| Deletions are marked like this. | Additions are marked like this. |
| Line 6: | Line 6: |
| A volume stores information about 3D space, whereas a surface stores 2D space. | *A volume stores information about 3D space, whereas a surface stores 2D space. |
| Line 9: | Line 9: |
| No, you do not have to use two structural scans as input to recon-all. If a multi-channel head coil is being used, then generally the SNR will be high enough where averaging two scans is no longer beneficial (and can even worsen a perfectly good scan). | *No, you do not have to use two structural scans as input to recon-all. If a multi-channel head coil is being used, then generally the SNR will be high enough where averaging two scans is no longer beneficial (and can even worsen a perfectly good scan). |
| Line 12: | Line 12: |
| *answer goes here | *You can draw a region of interest either in the volume (using tkmedit and the Select Voxels tool) or on the surface (using tkmedit or qdec). |
| Line 15: | Line 15: |
| It is constructed of MRI scans of 40 subjects that have been manually segmented. 10 are young adults, 10 are middle-ages, 10 are older cognitively normal, and 10 are older demented patients. | *It is constructed of MRI scans of 40 subjects that have been manually segmented. 10 are young adults, 10 are middle-ages, 10 are older cognitively normal, and 10 are older demented patients. |
| Line 21: | Line 21: |
| 20-24 hours. | *20-24 hours. |
| Line 24: | Line 24: |
| *answer goes here | *To manually label the wm, gm, and subcortical structures of one case will likely take a month. |
| Line 27: | Line 27: |
| The variables indicate the location of code and data sets. Setting them once at the beginning of your data processing ensures that the right version of the code is executed, all the binaries will be found and that the data files are also correctly located. | *The variables indicate the location of code and data sets. Setting them once at the beginning of your data processing ensures that the right version of the code is executed, all the binaries will be found and that the data files are also correctly located. |
| Line 34: | Line 34: |
| *answer goes here | *The stats output for each subject can be found in <subjid>/stats where subjid is the the name of one particular subject. To grab the stats files for several subjects to put them in spreadsheet-ready format, use the commands asegstats2table or aparcstats2table. |
| Line 37: | Line 37: |
| Current volume-based registration methods cannot achieve high accuracy in aligning the cortical regions because of their high inter-subject variability. When we are only interested in finding correspondences between these areas (for example, in the case of functional studies), it is sufficient and also more accurate to register only the cortical areas with the spherical averaging method. | *Current volume-based registration methods cannot achieve high accuracy in aligning the cortical regions because of their high inter-subject variability. When we are only interested in finding correspondences between these areas (for example, in the case of functional studies), it is sufficient and also more accurate to register only the cortical areas with the spherical averaging method. |
| Line 40: | Line 40: |
| *answer goes here | *The alignment does not take into account the subcortical structures. |
| Line 43: | Line 43: |
| When computing the deformation fields between a subject and another or an atlas, the data itself is not changed. When the deformation field is computed, however, it can be applied to the subject, which means resampling its scan(s) in the target coordinate space. | *When computing the deformation fields between a subject and another or an atlas, the data itself is not changed. When the deformation field is computed, however, it can be applied to the subject, which means resampling its scan(s) in the target coordinate space. |
| Line 51: | Line 51: |
| *answer goes here | *You only need to remove skull or dura if it affects the surfaces since we get our measurements from the surfaces. |
| Line 55: | Line 55: |
| *answer goes here | *If you have already made edits to a dataset, you can rerun it with a new version of !FreeSurfer and it will keep all of the edits you have already made as long as you run it on the existing dataset. In other words, you would just want to do "recon-all -all -s existing_subject". |
FreeSurfer Tutorial and Workshop Quiz
Discuss the answers to these questions with your partner.
What is the difference between a volume and a surface?
- A volume stores information about 3D space, whereas a surface stores 2D space.
Do I have to use two MPRAGEs to run recon-all? Explain.
- No, you do not have to use two structural scans as input to recon-all. If a multi-channel head coil is being used, then generally the SNR will be high enough where averaging two scans is no longer beneficial (and can even worsen a perfectly good scan).
Can FreeSurfer help me select a region of interest and measure certain quantities within? How?
- You can draw a region of interest either in the volume (using tkmedit and the Select Voxels tool) or on the surface (using tkmedit or qdec).
What is fsaverage made of?
- It is constructed of MRI scans of 40 subjects that have been manually segmented. 10 are young adults, 10 are middle-ages, 10 are older cognitively normal, and 10 are older demented patients.
What measures will FreeSurfer give me?
- answer goes here
How long does it take for recon-all to finish processing one subject?
- 20-24 hours.
How long would it take you to do this manually?
- To manually label the wm, gm, and subcortical structures of one case will likely take a month.
Why do I have to set so many variables before using FreeSurfer?
- The variables indicate the location of code and data sets. Setting them once at the beginning of your data processing ensures that the right version of the code is executed, all the binaries will be found and that the data files are also correctly located.
Where do I find all those fantastic stats files FreeSurfer created for me?
- answer goes here
When mailing the FreeSurfer list about a problem, what information should I include?
The stats output for each subject can be found in <subjid>/stats where subjid is the the name of one particular subject. To grab the stats files for several subjects to put them in spreadsheet-ready format, use the commands asegstats2table or aparcstats2table.
Why is spherical averaging better than current volume-based methods out there?
- Current volume-based registration methods cannot achieve high accuracy in aligning the cortical regions because of their high inter-subject variability. When we are only interested in finding correspondences between these areas (for example, in the case of functional studies), it is sufficient and also more accurate to register only the cortical areas with the spherical averaging method.
What is a limitation of this procedure?
- The alignment does not take into account the subcortical structures.
When you do all that crazy morph stuff, are you changing the data?
- When computing the deformation fields between a subject and another or an atlas, the data itself is not changed. When the deformation field is computed, however, it can be applied to the subject, which means resampling its scan(s) in the target coordinate space.
When I report my findings in a paper, is there any way to report the Talairach coordinates?
- answer goes here
Do I have to remove every bit of skull, dura, etc. that I see in the brainmask? Why or why not?
- You only need to remove skull or dura if it affects the surfaces since we get our measurements from the surfaces.
Oh no! I made all these edits to a subject but now I want to rerun recon-all on the subject again with a new version of FreeSurfer. Will I lose all my work?
If you have already made edits to a dataset, you can rerun it with a new version of FreeSurfer and it will keep all of the edits you have already made as long as you run it on the existing dataset. In other words, you would just want to do "recon-all -all -s existing_subject".
Where do all those atlases come from that FreeSurfer uses?
The different FreeSurfer atlases were generated from manually segmented data sets. Given each definition of the manual segmentation procedure and its labels, we constructed an atlas.
If a ran my subjects with version 4.0, can I run the rest with the newest version?
For population studies and large scale comparisons, the best is to process all your data sets with the same version of FreeSurfer.
How do I control for head size?
- answer goes here