist? /nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Douglas N Greve
rüngliche Mail - > Von: "Douglas N Greve" > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 21. Februar 2017 17:47:23 > Betreff: Re: [Freesurfer] cluster as ROI > > Can you send the terminal output? > > > On 02/21/2017 11:44 AM, Clara Kühn wrote: >> Hm.

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Clara Kühn
I've attached it for you as a .txt file - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 21. Februar 2017 17:47:23 Betreff: Re: [Freesurfer] cluster as ROI Can you send the terminal output? On 02/21/2017 11:44 AM, C

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Douglas N Greve
--cache-dir > $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces > > Cheers Clara > > - Ursprüngliche Mail - > Von: "Douglas N Greve" > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 21. Februar 2017 17:24:02 > Betreff: Re: [Fr

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Clara Kühn
- Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 21. Februar 2017 17:24:02 Betreff: Re: [Freesurfer] cluster as ROI You will have to run mri_glmfit-sim On 02/21/2017 04:07 AM, Clara Kühn wrote: > Hi Doug, > > I have a gamma

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Douglas N Greve
ig.ocn.mgh? Or how could I > retrieve this file? > > Thanks for your help! > Clara > > - Ursprüngliche Mail - > Von: "Douglas N Greve" > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Donnerstag, 16. Februar 2017 19:22:01 > Betreff: Re: [Freesurfer] c

Re: [Freesurfer] cluster as ROI

2017-02-21 Thread Clara Kühn
- Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 16. Februar 2017 19:22:01 Betreff: Re: [Freesurfer] cluster as ROI On 02/16/2017 04:24 AM, Clara Kühn wrote: > Hi Doug, > > thanks for your input. Could you specify some of the flags for me? > &g

Re: [Freesurfer] cluster as ROI

2017-02-16 Thread Douglas N Greve
-sim output may not be there. you'll have to run it separately. But there should be, eg, gamma.mgh there > > Cheers > Clara > > - Ursprüngliche Mail - > Von: "Douglas N Greve" > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Mittwoch, 15. Februar 2017 2

Re: [Freesurfer] cluster as ROI

2017-02-16 Thread Clara Kühn
file. The only files I have in the contrast folder are 2 .mat files Cheers Clara - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 15. Februar 2017 23:35:54 Betreff: Re: [Freesurfer] cluster as ROI Use something like this m

Re: [Freesurfer] cluster as ROI

2017-02-15 Thread Douglas N Greve
Use something like this mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh --excludeid 0 --avgwf tp1.clustermean.dat The output tp1.clustermean.dat will be a matrix with nsubjects rows and nclusters columns where the value represents the mean for that subject in that clu

[Freesurfer] cluster as ROI

2017-02-14 Thread Clara Kühn
Dear FreeSurfer Experts, I compared 2 groups in QDEC in spc (from pre to post) and found a cluster that survives Monte Carlo correction. Now I would like to extract the data for each participant and each time point from that cluster so that I can plot the change. How could I do this? I tried th