Hello Freesurfers,
I'm been experimenting with creating timecourses for tksurfer and tkmedit using the -hrf flag. However I've noticed that the h.nii files created provide the HDR timecourse are only based on the original analysis under which isxconcat-sess was run (in my case, error vs correct). I was wondering if there was a way to tailor the timecourse in such a way that, instead of plotting only the conditions of the analysis, it would plot lines based on subject groups (e.g. Patients and Controls from an fsgd file).
Basically, is there a way that I can create an HDR timecourse plot that can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct?
Thanks!
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
Do you mean something like you have two conditions (say A and B) and two groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B?
Adam Nitenson wrote:
Hello Freesurfers,
I'm been experimenting with creating timecourses for tksurfer andtkmedit using the -hrf flag. However I've noticed that the h.nii files created provide the HDR timecourse are only based on the original analysis under which isxconcat-sess was run (in my case, error vs correct). I was wondering if there was a way to tailor the timecourse in such a way that, instead of plotting only the conditions of the analysis, it would plot lines based on subject groups (e.g. Patients and Controls from an fsgd file).
Basically, is there a way that I can create an HDR timecourse plotthat can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct?
Thanks!
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously.
-Adam
Do you mean something like you have two conditions (say A and B) and two groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B?
Adam Nitenson wrote:
Hello Freesurfers,
I'm been experimenting with creating timecourses for tksurfer andtkmedit using the -hrf flag. However I've noticed that the h.nii files created provide the HDR timecourse are only based on the original analysis under which isxconcat-sess was run (in my case, error vs correct). I was wondering if there was a way to tailor the timecourse in such a way that, instead of plotting only the conditions of the analysis, it would plot lines based on subject groups (e.g. Patients and Controls from an fsgd file).
Basically, is there a way that I can create an HDR timecourse plotthat can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct?
Thanks!
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
Create two contrasts, A-vs-fixation and B-vs-fixation, then run isxconcat-sess separately for each group. This will create ces files for each contrast. There will be a ces file for each time point in the FIR; each of these will have a frame for all the members of the group.
1. Compute the mean of each time point mri_concat ces.000.nii --mean --o mean.ces.000.nii ... 2. Concat all the means into a single file: mri_concat mean.ces.???.nii --o all.mean.ces.nii
This will give you 4 mean files, one for each group/condition. Concatenate them together: mri_concat g1/A/all.mean.ces.nii g1/B/all.mean.ces.nii g2/A/all.mean.ces.nii g2/B/all.mean.ces.nii --o g1A.g1B.g2A.g2B.nii
Now run
beta2sxa -b g1A.g1B.g2A.g2B.nii --nc 4 --nper Ntp --o h.g1A.g1B.g2A.g2B.nii
where "--nc 4" is the four waveforms (2 groups * 2 conditions) and Ntp is the number of time points in each waveform.
you can then run
tksurfer fsaverage lh inflated -t h.g1A.g1B.g2A.g2B.nii
or tkmedit if these are volumes.
doug
Adam Nitenson wrote:
Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously.
-Adam
Do you mean something like you have two conditions (say A and B) and two groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B?
Adam Nitenson wrote:
Hello Freesurfers,
I'm been experimenting with creating timecourses for tksurfer andtkmedit using the -hrf flag. However I've noticed that the h.nii files created provide the HDR timecourse are only based on the original analysis under which isxconcat-sess was run (in my case, error vs correct). I was wondering if there was a way to tailor the timecourse in such a way that, instead of plotting only the conditions of the analysis, it would plot lines based on subject groups (e.g. Patients and Controls from an fsgd file).
Basically, is there a way that I can create an HDR timecourse plotthat can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct?
Thanks!
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
Ok, I have previously created these group specific concatenations, but not with the -hrf flag. Would I need to reconcatenate them with this flag or does your method not require it?
-Adam
Create two contrasts, A-vs-fixation and B-vs-fixation, then run isxconcat-sess separately for each group. This will create ces files for each contrast. There will be a ces file for each time point in the FIR; each of these will have a frame for all the members of the group.
- Compute the mean of each time point mri_concat ces.000.nii --mean --o mean.ces.000.nii ...
- Concat all the means into a single file: mri_concat mean.ces.???.nii --o all.mean.ces.nii
This will give you 4 mean files, one for each group/condition. Concatenate them together: mri_concat g1/A/all.mean.ces.nii g1/B/all.mean.ces.nii g2/A/all.mean.ces.nii g2/B/all.mean.ces.nii --o g1A.g1B.g2A.g2B.nii
Now run
beta2sxa -b g1A.g1B.g2A.g2B.nii --nc 4 --nper Ntp --o h.g1A.g1B.g2A.g2B.nii
where "--nc 4" is the four waveforms (2 groups * 2 conditions) and Ntp is the number of time points in each waveform.
you can then run
tksurfer fsaverage lh inflated -t h.g1A.g1B.g2A.g2B.nii
or tkmedit if these are volumes.
doug
Adam Nitenson wrote:
Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously.
-Adam
Do you mean something like you have two conditions (say A and B) and two groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B?
Adam Nitenson wrote:
Hello Freesurfers,
I'm been experimenting with creating timecourses for tksurfer andtkmedit using the -hrf flag. However I've noticed that the h.nii files created provide the HDR timecourse are only based on the original analysis under which isxconcat-sess was run (in my case, error vs correct). I was wondering if there was a way to tailor the timecourse in such a way that, instead of plotting only the conditions of the analysis, it would plot lines based on subject groups (e.g. Patients and Controls from an fsgd file).
Basically, is there a way that I can create an HDR timecourse plotthat can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct?
Thanks!
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
The -hrf flag is not necessary.
Adam Nitenson wrote:
Ok, I have previously created these group specific concatenations, but not with the -hrf flag. Would I need to reconcatenate them with this flag or does your method not require it?
-Adam
Create two contrasts, A-vs-fixation and B-vs-fixation, then run isxconcat-sess separately for each group. This will create ces files for each contrast. There will be a ces file for each time point in the FIR; each of these will have a frame for all the members of the group.
- Compute the mean of each time point mri_concat ces.000.nii --mean --o mean.ces.000.nii ...
- Concat all the means into a single file: mri_concat mean.ces.???.nii --o all.mean.ces.nii
This will give you 4 mean files, one for each group/condition. Concatenate them together: mri_concat g1/A/all.mean.ces.nii g1/B/all.mean.ces.nii g2/A/all.mean.ces.nii g2/B/all.mean.ces.nii --o g1A.g1B.g2A.g2B.nii
Now run
beta2sxa -b g1A.g1B.g2A.g2B.nii --nc 4 --nper Ntp --o h.g1A.g1B.g2A.g2B.nii
where "--nc 4" is the four waveforms (2 groups * 2 conditions) and Ntp is the number of time points in each waveform.
you can then run
tksurfer fsaverage lh inflated -t h.g1A.g1B.g2A.g2B.nii
or tkmedit if these are volumes.
doug
Adam Nitenson wrote:
Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously.
-Adam
Do you mean something like you have two conditions (say A and B) and two groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B?
Adam Nitenson wrote:
Hello Freesurfers,
I'm been experimenting with creating timecourses for tksurfer andtkmedit using the -hrf flag. However I've noticed that the h.nii files created provide the HDR timecourse are only based on the original analysis under which isxconcat-sess was run (in my case, error vs correct). I was wondering if there was a way to tailor the timecourse in such a way that, instead of plotting only the conditions of the analysis, it would plot lines based on subject groups (e.g. Patients and Controls from an fsgd file).
Basically, is there a way that I can create an HDR timecourse plotthat can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct?
Thanks!
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
Hey Doug,
Everything is working out well with this pathway....but beta2sxa is not recognized as a valid command. I've sourced to nmr (Stable 4 if that matters at all) and have been on the same terminal on which I've done the previous steps. Any ideas?
Specifically, I entered:
beta2sxa -b 12ConT.13ConC.14SchC.17SchT.nii --nc 8 --nper 12 --o h.12ConT.13ConC.14SchC.17SchT.nii
(I have 4 groups, 2 conditions, 12 time points)
-Adam
Create two contrasts, A-vs-fixation and B-vs-fixation, then run isxconcat-sess separately for each group. This will create ces files for each contrast. There will be a ces file for each time point in the FIR; each of these will have a frame for all the members of the group.
