Dear freesurfer experts,
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*
Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel
