Hi Doug,
Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well.
We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are?
Thanks so much! Alex
Hi Alexandra, what structure are you looking to analyze? Ie, the volume of what? The volume of cortex? doug ps. In the future, please post such questions to the freesurfer list as it gives others the opportunity to answer and to learn. thanks!
On 07/23/2012 12:03 PM, Alexandra Tanner wrote:
Hi Mr. Greve,
My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain Genomics Lab. I had a question regarding conducting volume analyses. On the freesurfer wiki there are commands that show how to conduct Paired Analyses to look at average surface, and I was curious if it was possible to do a paired analysis looking at volume instead. Any information you have would be very helpful.
Thanks so much!
Best,
Alexandra Tanner Clinical Research Coordinator Laboratory for Brain Genomics Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p) 617.643.3215
-- 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
Hi Alex, do you want to do it on an ROI basis? If so, you can use asegstats2table to create a table of your subjects at the two time points, then import this table into SPSS. Or you can run the table through mri_glmfit to do the paired-t analysis. doug
On 07/24/2012 01:56 PM, Alexandra Tanner wrote:
Hi Doug,
Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well.
We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are?
Thanks so much! Alex
Hi Alexandra, what structure are you looking to analyze? Ie, the volume of what? The volume of cortex? doug ps. In the future, please post such questions to the freesurfer list as it gives others the opportunity to answer and to learn. thanks!
On 07/23/2012 12:03 PM, Alexandra Tanner wrote:
Hi Mr. Greve,
My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain Genomics Lab. I had a question regarding conducting volume analyses. On the freesurfer wiki there are commands that show how to conduct Paired Analyses to look at average surface, and I was curious if it was possible to do a paired analysis looking at volume instead. Any information you have would be very helpful.
Thanks so much!
Best,
Alexandra Tanner Clinical Research Coordinator Laboratory for Brain Genomics Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p) 617.643.3215
-- 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
Hi Doug,
We don't want to do ROIs because we're trying to get a thickness map of the entire subcortical region of the brain.
Prior to trying this, we ran a within subjects paired analysis that gave us thickness maps of cortical surface. We ran these commands to look at the thickness maps in each of our two groups:
mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --paired-diff
mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx
cd /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH
mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED2_Structural.fsgd osgm
(and then the same for our second group)
And then we ran these commands to get a thickness map for the interaction between the two groups:
mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural.fsgd paired-diff
mri_surf2surf --s fsaverage1 --hemi lh --fwhm 5 --sval lh.paired-diff.thickness.mgh --tval lh.paired-diff.thickness.sm05.mgh
mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.sm05.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED2_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx
Basically what we're wondering is if there's a way to do the same type of paired within subjects analyses on the same data that will instead generate volume thickness maps of the subcortical brain. I hope this clarifies my question a bit better, and if anyone has any ideas that'd be great!
Thanks, Alex
Hi Alex, do you want to do it on an ROI basis? If so, you can use asegstats2table to create a table of your subjects at the two time points, then import this table into SPSS. Or you can run the table through mri_glmfit to do the paired-t analysis. doug
On 07/24/2012 01:56 PM, Alexandra Tanner wrote:
Hi Doug,
Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well.
We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are?
Thanks so much! Alex
Hi Alexandra, what structure are you looking to analyze? Ie, the volume of what? The volume of cortex? doug ps. In the future, please post such questions to the freesurfer list as it gives others the opportunity to answer and to learn. thanks!
On 07/23/2012 12:03 PM, Alexandra Tanner wrote:
Hi Mr. Greve,
My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain Genomics Lab. I had a question regarding conducting volume analyses. On the freesurfer wiki there are commands that show how to conduct Paired Analyses to look at average surface, and I was curious if it was possible to do a paired analysis looking at volume instead. Any information you have would be very helpful.
Thanks so much!
Best,
Alexandra Tanner Clinical Research Coordinator Laboratory for Brain Genomics Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p) 617.643.3215
-- 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
-- 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
Hi Alex, what do you mean by a thickness map of the subcortical region? The subcortical structure are usually characterized by simple volume measurements (eg, hippocampus has a volume of XXX mm3). There are tools out there to do voxel based morphometry. Is this what you mean? doug
On 07/24/2012 03:02 PM, Alexandra Tanner wrote:
Hi Doug,
We don't want to do ROIs because we're trying to get a thickness map of the entire subcortical region of the brain.
