Hello Freesurfer experts,
My question may have already been solved in a previous thread. I have three runs of block-design bold scans. All three are quite similar. They all have only 2 blocks, one for rest and one for task. I’m trying to create a functional map that displays where the functional activation of these three runs overlap. I used the code below with no errors:
preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
mkanalysis-sess \ -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ -event-related -paradigm para.tsv -nconditions 1 \ -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \ -analysis TaskOverlap.lh -per-run -force
mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1
selxavg3-sess -s subj01 -analysis TaskOverlap.lh
And to display: tksurfer-sess -s subj01 \ -analysis TaskOverlap.lh \ -c con1
Or
tksurfer-sess -s subj01 \ -analysis TaskOverlap.lh \ -c con1 -map fsig
The problem is that when I view the output it seems that there’s far more activation than there should be when trying to find mutual overlap between the three tasks. If anyone has any suggestions it would be much appreciated.
Have a great day!
I'm not entirely sure what you are doing. It sounds like you have 3 different conditions and want to find out where the activation for all conditions overlaps. But what you have done is to combine all conditions into a single condition, so you are seeing where the average activation is, which is different than the overlap (and why it looks to have to much of an extent). To do what you want to do, you should model each condition as a separate condition in mkanalysis (ie, -nconditions 3 and change your paradigm file), set up 3 contrasts (one for each condition, ie, -a 1, -a 2, -a 3), then you will need to do a conjunction analysis (mri_concat con1/sig.nii.gz con2/sig.nii.gz con3/sig.nii.gz --conjunct --o conjunction.nii.gz). You can then view the conjunction with freeview (or tksurfer/tkmedit)
On 03/20/2018 06:30 PM, nm644 wrote:
Hello Freesurfer experts,
My question may have already been solved in a previous thread. I have three runs of block-design bold scans. All three are quite similar. They all have only 2 blocks, one for rest and one for task. I’m trying to create a functional map that displays where the functional activation of these three runs overlap. I used the code below with no errors:
preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
mkanalysis-sess \
-fsd bold -stc up -surface fsaverage lh -fwhm 5 \
-event-related -paradigm para.tsv -nconditions 1 \
-spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \
-analysis TaskOverlap.lh -per-run -force
mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1
selxavg3-sess -s subj01 -analysis TaskOverlap.lh
And to display:
tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1
Or
tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1 -map fsig
The problem is that when I view the output it seems that there’s far more activation than there should be when trying to find mutual overlap between the three tasks. If anyone has any suggestions it would be much appreciated.
Have a great day!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for the quick reply.
As you may be able to tell I'm a bit new at this so am still unsure about some things but yes a conjunction analysis is exactly what I want to do. Just a little more background, all the tasks are exactly the same in that they all have a null condition (set to 0 in all the paradigm files) with the same duration and the ON of all tasks also has the same duration across all tasks. I've also set the ON blocks in the 3 different paradigm files to be 1,2,3 instead of all being 1.
Thus far I've done:
1)
mkanalysis-sess \ -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ -event-related -paradigm para.tsv -nconditions 3 \ -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \ -analysis conjunction_analysis.lh -per-run -force
2) Create all the contrasts mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-1 -a 1 mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-2 -a 2 mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-3 -a 3
3) Run the analysis with
selxavg3-sess -s subj01 -analysis conjunction_analysis.lh \ -c task-1 \ -c task-2 \ -c task-3
Then cd into subj01/bold/conjunction_analysis.lh
and finally
4) mri_concat
mri_concat lang-cond-1/sig.nii.gz lang-cond-2/sig.nii.gz lang-cond-3/sig.nii.gz --conjunct --o conjunction.nii.gz
Does this look right? Also, what would be the proper command to view the conjunction after running this? Sorry this is very long winded, I just want to make sure I'm doing everything properly.
Thank you again!
