Dear Freesurfer experts, My dataset was processed by Brainsuite, so that after registration they are in .dfs format. Now I wanted to do multiple comparison correction. How do I import the data to freesurfer and do the corrections? Thanks. Miao
Hi Mio, sorry, I have no clue, I've never used Brainsuite. If you have each subject's thickness in a common space, you could convert it to mgh format and then run mri_glmfit and mri_glmfit-sim doug
On 06/24/2014 01:16 PM, Miao Wei wrote:
Dear Freesurfer experts, My dataset was processed by Brainsuite, so that after registration they are in .dfs format. Now I wanted to do multiple comparison correction. How do I import the data to freesurfer and do the corrections? Thanks. Miao
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Douglas, Thanks for getting back to me. Which software can help me to convert the files to mgh format? I found one called MNE. Do you happen to have any experience with this one? Miao
Douglas N Greve <greve@nmr.mgh.harvard.edu javascript:_e(%7B%7D,'cvml','greve@nmr.mgh.harvard.edu');
于2014年6月24日星期二写道：
Hi Mio, sorry, I have no clue, I've never used Brainsuite. If you have each subject's thickness in a common space, you could convert it to mgh format and then run mri_glmfit and mri_glmfit-sim doug
On 06/24/2014 01:16 PM, Miao Wei wrote:
Dear Freesurfer experts, My dataset was processed by Brainsuite, so that after registration they are in .dfs format. Now I wanted to do multiple comparison correction. How do I import the data to freesurfer and do the corrections? Thanks. Miao
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 greve@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/
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I have not used MNE. I'm cc'ing Matti who is the MNE author doug
On 06/24/2014 04:32 PM, Miao Wei wrote:
Hi Douglas, Thanks for getting back to me. Which software can help me to convert the files to mgh format? I found one called MNE. Do you happen to have any experience with this one? Miao
Douglas N Greve <greve@nmr.mgh.harvard.edu javascript:_e(%7B%7D,'cvml','greve@nmr.mgh.harvard.edu');>于2014年6 月24日星期 二写道：
Hi Mio, sorry, I have no clue, I've never used Brainsuite. If you have each subject's thickness in a common space, you could convert it to mgh format and then run mri_glmfit and mri_glmfit-sim doug On 06/24/2014 01:16 PM, Miao Wei wrote: > Dear Freesurfer experts, > My dataset was processed by Brainsuite, so that after registration > they are in .dfs format. > Now I wanted to do multiple comparison correction. How do I import the > data to freesurfer and do the corrections? > Thanks. > Miao > > > _______________________________________________ > 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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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.
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Thank you. Hopefully I can do this since my data won't survive fdr correction in matlab. And there are no other options available for the correction.
Miao
On Tue, Jun 24, 2014 at 1:19 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Mio, sorry, I have no clue, I've never used Brainsuite. If you have each subject's thickness in a common space, you could convert it to mgh format and then run mri_glmfit and mri_glmfit-sim doug
On 06/24/2014 01:16 PM, Miao Wei wrote:
Dear Freesurfer experts, My dataset was processed by Brainsuite, so that after registration they are in .dfs format. Now I wanted to do multiple comparison correction. How do I import the data to freesurfer and do the corrections? Thanks. Miao
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 greve@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.
Hi Doug, Now I am able to convert .dfs files to freesurfer readable files (although I am not sure what is the format of the file, but now I can view it in Freeview). The command I used was write_surf. Basically I want to get a significance thickness map to see the regions that make contribution to the GLM model. My dependent variable is the learning outcome of a second language. My independent variable include the thickness and one test score (word reading efficiency). In the meanwhile we have to exclude IQ score and age in the model.
To achieve this goal, the followings should be done: 1. Convert all my .dfs files and get each subject's thickness and get average subject thickness using "make_average_subject http://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject" 2. convert this average to mgh file format (how to do this)? 3. and run my own monte carlo using "mri_mcsim " to the average subject. 4. after 3 run "mri_glmfit-sim" 5. using qdec to build my GLM model : y= training outcome, x=thickness and cognitive scores, excluding age and IQ as covariates.
Could you please give me some suggestions on whether this looks like the right procedure? Thanks. Miao
On Tue, Jun 24, 2014 at 3:44 PM, Miao Wei weimiao@usc.edu wrote:
Thank you. Hopefully I can do this since my data won't survive fdr correction in matlab. And there are no other options available for the correction.
Miao
On Tue, Jun 24, 2014 at 1:19 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Hi Mio, sorry, I have no clue, I've never used Brainsuite. If you have each subject's thickness in a common space, you could convert it to mgh format and then run mri_glmfit and mri_glmfit-sim doug
On 06/24/2014 01:16 PM, Miao Wei wrote:
Dear Freesurfer experts, My dataset was processed by Brainsuite, so that after registration they are in .dfs format. Now I wanted to do multiple comparison correction. How do I import the data to freesurfer and do the corrections? Thanks. Miao
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 greve@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.
You can't use make_average_subject. Actually, now that I think about it, I don't think this will work because your surfaces need to be on a FreeSurfer subject like fsaverage. Unless you can do this, you will not be able to use our tools. doug
On 06/26/2014 02:42 PM, Miao Wei wrote:
Hi Doug, Now I am able to convert .dfs files to freesurfer readable files (although I am not sure what is the format of the file, but now I can view it in Freeview). The command I used was write_surf. Basically I want to get a significance thickness map to see the regions that make contribution to the GLM model. My dependent variable is the learning outcome of a second language. My independent variable include the thickness and one test score (word reading efficiency). In the meanwhile we have to exclude IQ score and age in the model.
To achieve this goal, the followings should be done:
- Convert all my .dfs files and get each subject's thickness and get
average subject thickness using "make_average_subject http://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject" 2. convert this average to mgh file format (how to do this)? 3. and run my own monte carlo using "mri_mcsim " to the average subject. 4. after 3 run "mri_glmfit-sim" 5. using qdec to build my GLM model : y= training outcome, x=thickness and cognitive scores, excluding age and IQ as covariates.
Could you please give me some suggestions on whether this looks like the right procedure? Thanks. Miao
On Tue, Jun 24, 2014 at 3:44 PM, Miao Wei <weimiao@usc.edu mailto:weimiao@usc.edu> wrote:
Thank you. Hopefully I can do this since my data won't survive fdr correction in matlab. And there are no other options available for the correction. Miao On Tue, Jun 24, 2014 at 1:19 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Mio, sorry, I have no clue, I've never used Brainsuite. If you have each subject's thickness in a common space, you could convert it to mgh format and then run mri_glmfit and mri_glmfit-sim doug On 06/24/2014 01:16 PM, Miao Wei wrote: > Dear Freesurfer experts, > My dataset was processed by Brainsuite, so that after registration > they are in .dfs format. > Now I wanted to do multiple comparison correction. How do I import the > data to freesurfer and do the corrections? > Thanks. > Miao > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <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.
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Miao Wei