Prior to trying this, we ran a within subjects paired analysis that gave us thickness maps of cortical surface. We ran these commands to look at the thickness maps in each of our two groups:
mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --paired-diff
mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx
cd /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH
mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED2_Structural.fsgd –osgm
(and then the same for our second group)
And then we ran these commands to get a thickness map for the interaction between the two groups:
mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural.fsgd –paired-diff
mri_surf2surf --s fsaverage1 --hemi lh --fwhm 5 --sval lh.paired-diff.thickness.mgh --tval lh.paired-diff.thickness.sm05.mgh
mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.sm05.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED2_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx
Basically what we're wondering is if there's a way to do the same type of paired within subjects analyses on the same data that will instead generate volume thickness maps of the subcortical brain. I hope this clarifies my question a bit better, and if anyone has any ideas that'd be great!
Thanks, Alex
Hi Alex, do you want to do it on an ROI basis? If so, you can use asegstats2table to create a table of your subjects at the two time points, then import this table into SPSS. Or you can run the table through mri_glmfit to do the paired-t analysis. doug
On 07/24/2012 01:56 PM, Alexandra Tanner wrote:
Hi Doug,
Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well.
We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are?
Thanks so much! Alex
Hi Alexandra, what structure are you looking to analyze? Ie, the volume of what? The volume of cortex? doug ps. In the future, please post such questions to the freesurfer list as it gives others the opportunity to answer and to learn. thanks!
On 07/23/2012 12:03 PM, Alexandra Tanner wrote:
Hi Mr. Greve,
My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain Genomics Lab. I had a question regarding conducting volume analyses. On the freesurfer wiki there are commands that show how to conduct Paired Analyses to look at average surface, and I was curious if it was possible to do a paired analysis looking at volume instead. Any information you have would be very helpful.
Thanks so much!
Best,
Alexandra Tanner Clinical Research Coordinator Laboratory for Brain Genomics Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p) 617.643.3215
-- 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
-- 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
Hi Doug,
Sorry for all the confusion, I misunderstood what we were looking for. Right now what we want is the volume measurement in each of the subcortical regions for each subject, which you suggested with the asegstats2table command.
Thanks so much for your help! Alex
Hi Alex, what do you mean by a thickness map of the subcortical region? The subcortical structure are usually characterized by simple volume measurements (eg, hippocampus has a volume of XXX mm3). There are tools out there to do voxel based morphometry. Is this what you mean? doug
On 07/24/2012 03:02 PM, Alexandra Tanner wrote:
Hi Doug,
We don't want to do ROIs because we're trying to get a thickness map of the entire subcortical region of the brain.
Prior to trying this, we ran a within subjects paired analysis that gave us thickness maps of cortical surface. We ran these commands to look at the thickness maps in each of our two groups:
mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --paired-diff
mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx
cd /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH
mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED2_Structural.fsgd osgm
(and then the same for our second group)
And then we ran these commands to get a thickness map for the interaction between the two groups:
mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural.fsgd paired-diff
mri_surf2surf --s fsaverage1 --hemi lh --fwhm 5 --sval lh.paired-diff.thickness.mgh --tval lh.paired-diff.thickness.sm05.mgh
mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.sm05.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED2_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx
Basically what we're wondering is if there's a way to do the same type of paired within subjects analyses on the same data that will instead generate volume thickness maps of the subcortical brain. I hope this clarifies my question a bit better, and if anyone has any ideas that'd be great!
Thanks, Alex
Hi Alex, do you want to do it on an ROI basis? If so, you can use asegstats2table to create a table of your subjects at the two time points, then import this table into SPSS. Or you can run the table through mri_glmfit to do the paired-t analysis. doug
On 07/24/2012 01:56 PM, Alexandra Tanner wrote:
Hi Doug,
Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well.
We were hoping to look at volume in subcortical regions of the brain
basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are?
Thanks so much! Alex
Hi Alexandra, what structure are you looking to analyze? Ie, the volume of what? The volume of cortex? doug ps. In the future, please post such questions to the freesurfer list as it gives others the opportunity to answer and to learn. thanks!
On 07/23/2012 12:03 PM, Alexandra Tanner wrote:
Hi Mr. Greve,
My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain Genomics Lab. I had a question regarding conducting volume analyses. On the freesurfer wiki there are commands that show how to conduct Paired Analyses to look at average surface, and I was curious if it was possible to do a paired analysis looking at volume instead. Any information you have would be very helpful.
Thanks so much!
Best,
Alexandra Tanner Clinical Research Coordinator Laboratory for Brain Genomics Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p) 617.643.3215
-- 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
-- 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
-- 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
-
Alexandra Tanner -
Douglas N Greve