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, March 20, 2018 7:25:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Functional Overlap Map
I'm not entirely sure what you are doing. It sounds like you have 3 different conditions and want to find out where the activation for all conditions overlaps. But what you have done is to combine all conditions into a single condition, so you are seeing where the average activation is, which is different than the overlap (and why it looks to have to much of an extent). To do what you want to do, you should model each condition as a separate condition in mkanalysis (ie, -nconditions 3 and change your paradigm file), set up 3 contrasts (one for each condition, ie, -a 1, -a 2, -a 3), then you will need to do a conjunction analysis (mri_concat con1/sig.nii.gz con2/sig.nii.gz con3/sig.nii.gz --conjunct --o conjunction.nii.gz). You can then view the conjunction with freeview (or tksurfer/tkmedit)
On 03/20/2018 06:30 PM, nm644 wrote:
Hello Freesurfer experts,
My question may have already been solved in a previous thread. I have three runs of block-design bold scans. All three are quite similar. They all have only 2 blocks, one for rest and one for task. I’m trying to create a functional map that displays where the functional activation of these three runs overlap. I used the code below with no errors:
preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
mkanalysis-sess \
-fsd bold -stc up -surface fsaverage lh -fwhm 5 \
-event-related -paradigm para.tsv -nconditions 1 \
-spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \
-analysis TaskOverlap.lh -per-run -force
mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1
selxavg3-sess -s subj01 -analysis TaskOverlap.lh
And to display:
tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1
Or
tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1 -map fsig
The problem is that when I view the output it seems that there’s far more activation than there should be when trying to find mutual overlap between the three tasks. If anyone has any suggestions it would be much appreciated.
Have a great day!
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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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 view it with
tksurferfv fsaverage lh inflated -aparc -overlay conjunction.nii.gz -fminmax 2 5
tksurferfv is a front-end for freeview. You can change the thresholds in freeview
On 3/22/18 12:27 PM, nm644 wrote:
Thank you for the quick reply.
As you may be able to tell I'm a bit new at this so am still unsure about some things but yes a conjunction analysis is exactly what I want to do. Just a little more background, all the tasks are exactly the same in that they all have a null condition (set to 0 in all the paradigm files) with the same duration and the ON of all tasks also has the same duration across all tasks. I've also set the ON blocks in the 3 different paradigm files to be 1,2,3 instead of all being 1.
Thus far I've done:
mkanalysis-sess \ -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ -event-related -paradigm para.tsv -nconditions 3 \ -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \ -analysis conjunction_analysis.lh -per-run -force
- Create all the contrasts
mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-1 -a 1 mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-2 -a 2 mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-3 -a 3
- Run the analysis with
selxavg3-sess -s subj01-analysis conjunction_analysis.lh \ -c task-1 \ -c task-2 \ -c task-3
Then cd into subj01/bold/conjunction_analysis.lh
and finally
- mri_concat
mri_concat lang-cond-1/sig.nii.gz lang-cond-2/sig.nii.gz lang-cond-3/sig.nii.gz --conjunct --o conjunction.nii.gz
Does this look right? Also, what would be the proper command to view the conjunction after running this? Sorry this is very long winded, I just want to make sure I'm doing everything properly.
Thank you again!
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Tuesday, March 20, 2018 7:25:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Functional Overlap Map I'm not entirely sure what you are doing. It sounds like you have 3 different conditions and want to find out where the activation for all conditions overlaps. But what you have done is to combine all conditions into a single condition, so you are seeing where the average activation is, which is different than the overlap (and why it looks to have to much of an extent). To do what you want to do, you should model each condition as a separate condition in mkanalysis (ie, -nconditions 3 and change your paradigm file), set up 3 contrasts (one for each condition, ie, -a 1, -a 2, -a 3), then you will need to do a conjunction analysis (mri_concat con1/sig.nii.gz con2/sig.nii.gz con3/sig.nii.gz --conjunct --o conjunction.nii.gz). You can then view the conjunction with freeview (or tksurfer/tkmedit)
On 03/20/2018 06:30 PM, nm644 wrote:
Hello Freesurfer experts,
My question may have already been solved in a previous thread. I have three runs of block-design bold scans. All three are quite similar. They all have only 2 blocks, one for rest and one for task. I’m trying to create a functional map that displays where the functional activation of these three runs overlap. I used the code below with no errors:
preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
mkanalysis-sess \
-fsd bold -stc up -surface fsaverage lh -fwhm 5 \
-event-related -paradigm para.tsv -nconditions 1 \
-spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \
-analysis TaskOverlap.lh -per-run -force
mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1
selxavg3-sess -s subj01 -analysis TaskOverlap.lh
And to display:
tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1
Or
tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1 -map fsig
The problem is that when I view the output it seems that there’s far more activation than there should be when trying to find mutual overlap between the three tasks. If anyone has any suggestions it would be much appreciated.
