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
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? I have tried to draw the cluster as an ROI in QDEC but that didn't work (I could draw only on the medial surface and around the temporal sulcus). I'm guessing because I'm using a study specific template and not the fsaverage.
Any help is much appreciated! Thank you
Clara
Hi Clara,
I don't know, but this is not specific to longitudinal question. You don't need to warp to individual time points. The SPC is defined in each base and everything is a cross sectional analysis.
So you have a cluster in QDEC and want to do an ROI analysis. I am sure someone else knows.
Best, Martin
On 02/15/2017 04:41 PM, 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? I have tried to draw the cluster as an ROI in QDEC but that didn't work (I could draw only on the medial surface and around the temporal sulcus). I'm guessing because I'm using a study specific template and not the fsaverage.
Any help is much appreciated! Thank you
Clara
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
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? --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
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
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
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
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
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
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
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
that doesn't change the values. I've attached the file for you.
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu 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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry, gave you the wrong flag. Use --sumwf instead of --accumulate
On 02/21/2017 01:08 PM, Clara Kühn wrote:
that doesn't change the values. I've attached the file for you.
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu 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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Clara Kühn -
Douglas N Greve -
Martin Reuter