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Subject:

Re: Question regarding Neuromorphometrics CSF/Ventricle segmentation

From:

Torben Lund <[log in to unmask]>

Reply-To:

Torben Lund <[log in to unmask]>

Date:

Thu, 20 Sep 2018 10:33:09 +0200

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (10 lines) , myvol.m (10 lines) , Unknown Name (55 lines)

Dear Julian

If you want the volumes in native space you can either use the inverse deformation field from the segmentation and use to to warp the atlas to native space, set up an imcclc job to isolate the region you are interested in an calculate its volume using the attached function. Alternatively a similar the calculation can be made in MNI space if you remember to use the posterior probability modulated with the Jacobian determinant.

Best
Torben





> On 19 Sep 2018, at 10.10, Christian Gaser <[log in to unmask]> wrote: > > Dear Julian, > > the abbreviations of the atlas are explained here: > spm12/atlas/labels_dartel_neuromorphometrics.xml > cat12/templates_1.50mm/neuromorphometrics.csv > > VenVen stands for "Ventral Ventricle". You can use the overlay function in CAT12 or the context menu in SPM12 (e.g. using CheckReg) to overlay the atlas labels. > > You can find more information about the atlas also here: > cat12/templates_1.50mm/neuromorphometrics.txt > > Best, > > Christian > > On Tue, 18 Sep 2018 11:20:42 +0200, Wolf-Julian Neumann <[log in to unmask]> wrote: > >> Dear SPMers/CATers, >> we are trying to quantify intraventricular CSF volumes and have stumbled >> upon the Neuromorphometrics atlas labels in the CAT labels catROI file. The >> labels for 3rd,4th and lateral ventricles are clear, but there is an >> additional label called venven (33:44). Does anyone know what this refers >> to? Is there a way to visualize the Neuromorphometrics labels in native >> space of the individual segmentation images? >> >> Alternatively, could you suggest a strategy to quantify all >> intraventricular CSF volumes? >> >> Best wishes, >> Julian >> -- >> >> >> Dr. med. Wolf-Julian Neumann >> >> Assistenzarzt >> Institut für Neuroradiologie >> >> Associate Researcher >> Movement Disorder and Neuromodulation Unit >> >> 030 450 660 359 >> 0152 539 262 90 >> >> Google Scholar: http://goo.gl/UJqj7j >> ResearchGate: http://goo.gl/DjguBx >> >> Charité - Universitätsmedizin Berlin >>

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