I'm wondering if it is possible to import the anatomy (and perhaps functional data too) onto my laptop for a subject, and after this import and subject preparation, copy/import this subject and their respective data to a different protocol on another computer. Is this possible?
This capability would be helpful because coherence computations take a while and being able to prepare the next subject's data while the current subject's coherence computations are running would be helpful to streamline postprocessing. Note: these are two separate protocols using different brainstorm_db directories to minimize risk of breaking a database or protocol structure.
Please let me know if this is a possibility or if you need clarification on anything I mentioned. Thank you!
Or it can be done by manipulated the files in the database. This would be to merge different Subjects (from laptop) once at the time into the Group protocol (other computer).
It is a good idea to make backups before merging protocols. Also, use copy, paste, delete, instead of moving files, in case something fails during reading/writing.
Thank you for the explanation! I was successful in importing some subjects.
After doing this, I noticed something within the default anatomy folder that I wanted to ask about.
It seems that for one of these protocols, the default anatomy folder has significantly less items in the folder than the other protocols we're using. For an example, please see the screenshots.
I'm asking this question because it seems the Desikan-Killiany atlas is slightly different on the default anatomy in the protocol with less items than others that have many more items, and I'm wondering how this affects source localization, etc..
Was there an update to the default anatomy templates that we should know about? Such as the difference between the ICBM152 and ICBM152 2023b noted in the screenshot?
Exporting a Subject from ProtocolX, also export the Default anatomy in that ProtocolX. So, when it is imported in ProtocolY, the default anatomy is overwritten. This is not an issue if you subjects are using their individual anatomies, as source estimation will rely on the individual anatomy.
I see. Thank you. One protocol we're using has the ICBM152 template while the other has the ICBM152 2023b version. After seeing that, I became concerned of inconsistent results if two different ICBM templates were used within the same study for participants using default anatomy. However, your link states that these (ICBM152 & ICBM152 2023b) are the same except a couple of surfaces. Would the absence of the white matter & mid surfaces in ICBM152 bias EEG source localization if one subject were to be run on the ICBM152 and another on ICBM152 2023b?
We already have run coherence computations for one of our subjects registered to the ICBM152 template; if I were to change the default anatomy in the this protocol to the ICBM152 2023b version, how would this affect their results? Would I need to re-run their coherence computations?
If you Subjects are using different default anatomies they should not be combined in one Protocol. Apologies if I mislead you, I had the impression that subjects had their individual anatomies.
It will not unless, those surfaces (white matter or mid) were used as default surfaces (indicated with a green font in the database). This is true only for ICBM152 templates (2022, 2023 and 2023b)
Edit. Be careful as the default anatomy ICBM152 2019 have different surfaces from all the other ICBM152 templates (2022, 2023 and 2023b). Which I believe is the Anatomy you have in the first screenshot.
It seems the default surfaces in all protocols were the cortical surface that we desired (cortex_15002v), it was just one of the protocols (screenshot 1 above) that seems to have the older default anatomy.
My apologies if I was unclear about our situation. For many of our participants, we have individual anatomy via MRI. However, we also have a number of individuals who were ineligible for MRI, in which case we are using the default anatomy. There are some participants in each protocol who have MRI's and others who do not. Our desire is to have the same default anatomy template used in all three protocols for the participants that do not have an MRI.
Is there a way to find out if what I have in screenshot 1 above is the 2019 version that you mentioned is different than the other ICBM versions? I see slight differences in the Desikan atlas parcellations between the protocol from screenshot 1 and the other protocols, leading me to think that this is the 2019 version in screenshot 1.
Overall, I think the safe bet is to import the ICBM 152 2023b default anatomy and overwrite the default anatomy in protocol 1 (this 2023b anatomy template is in the other protocols), and re-run computations for any subject that used the older ICBM template.
This only indicates the number of vertices in the surfaces. There could be two different cortical surfaces with the same number of vertices, that would be a problem, because the projection will be messed up. (In fact this is the case between the 2019 and 202xx default anatomies)
Yes, you can compare the surface against the ICBM152 2019
Create a new Subject in that Protocol, select No, use individual anatomy
Set the new user to use the ICBM152_2019 anatomy as their own
Right-click the new subject > Use template > MNI > ICBM152_2019
Export both cortex_15002V surfaces to Matlab
Right-click the cortex_15002V in the Default anatomy> File > Export to Matlab name it surf_defAnat
Right-click the cortex_15002V in the New Subject> File > Export to Matlab name it surf_2019
Compare the mean distance across all the vertices. In Matlab run the command
meanDistSurfVertices = mean(sqrt(sum((surf_defAnat.Vertices - surf_2019.Vertices).^2, 2)));
fprintf('Mean distance across all pairs of vertices: %0.3f mm \n', meanDistSurfVertices*1000);
This distance should be 0 for the exactly same surfaces.
FYI, this distance is more than 50 mm!!! between the 2019 and 2023 versions of the ICBM152 Default anatomy
Thanks for the quick reply. I followed these steps and indeed the mean distance across the vertices was 0mm, therefore the template in this protocol is the 2019 ICBM template. I'm going to update the default anatomy template in this protocol. Thanks for your help!
It is a good idea to make backups before merging protocols. Also, use copy, paste, delete, instead of moving files, in case something fails during reading/writing.
Be careful as the default anatomy ICBM152 2019 have different surfaces from all the other ICBM152 templates (2022, 2023 and 2023b). Which I believe is the Anatomy you have in the first screenshot.