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Hi Martin,
I run the followig:
run_fastsurfer.sh --t1 $image_path --sd $output_dir/fastsurfer --sid results --seg_only --no_cereb --no_hypothal --3T
Should I remove --seg_only and add --tal_reg ?
Is the TIV estimated using a factor computed during the non linear registration to a template?
Best, Marco
From: Reuter, Martin,Ph.D. MREUTER@mgh.harvard.edu Date: Wednesday, 13 August 2025 at 15:53 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: TIV estimation from Fastsurfer
EXTERNAL SENDER Hi Marco,
What command did you run and what FastSurfer version? If you run the full pipeline you should have the eTIV measure in the stats files.
If you run --seg_only then you will not get etiv by default, as that requires the talairach registration. So in that case just switch on the talairach registration via --tal_reg You may also want other use the --3T flag for 3T images so that the correct atlas is used (same as in FreeSurfer).
Best, Martin
On 16. Jul 2025, at 15:22, Marco Ganzetti marco.ganzetti@biogen.com wrote:
Dear, I would like to know how to extract the total intracranial volume after running Fastsurfer. The aseg.stats file only report the following regions:
# Measure Mask, MaskVol, Mask Volume, 1378561.000000, mm^3 # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1112716.172377, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1095647.392151, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 966887.205081, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 949818.424855, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 58370.262413, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 235981.558256, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 231717.193880, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 467698.752136, mm^3
I don’t see any eTIV.
Regards Marco _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edumailto:freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1trt9nLNosmuFprv9cQ7DNEUAW3weAjy_WYWFdLOXSFA3aI...