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 the total area
On 02/21/2017 12:43 PM, Clara Kühn wrote:
I have one last question about the whole thing.
What is the measurement in the output file? My subjects have values between 0.6 and 1.5. As the measure is surface area I was expecting different numbers. Do I have to multiply by some constant to get to mm²?
Thank you Clara
----- Ursprüngliche Mail ----- Von: "ckuehn" ckuehn@cbs.mpg.de An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu 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" greve@nmr.mgh.harvard.edu 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_segstats
On 02/21/2017 12:18 PM, Clara Kühn wrote:
yes!
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu 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_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
On 02/21/2017 11:54 AM, Clara Kühn wrote:
I've attached it for you as a .txt file
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu 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 already did that. In none of my glmdirs are files like the csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu 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.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I also have a contrasts.sig.mgh file in the gmldir.
Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could I retrieve this file?
Thanks for your help! Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu 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?
--i tp1.stack.mgh - is this supposed to be the cluster or file in my /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
input from preproc/surf2surf
--seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this file. The only files I have in the contrast folder are 2 .mat files
there should be a bunch of output there from mri_glmfit and mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-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" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 15. Februar 2017 23:35:54 Betreff: Re: [Freesurfer] cluster as ROI
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 cluster.
On 02/14/2017 11:47 AM, Clara Kühn wrote: > 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 this so far: > aparcstats2table --qdec-long $SUBJECTS DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt --parc $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh > > But I get this error: > ERROR: The stats file /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats is not found or is too small to be a valid statsfile > Use --skip flag to automatically skip bad stats files > > > Do I have to define my cluster as a ROI and then warp it onto the single time points? How would I do that? > > Any help is much appreciated! > Thank you > > Clara
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