It should be the sig.mgh file in your contrast directory. doug ps. Please post to the list and not me directly. thanks!
On 07/18/2012 11:56 AM, Antonella Kis wrote:
Hi Doug,
Many thanks for your prompt response and your help. I have one more question please. I searched for mri_surfcluster command and I am not sure what should be my input file.
Can you please clarify this for me? Should this be L-frontal.fsgd since I have more subjects?
Thank you. Antonella
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, July 18, 2012 11:39 AM *Subject:* Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option
Hi Antonella, first of all, FDR and clusterwise correction are doing different things. Technically, you don't get clusters from FDR. FDR will choose a voxel-wise threshold for you, and any voxel above threshold can be interpreted as surviving FDR (but you should know how to interpret it -- see Tom Nichols' paper). Of course, many of the voxels may appear as clusters. In your case, FDR found a voxel-wise threshold of 3.8 (meaning p<1.5849e-04). The fastest way to get the values you want is to go outside of QDEC. First, run mri_surfcluster using a threshold of 3.8 (--thmin 3.8). Specify an output cluster number map (--ocn ocn.mgh) and a summary file (--sum sum.dat). This will produce a lot of "clusters", two of which should be the ones below (you can prune the list by specifying that the clusters need to be a certain size (--minarea). Once you have the ocn file, you can run mri_segstats, something like mri_segstats --seg ocn.mgh --i y.mgh --avgwf avgwf.dat --excludeid 0 y.mgh is the glmfit input file created by qdec. This will produce avgwf.dat which will have a column for each cluster, the order will be the same as that in sum.dat.
douig
On 07/18/2012 11:25 AM, Antonella Kis wrote:
Dear FS team,
I am doing a cortical thickness study using QDEC. I used FDR and got the following clusters:
Generating cluster stats using min threshold of 3.8... Found 2 clusters Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation
1 -3.8743 18231 4.55 -39.8 1.5 14.1 14 precentral 2 -3.8065 47386 2.66 -8.2 33.1 33.9 4superiorfrontal
============================================================ I need to get the cortical thickness values from each subject within this clusters so I am trying to use mri_glmfit-sim with --cache option and I wonder what value should I choose in this case for cache (2, 3.3 or 4) and what --cwpvalthresh 0.05 or .025 to get the same results as FDR's results.
I tried: mri_glmfit-sim \ --glmdir lh.L_frontal.glmdir \ --cache 3 neg \ --cwpvalthresh .05 \ --overwrite
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.874 18231 320.36 -39.8 1.5 14.1 0.02610 0.02410 0.02820 949 precentral 2 -3.807 47386 700.61 -8.2 33.1 33.9 0.00020 0.00000 0.00040 1053 superiorfrontal
so as you can see the clusters are the same but their Size and NVtxs is so different. What is wrong?
Thank you for your time and help. Antonella
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Thanks Doug,
So I suppose should be the sig.mgh from running mri_glmfit:
mri_glmfit \ --y lh.L_frontal.15.mgh \ --fsgd L_frontal.fsgd dods\ --C lh-Avg-thickness-Cor.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.L_frontal.glmdir Is this right?
Thank you. Antonella
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com; "Freesurfer@nmr.mgh.harvard.edu" Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 18, 2012 12:03 PM Subject: Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option
It should be the sig.mgh file in your contrast directory. doug ps. Please post to the list and not me directly. thanks!
On 07/18/2012 11:56 AM, Antonella Kis wrote:
Hi Doug,
Many thanks for your prompt response and your help. I have one more question please. I searched for mri_surfcluster command and I am not sure what should be my input file.
Can you please clarify this for me? Should this be L-frontal.fsgd since I have more subjects?
Thank you. Antonella
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, July 18, 2012 11:39 AM *Subject:* Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option
Hi Antonella, first of all, FDR and clusterwise correction are doing different things. Technically, you don't get clusters from FDR. FDR will choose a voxel-wise threshold for you, and any voxel above threshold can be interpreted as surviving FDR (but you should know how to interpret it -- see Tom Nichols' paper). Of course, many of the voxels may appear as clusters. In your case, FDR found a voxel-wise threshold of 3.8 (meaning p<1.5849e-04). The fastest way to get the values you want is to go outside of QDEC. First, run mri_surfcluster using a threshold of 3.8 (--thmin 3.8). Specify an output cluster number map (--ocn ocn.mgh) and a summary file (--sum sum.dat). This will produce a lot of "clusters", two of which should be the ones below (you can prune the list by specifying that the clusters need to be a certain size (--minarea). Once you have the ocn file, you can run mri_segstats, something like mri_segstats --seg ocn.mgh --i y.mgh --avgwf avgwf.dat --excludeid 0 y.mgh is the glmfit input file created by qdec. This will produce avgwf.dat which will have a column for each cluster, the order will be the same as that in sum.dat.
douig
On 07/18/2012 11:25 AM, Antonella Kis wrote:
Dear FS team,
I am doing a cortical thickness study using QDEC. I used FDR and got the following clusters:
Generating cluster stats using min threshold of 3.8... Found 2 clusters Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -3.8743 18231 4.55 -39.8 1.5 14.1 14 precentral 2 -3.8065 47386 2.66 -8.2 33.1 33.9 4 superiorfrontal ============================================================ I need to get the cortical thickness values from each subject within this clusters so I am trying to use mri_glmfit-sim with --cache option and I wonder what value should I choose in this case for cache (2, 3.3 or 4) and what --cwpvalthresh 0.05 or .025 to get the same results as FDR's results.
I tried: mri_glmfit-sim \ --glmdir lh.L_frontal.glmdir \ --cache 3 neg \ --cwpvalthresh .05 \ --overwrite
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.874 18231 320.36 -39.8 1.5 14.1 0.02610 0.02410 0.02820 949 precentral 2 -3.807 47386 700.61 -8.2 33.1 33.9 0.00020 0.00000 0.00040 1053 superiorfrontal
so as you can see the clusters are the same but their Size and NVtxs is so different. What is wrong?
Thank you for your time and help. Antonella
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Antonella Kis -
Douglas N Greve