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Sure, please send a dropbox link to ajoshi@usc.edu or ajoshi@sipi.usc.edu and I will take a look.
Thank you, best, AnandAlso, since you see atlas.pvc-thickness_0-6mm.right.mid.cortex.dfs and atlas.pvc-thickness_0-6mm.left.mid.cortex.dfs
the execution of cortical thickness script seems to have finished.You can check *left.inner.cortex.dfs, *right.inner.cortex.dfs
*left.pial.cortex.dfs, *right.pial.cortex.dfsMost likely this is due to processing error at earlier stages.
Can you check if your extracted brain surfaces look realistic?You can apply the deformation map stored in that file using svreg_apply_map.sh script that should be in <BrainSuite18a>svreg/bin folder.
The usage is described here.
#13 here http://brainsuite.org/processing/svreg/svreg_modules/The map in svreg is stored in a slightly different format than the one in fnirt, so svreg_apply_map shoudl be used for the svreg map and FSL’s function for applying maps from fnirt.
Are you running win 7 by any chance?
There seems to be some discussion on this at
https://www.mathworks.com/matlabcentral/answers/98050-why-do-i-get-an-error-saying-undefined-function-or-variable-matlabrc-when-executing-a-program-thPlease try deleting the folder mentioned there:
(C:\Users\[username]\AppData\Local\Temp\[username]\mcrCache[version])If you ran the full BrainSuite and SVReg sequence, the volumes are already computed. You can find them in {subject}.roiwise.stats.txt file. Just load this in excel and you can see the table of all the statistics. Please let me know if there is any issue.
Can you please explain what you are trying to do? I want to have a better idea of what you are doing so that I have a better idea and suggest the correct command.
There is a cortical_extraction.sh script that runs through the surface generation and there is a script for labeling svreg.sh
These scripts are included in bin and svreg/bin directories respectively.
You can save the extraction settings from here:
file -> save extraction settingsHi CRW,
Can you please describe the issue a little more? Which script are you trying to run and what is the error?You could edit the inner cortical mask.
Just before you press generate inner cortical surface, goto tools->mask tool
There I assume that the ventricle would be empty in the mask. You can edit it and fill the ventricles.
Then generate the inner cortical surface and continue.
This should take care of the issue.
You can also manually edit the final labels manually using the label tool.
In case of abnormal anatomy, the results would depend on the extent of the abnormality. In general, the unaffected hemisphere should still be fine.does this file exist?
/Users/mspocter/Users/mspocter/Desktop/TrialBrainsuite/BrainSuiteTutorialCSE/2523412.left.inner.cortex.svreg.dfsI am not sure if I follow the question. The ROIs produced by SVReg are labeled both on the cortical surface as well as in the volume. The ROI based analysis will use the surface statistics, such as surface area, or it can use volumetric statistic such as volume of the ROI for comparison. It would depend on how you configured BSS when you ran the study.
The BSS module in BrainSuite can perform both surface-based and volume based analysis.
Not sure if this helps, but if not, can you please explain what you are trying to do?
