I'm performing anatomical segmentation for Philips dicoms (3T scanner). I got these two images from the same slice while performing step number 4 in the script below – from some reason, the two images don't fit. Should I use "scale brain" ? I know this is not recommended thus want to consult with u first – Can u please comment on why this is happening? Is there any value that corresponds to "how good is the segmentation" ? if yes, where can I find it ?

My script is written below.

Thanks,

Rotem

Anatomical segmentation:

first step- 23 hours:

recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s FOLDER-NAME

second step:(gyrus=green, sulcus=red)

tksurfer -curv FOLDER-NAME lh/rh inflated

third step: (talairch registretion)

tkmedit FOLDER-NAME brainmask.mgz

File-> transforms-> load transform AUX-> Browse-> talairch.xfm

forth step: (simetry - allows changing 12df transformation. if we made any changes we should click "save reg" and run this command again)

tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig

IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING POING: recon-all -all -subjectid FOLDER-NAME

fifth step: (scalp removal: if removed too much, rise up from the value 25:

recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s FOLDER-NAME                     

to check the result press: tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white )

for hand correction: tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz

tools-> configure volume brush -> MARK: mode=clone, source=Aux

tools-> configure brush info (for choosing brush size)

click on edit voxels: click in MIDDLE for adding voxels, RIGHT for removing voxels : slice by slice.

when finish, click: File-> save main volume

sisxt step: (cp for correcting segmentation)

tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white

seventh step: (done)

recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME