[Freesurfer] questions about mri_glmfit

2022-12-20 Thread James Brown 
External Email - Use Caution

Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your help.
1- Are there any settings or flags that can be used in mri_glmfit to
restrict statistical comparison of surface based analysis to specific ROIs
rather than whole brain analysis. I would like to show the difference on
the brain surface in lobes rather than in sub lobar labels.
2- I understand that the flag "--table" in command mri_glmfit allows for
feeding spreadsheets instead of images. Can we restrict the number of
columns in this spreadsheet to 8 columns for lobs (frontal, temporal,
occipital and parietal) left and right? Also, is there any way to generate
a statistical map from the spreadsheet statistics?

Thank you and happy holidays :)
James
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] questions about mri_glmfit

2022-12-20 Thread Douglas N. Greve 



On 12/20/2022 12:22 PM, James Brown wrote:


External Email - Use Caution

Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your 
help.
1- Are there any settings or flags that can be used in mri_glmfit to 
restrict statistical comparison of surface based analysis to specific 
ROIs rather than whole brain analysis. I would like to show the 
difference on the brain surface in lobes rather than in sub lobar labels.
You can create a mask or label and feed it into mri_glmfit with --mask 
or --label
2- I understand that the flag "--table" in command mri_glmfit allows 
for feeding spreadsheets instead of images. Can we restrict the number 
of columns in this spreadsheet to 8 columns for lobs (frontal, 
temporal, occipital and parietal) left and right? Also, is there any 
way to generate a statistical map from the spreadsheet statistics?

Remove the columns you don't want?


Thank you and happy holidays :)
James

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] questions about mri_glmfit

2022-12-21 Thread James Brown 
External Email - Use Caution

Dear Dr Greve, thank you so much for answers to my questions.
Regarding question 2, yes I meant leaving only columns I need, for instance
I am interested in lobes. I ran these commands on my data

# mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
# mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
# mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
#   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
#   --annot lobes --base-offset 200 [--base-offset must be last arg]

then mri_segstats and I got the final stats file which contain data for the
lobes rois

3201wm-lh-frontal-lobe
3203wm-lh-cingulate-lobe
3204wm-lh-occiptal-lobe
3205wm-lh-temporal-lobe
3206wm-lh-parietal-lobe
3207wm-lh-insula-lobe

4201wm-rh-frontal-lobe
4203wm-rh-cingulate-lobe
4204wm-rh-occiptal-lobe
4205wm-rh-temporal-lobe
4206wm-rh-parietal-lobe
4207wm-rh-insula-lobe


My question is can I revise the spreadsheet from the output of
aparcstats2table or asegstats2table to keep the lobar ROIs above (8
columns) then feed that data to mri_glmfit?

On 12/20/2022 12:22 PM, James Brown wrote:

Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your help.
1- Are there any settings or flags that can be used in mri_glmfit to
restrict statistical comparison of surface based analysis to specific ROIs
rather than whole brain analysis. I would like to show the difference on
the brain surface in lobes rather than in sub lobar labels.

You can create a mask or label and feed it into mri_glmfit with --mask or
--label

2- I understand that the flag "--table" in command mri_glmfit allows for
feeding spreadsheets instead of images. Can we restrict the number of
columns in this spreadsheet to 8 columns for lobs (frontal, temporal,
occipital and parietal) left and right? Also, is there any way to generate
a statistical map from the spreadsheet statistics?

Remove the columns you don't want?

On Tue, Dec 20, 2022 at 12:22 PM James Brown  wrote:

> Dear Freesurfer experts,
> I have 2 questions about the command mri_glmfit and I appreciate your help.
> 1- Are there any settings or flags that can be used in mri_glmfit to
> restrict statistical comparison of surface based analysis to specific ROIs
> rather than whole brain analysis. I would like to show the difference on
> the brain surface in lobes rather than in sub lobar labels.
> 2- I understand that the flag "--table" in command mri_glmfit allows for
> feeding spreadsheets instead of images. Can we restrict the number of
> columns in this spreadsheet to 8 columns for lobs (frontal, temporal,
> occipital and parietal) left and right? Also, is there any way to generate
> a statistical map from the spreadsheet statistics?
>
> Thank you and happy holidays :)
> James
>
>
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.