Have a great day!
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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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
Thank you very much!
On Mar 22, 2018, at 2:31 PM, Douglas Greve dgreve@mgh.harvard.edu wrote:
you can view it with tksurferfv fsaverage lh inflated -aparc -overlay conjunction.nii.gz -fminmax 2 5 tksurferfv is a front-end for freeview. You can change the thresholds in freeview
On 3/22/18 12:27 PM, nm644 wrote:
Thank you for the quick reply.
As you may be able to tell I'm a bit new at this so am still unsure about some things but yes a conjunction analysis is exactly what I want to do. Just a little more background, all the tasks are exactly the same in that they all have a null condition (set to 0 in all the paradigm files) with the same duration and the ON of all tasks also has the same duration across all tasks. I've also set the ON blocks in the 3 different paradigm files to be 1,2,3 instead of all being 1.
Thus far I've done:
mkanalysis-sess \ -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ -event-related -paradigm para.tsv -nconditions 3 \ -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \ -analysis conjunction_analysis.lh -per-run -force
- Create all the contrasts
mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-1 -a 1 mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-2 -a 2 mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-3 -a 3
- Run the analysis with
selxavg3-sess -s subj01 -analysis conjunction_analysis.lh \ -c task-1 \ -c task-2 \ -c task-3
Then cd into subj01/bold/conjunction_analysis.lh
and finally
- mri_concat
mri_concat lang-cond-1/sig.nii.gz lang-cond-2/sig.nii.gz lang-cond-3/sig.nii.gz --conjunct --o conjunction.nii.gz
Does this look right? Also, what would be the proper command to view the conjunction after running this? Sorry this is very long winded, I just want to make sure I'm doing everything properly.
Thank you again! From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, March 20, 2018 7:25:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Functional Overlap Map
I'm not entirely sure what you are doing. It sounds like you have 3 different conditions and want to find out where the activation for all conditions overlaps. But what you have done is to combine all conditions into a single condition, so you are seeing where the average activation is, which is different than the overlap (and why it looks to have to much of an extent). To do what you want to do, you should model each condition as a separate condition in mkanalysis (ie, -nconditions 3 and change your paradigm file), set up 3 contrasts (one for each condition, ie, -a 1, -a 2, -a 3), then you will need to do a conjunction analysis (mri_concat con1/sig.nii.gz con2/sig.nii.gz con3/sig.nii.gz --conjunct --o conjunction.nii.gz). You can then view the conjunction with freeview (or tksurfer/tkmedit)
On 03/20/2018 06:30 PM, nm644 wrote:
Hello Freesurfer experts,
My question may have already been solved in a previous thread. I have three runs of block-design bold scans. All three are quite similar. They all have only 2 blocks, one for rest and one for task. I’m trying to create a functional map that displays where the functional activation of these three runs overlap. I used the code below with no errors:
preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
mkanalysis-sess \
-fsd bold -stc up -surface fsaverage lh -fwhm 5 \
-event-related -paradigm para.tsv -nconditions 1 \
-spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \
-analysis TaskOverlap.lh -per-run -force
mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1
selxavg3-sess -s subj01 -analysis TaskOverlap.lh
And to display:
tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1
Or
tksurfer-sess -s subj01 \
-analysis TaskOverlap.lh \
-c con1 -map fsig
The problem is that when I view the output it seems that there’s far more activation than there should be when trying to find mutual overlap between the three tasks. If anyone has any suggestions it would be much appreciated.
Have a great day!
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 Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N. Greve
-
nm644