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
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
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
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
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
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
>
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
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.
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
--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
- 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
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
-
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
-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
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
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
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
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