- Compute the mean of each time point mri_concat ces.000.nii --mean --o mean.ces.000.nii ...
- Concat all the means into a single file: mri_concat mean.ces.???.nii --o all.mean.ces.nii
This will give you 4 mean files, one for each group/condition. Concatenate them together: mri_concat g1/A/all.mean.ces.nii g1/B/all.mean.ces.nii g2/A/all.mean.ces.nii g2/B/all.mean.ces.nii --o g1A.g1B.g2A.g2B.nii
Now run
beta2sxa -b g1A.g1B.g2A.g2B.nii --nc 4 --nper Ntp --o h.g1A.g1B.g2A.g2B.nii
where "--nc 4" is the four waveforms (2 groups * 2 conditions) and Ntp is the number of time points in each waveform.
you can then run
tksurfer fsaverage lh inflated -t h.g1A.g1B.g2A.g2B.nii
or tkmedit if these are volumes.
doug
Adam Nitenson wrote:
Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously.
-Adam
Do you mean something like you have two conditions (say A and B) and two groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B?
Adam Nitenson wrote:
Hello Freesurfers,
I'm been experimenting with creating timecourses for tksurfer andtkmedit using the -hrf flag. However I've noticed that the h.nii files created provide the HDR timecourse are only based on the original analysis under which isxconcat-sess was run (in my case, error vs correct). I was wondering if there was a way to tailor the timecourse in such a way that, instead of plotting only the conditions of the analysis, it would plot lines based on subject groups (e.g. Patients and Controls from an fsgd file).
Basically, is there a way that I can create an HDR timecourse plotthat can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct?
Thanks!
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
use stable5
Adam Nitenson wrote:
Hey Doug,
Everything is working out well with this pathway....but beta2sxa is not recognized as a valid command. I've sourced to nmr (Stable 4 if that matters at all) and have been on the same terminal on which I've done the previous steps. Any ideas?
Specifically, I entered:
beta2sxa -b 12ConT.13ConC.14SchC.17SchT.nii --nc 8 --nper 12 --o h.12ConT.13ConC.14SchC.17SchT.nii
(I have 4 groups, 2 conditions, 12 time points)
-Adam
Create two contrasts, A-vs-fixation and B-vs-fixation, then run isxconcat-sess separately for each group. This will create ces files for each contrast. There will be a ces file for each time point in the FIR; each of these will have a frame for all the members of the group.
- Compute the mean of each time point mri_concat ces.000.nii --mean --o mean.ces.000.nii ...
- Concat all the means into a single file: mri_concat mean.ces.???.nii --o all.mean.ces.nii
This will give you 4 mean files, one for each group/condition. Concatenate them together: mri_concat g1/A/all.mean.ces.nii g1/B/all.mean.ces.nii g2/A/all.mean.ces.nii g2/B/all.mean.ces.nii --o g1A.g1B.g2A.g2B.nii
Now run
beta2sxa -b g1A.g1B.g2A.g2B.nii --nc 4 --nper Ntp --o h.g1A.g1B.g2A.g2B.nii
where "--nc 4" is the four waveforms (2 groups * 2 conditions) and Ntp is the number of time points in each waveform.
you can then run
tksurfer fsaverage lh inflated -t h.g1A.g1B.g2A.g2B.nii
or tkmedit if these are volumes.
doug
Adam Nitenson wrote:
Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously.
-Adam
Do you mean something like you have two conditions (say A and B) and two groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B?
Adam Nitenson wrote:
Hello Freesurfers,
I'm been experimenting with creating timecourses for tksurfer andtkmedit using the -hrf flag. However I've noticed that the h.nii files created provide the HDR timecourse are only based on the original analysis under which isxconcat-sess was run (in my case, error vs correct). I was wondering if there was a way to tailor the timecourse in such a way that, instead of plotting only the conditions of the analysis, it would plot lines based on subject groups (e.g. Patients and Controls from an fsgd file).
Basically, is there a way that I can create an HDR timecourse plotthat can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct?
Thanks!
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
freesurfer@nmr.mgh.harvard.edu
-
Adam Nitenson -
Douglas N Greve