Convert sulcal labels

[HusBunia]

Hi,
I ran the Morphologist pipeline using FreeSurfer inputs and generated a series of .arg files. I would like to convert the .arg outputs to a label file. I used the following command:
AimsGraphConvert -i Lsub-001_default_session_auto.arg --volume 1 -b L_labelvol.data --verbose 1
The resulting volume does not appear to match my original native T1w image.
Is there a recommended way to export a sulcal label volume that is explicitly aligned to the native T1w space ?or Is there a way to get these sulcal labels onto the orginal native FreeSurfer meshes or HCP 32k meshes?

Thank you !
lei

[denisri]

Hi,
In Brainvisa, there is a process: "Morphologist/Sulci/Create sulcus label volume", which basically runs the command siGraph2Label, which will create a volume with sulci labels.
The AimsGraphConvert command you used keeps only the smallest possible volume (cropped to the actual bounding box of sulci data) and here, each label is the sulcus part identifier number (graph vertex number), not the sulci identification.
To project on a mesh, we don't have a very good tool: projecting on the surface is tricky as there are many ambiguities, but you can try the AimsVol2Tex command, or look at the Cortical Surface toolbox of BrainVisa, in the Hip Hop pipeline, the sulcal lines extraction step, which is specifically designed for sulci projection. Other people have worked on this kind of projection so you can also find other tools, I dare say that probably none is perfect.
Denis

[HusBunia]

Sorry for the late reply. Thank you for the guidence!