Dear all,
I am investigating volumes of deep brain structures with the use of FSL-FIRST and I have a few questoins that I need help with.
1. I have incomplete head acquisitions so that I am looking for a way to make FIRST run on a restricted range of standardized MNI Z-coordinates in a similar way that is possible with SIENAX (for instance, -t 60 -b -50). I would also like to have in my outputs head images that are cut at those standardized coordinate values by in native space.
2. Are volume measurements generated by FSL-FIRST normalised for head size such as in SIENAX, and if not, what normalisation process would be suitable (e.g. multiplication by the scaling factor derived from SIEANX?, other suggestions?)
3. I would like to compare FSL-FIRST measurements with those performed with Lesion Toads (part of MIPAV). For this, I would need to have head mages that are cut at the same MNI Z-coordinates as specified earlier in FSL-FIRST (e.g. -t 60, -b -50 when used SIENAX notation).
4. If I do everything successfully, I still have a question regarding the registration used for Lesion-Toads measurements. When comparing brain volume measurements carried out with FSL-SIENAX, the authors of Lesion-Toads registered images rigidly (6 DOF) to a standard brain and then performed measurements with Leison-Toads ("we rigidly registered the stripped MPRAGE scans to a single image atlas (“JHU_MNI_SS_T1”) " in http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0037049). My question is whether this rigid registration could interfere with the volumetric outputs as compared to native images (i.e. will volume measurments of native brains and such registered brains be different).
Any help wll be greatly appreciated.
Best wishes,
Lukasz
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