Thank you Doug,
Actually I was trying to apply what was mentioned in this link by replicating the method on the command "mri_glmfit" and not using the command "mri_mcsim".
I tried to use for example the label "BA4a" (it is available in the folder/fsaverage/label), but the command "mriglm_fit failed to see it!! I ran the command as follow:
mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --label BA4a --glmdir lh
Kindly, what I am doing wrong in this command ? and how can I create label? What command I need? Can I use mri_binarize for example and save the output as a label?
John
Sent: Thursday, January 26, 2017 at 1:15 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis
FS does not come with correction tables for all labels. You'll have to
build your own. here are the instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
On 01/26/2017 01:09 PM, John Anderson wrote:
> Hello Freesurfers,
> I am working on a PET surface based analysis between two groups. I did
> the following:
> 1. I concatentaed the PET images using the command "mris_preproce"
> and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right
> hemisphere.
> 2. I smoothed "lh.mgh and rh.mgh) using the command:
> mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.mgh --tval
> lh_sm10.mgh
> 3. I studdied the diffence between the groups usiing the command:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf
> fsaverage lh --cortex --glmdir lh
> 4. I corrected the results for multiple comparison using the command:
> mri_glmfit-sim --glmdir lh --cache 30 pos --cwp 0.01 --2spaces
> I want to narrow (reduce the strictness) of the correction for
> multiple comparision to a specific label (e.g. precentral gyrus). I
> changed the commands "mri_glmfit" and "mri_glmfit-sim" as follow:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf
> fsaverage lh --label precentral --glmdir lh
> mri_glmfit-sim --glmdir lh --cache 30 pos --cache-label precentral
> --cwp 0.01 --2spaces
> I got error that the label "precentral" is not exist. I was unable to
> find this label in the folder "fsaverage". Kindly:
> 1. whct I am doing wrong?
> 2. How can I create this label ? and in whcih folder it must be placed?
> Best,
> John
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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.
build your own. here are the instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
On 01/26/2017 01:09 PM, John Anderson wrote:
> Hello Freesurfers,
> I am working on a PET surface based analysis between two groups. I did
> the following:
> 1. I concatentaed the PET images using the command "mris_preproce"
> and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right
> hemisphere.
> 2. I smoothed "lh.mgh and rh.mgh) using the command:
> mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.mgh --tval
> lh_sm10.mgh
> 3. I studdied the diffence between the groups usiing the command:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf
> fsaverage lh --cortex --glmdir lh
> 4. I corrected the results for multiple comparison using the command:
> mri_glmfit-sim --glmdir lh --cache 30 pos --cwp 0.01 --2spaces
> I want to narrow (reduce the strictness) of the correction for
> multiple comparision to a specific label (e.g. precentral gyrus). I
> changed the commands "mri_glmfit" and "mri_glmfit-sim" as follow:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf
> fsaverage lh --label precentral --glmdir lh
> mri_glmfit-sim --glmdir lh --cache 30 pos --cache-label precentral
> --cwp 0.01 --2spaces
> I got error that the label "precentral" is not exist. I was unable to
> find this label in the folder "fsaverage". Kindly:
> 1. whct I am doing wrong?
> 2. How can I create this label ? and in whcih folder it must be placed?
> Best,
> John
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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.
_______________________________________________ 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.
