Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul
I think there is an example on the wiki in the ROI analysis section. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs and p-values
On 7/30/16 5:33 PM, miracle ozzoude wrote:
Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks doug. Also, Please can you verify if this are the right codes for performing ROI surface based analysis using the command line. I tried to reverse the whole brain analysis tutorial with some of the previous threads i read. I'm trying to mask the entorhinal and MT and then perform ROI on them using GLM. Thanks a lot
CREATE MASK USING MRI_BINARIZE setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri cd users/paul/desktop/ims/fsaverage/mri mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz
MERGE TO LABELS cd users/paul/desktop/ims/fsaverage/label mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label
MRIS_PREPROC cd users/paul/desktop/ims mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas thickness --out lh.filename.thickness.00.mgh
MRI_SURF2SURF mri_surf2surf --hemi lh --s fsaverage --sval lh.filename.thickness.00.mgh --fwhm 10 --label-trg fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh
GLM mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods --C contrastmatrix.mtx --surf fsaverage lh --label fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir
CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces
On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
I think there is an example on the wiki in the ROI analysis section. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs and p-values
On 7/30/16 5:33 PM, miracle ozzoude wrote:
Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
There are several things that need to be changed as I've indicated below
On 08/01/2016 10:09 PM, miracle ozzoude wrote:
Thanks doug. Also, Please can you verify if this are the right codes for performing ROI surface based analysis using the command line. I tried to reverse the whole brain analysis tutorial with some of the previous threads i read. I'm trying to mask the entorhinal and MT and then perform ROI on them using GLM. Thanks a lot
CREATE MASK USING MRI_BINARIZE setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri cd users/paul/desktop/ims/fsaverage/mri mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz
MERGE TO LABELS cd users/paul/desktop/ims/fsaverage/label mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label
MRIS_PREPROC cd users/paul/desktop/ims mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas thickness --out lh.filename.thickness.00.mgh
MRI_SURF2SURF mri_surf2surf --hemi lh --s fsaverage --sval lh.filename.thickness.00.mgh --fwhm 10 --label-trg fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh
Add --label-src lh.2mask.label This will cause it to smooth only in the mask
GLM mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods --C contrastmatrix.mtx --surf fsaverage lh --label fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir
CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces
You will need to create your own correction simulation since you have changed the search space. See here http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think there is an example on the wiki in the ROI analysis section. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs and p-values On 7/30/16 5:33 PM, miracle ozzoude wrote:Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello doug, Should I add --label-src in addition to --label-trg or should I replace the latter with the former? Thanks. Also, Just to conform, I should run mri_glmfit-sim after mri_mcsim. Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Douglas N Greve Sent: Friday, August 5, 2016 11:49 AM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] group analysis/ region of interest (ROI) approach
There are several things that need to be changed as I've indicated below
On 08/01/2016 10:09 PM, miracle ozzoude wrote:
Thanks doug. Also, Please can you verify if this are the right codes for performing ROI surface based analysis using the command line. I tried to reverse the whole brain analysis tutorial with some of the previous threads i read. I'm trying to mask the entorhinal and MT and then perform ROI on them using GLM. Thanks a lot
CREATE MASK USING MRI_BINARIZE setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri cd users/paul/desktop/ims/fsaverage/mri mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz
MERGE TO LABELS cd users/paul/desktop/ims/fsaverage/label mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label
MRIS_PREPROC cd users/paul/desktop/ims mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas thickness --out lh.filename.thickness.00.mgh
MRI_SURF2SURF mri_surf2surf --hemi lh --s fsaverage --sval lh.filename.thickness.00.mgh --fwhm 10 --label-trg fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh
Add --label-src lh.2mask.label This will cause it to smooth only in the mask
GLM mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods --C contrastmatrix.mtx --surf fsaverage lh --label fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir
CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces
You will need to create your own correction simulation since you have changed the search space. See here http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think there is an example on the wiki in the ROI analysis section. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs and p-values
On 7/30/16 5:33 PM, miracle ozzoude wrote:
Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 08/05/2016 02:35 PM, miracooloz@gmail.com wrote:
Hello doug, Should I add --label-src in addition to --label-trg or should I replace the latter with the former?
It does not matter as both the source and target are fsaveage
Thanks. Also, Just to conform, I should run mri_glmfit-sim after mri_mcsim.
correct
Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Douglas N Greve Sent: Friday, August 5, 2016 11:49 AM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] group analysis/ region of interest (ROI) approach
There are several things that need to be changed as I've indicated below
On 08/01/2016 10:09 PM, miracle ozzoude wrote:
Thanks doug. Also, Please can you verify if this are the right codes for performing ROI surface based analysis using the command line. I tried to reverse the whole brain analysis tutorial with some of the previous threads i read. I'm trying to mask the entorhinal and MT and then perform ROI on them using GLM. Thanks a lot
CREATE MASK USING MRI_BINARIZE setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri cd users/paul/desktop/ims/fsaverage/mri mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz
MERGE TO LABELS cd users/paul/desktop/ims/fsaverage/label mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label
MRIS_PREPROC cd users/paul/desktop/ims mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas thickness --out lh.filename.thickness.00.mgh
MRI_SURF2SURF mri_surf2surf --hemi lh --s fsaverage --sval lh.filename.thickness.00.mgh --fwhm 10 --label-trg fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh
Add --label-src lh.2mask.label This will cause it to smooth only in the mask
GLM mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods --C contrastmatrix.mtx --surf fsaverage lh --label fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir
CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces
You will need to create your own correction simulation since you have changed the search space. See here http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think there is an example on the wiki in the ROI analysis section. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs and p-values
On 7/30/16 5:33 PM, miracle ozzoude wrote:
Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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miracle ozzoude -
miracooloz＠gmail.com