Table 1.

Methodological variations in articles utilizing FreeSurfer, published between 2006 and 2013^a.

Study (Year)	Patient N	Pathology	Control N	Total N	Scanner type/Strength	Manual edits
Alner et al., 2012	26	Insertional mutation	10	36	1.5T GE Signa	S, C
Anticevic et al., 2012	20	HC	0	20	3T Siemens Allegra
Barnes et al., 2010	78	HC	0	78	1.5T GE Signa	S, C
Batty et al., 2010	25	ADHD (age 9–15)	24	49	1.5T Phillips Achieva	S, C, W
Benedict et al., 2009	50	MS	20	70	1.5T GE Signa	S
Bhojraj et al., 2011	56	SCZ	36	92	1.5T GE	S, C, W
Bomboi et al., 2011	24	MS	24	48	1.5T, 3T GE Signa	C, W
Bray et al., 2011	59	Fragile X	83	142	1.5T GE Signa	C
Cerasa et al., 2011	109	MAO-A alleles	0	109	3T Siemens Allegra	S, C, W
Cherbuin et al., 2009	403	HC	0	403	1.5T Phillips
Chiang et al., 2011	149	HC (elderly)	0	149	1.5T
Clarkson et al., 2011	106	AD and FTD	44	150	1.5T GE Signa
Dalaker et al., 2011	43	PD	41	84	1.5T Philips Intera	S, C
Desikan et al., 2010	162	MCI	0	162	1.5T GE, Siemens, or Phillips
Dickerson et al., 2007	15	HC	0	15	1.5T Siemens Avanto
Du et al., 2007	41	AD and FTD	23	64	1.5T Siemens Vision
Durand-Dubief et al., 2012	9	MS	0	9	1.5T Siemens Sonata + Intera
Dykstra et al., 2012	5	TLE	0	5	T1 Weighted MRI	S, C
Eggert et al., 2012	38	Simulated	0	38	3T Siemens TRIO
Ehrlich et al., 2012	131	SCZ	138	269	1.5T, 3T Siemens Sonata + TRIO	C
Eyler et al., 2011	202	HC (twins)	0	404	1.5T Siemens	C
Feczko et al., 2009	29	AD	76	105	1.5T Siemens	S, C, W
Fennema-Notestine et al., 2007	133	HC (elderly)	0	133	1.5T GE Signa + Siemens	C
Fennema-Notestine et al., 2009	259	AD and MCI	139	398	ADNI WEBSITE	C
Fennema-Notestine et al., 2006	16	Various diagnoses	0	16	1.5T GE
Fjell et al., 2009	883	HC (18-93)	0	883	1.5T	S, C
Francis et al., 2011	70	Children of SCZ patients	73	143	1.5T GE	S, C, W
Fujimoto et al., 2014	6	HC	0	6	7T Siemens	C
Furst and Lal, 2011	13	AD	11	24	1.5T Siemens Vision	C
Goghari et al., 2007a	19	Relatives of SCZ patients	22	41	3T GE Signa	S, C
Goghari et al., 2007b	19	Relatives of SCZ patients	22	41	3T GE Signa	S, C, W
Goldman et al., 2009	307	SCZ and unaffected siblings	196	503	1.5T GE
Gronenschild et al., 2012	10	Various diagnoses	20	30	3T Siemens Allegra
Gutierrez-Galve et al., 2009	38	APO-E allele	23	61	1.5T GE Signa	S, C, W
Han et al., 2006	15	HC	0	15	1.5T Siemens Sonata + 3T Siemens
Hinds et al., 2009	10	HC	0	10	3T TIM TRIO	C
Iglesias et al., 2011	92	HC	0	92	1.5T Siemens
Keller et al., 2012	10	JME	62	72	3T Philips Intera
Khan et al., 2008	50	Various diagnoses	0	50	1.5T GE + Siemens
Klein and Tourville, 2012	101	HC	0	101	3T, 7T	C
Kremen et al., 2010	474	HC (twins)	0	474	1.5T Siemens	C
Lee et al., 2006	30	Cases from ICBM	0	30	Database	C
Lehmann et al., 2010	51	AD and FTD	25	76	1.5T GE	S, C
Levinski et al., 2009					1.5	S, C, W
Mahone et al., 2011	42	ADHD	44	86	1.5T Phillips
Makris et al., 2007	24	ADHD (adults)	18	42	1.5T Siemens Sonata
Moore et al., 2012	15	NPH and AD	15	30	3T GE Signa	C
Morey et al., 2009	20	HC	0	20	3T GE Excite
Mueller et al., 2010	38	AD and MCI	53	91	4T BrukerMedSpec	S
Murakami et al., 2011	21	SCZ	21	42	3T GE Signa	S, C
Nesvåg et al., 2009	53	SCZ/SCA	0	53	1.5T GE	C
Noble et al., 2012	60	HC	0	60	1.5T Siemens Sonata	S, C
O'Donnell et al., 2005	35	HC (8–20)	0	35	1.5T GE Horizon	S, C
Oertel-Knöchel et al., 2013	54	SCZ and healthy relatives	37	91	3T Siemens Allegra	S, C, W
Oguz et al., 2008	9	HC	0	9	1.5T
Ostby et al., 2009	171	HC	0	171	1.5T Siemens Avanto	S, C
Panizzon et al., 2009	474	Publicly available images	0	474	1.5T Siemens	S, C
Park et al., 2004	1	Tumor	1	2	1.5T	S, C
Park et al., 2009	33	Blind from birth or after	35	68	3T Philips	S, C
Pellicano et al., 2010	24	MS	24	48	3T GE Signa	C
Pengas et al., 2009	11	SD	0	11	1.5T GE Signa
Pfefferbaum et al., 2012	114	HC	0	114	1.5T, 3T GE Signa	C
Poulin et al., 2011	367	AD from ADNI base	0	367	1.5T GE, Siemens, or Phillips
Putcha et al., 2011	16	MCI	18	34	3T Siemens Trio	S
Raj et al., 2010	27	Drug resistant TLE	30	57	4T BrukerMedSpec	C
Ramasamy et al., 2009	88	MS	38	126	1.5T GE Signa	C, W
Rimol et al., 2010	312	SCZ and BD	207	519	1.5T Siemens Sonata
Rohrer et al., 2009	76	SD and aphasia	29	105	1.5T GE Signa	S, C, W
Romero-Garcia et al., 2012	30	HC elderly	0	30	1.5T Phillips Intera	C
Safford et al., 2010	13	HC	0	13	3T Siemens Allegra
Schultz et al., 2010b	59	SCZ	59	118	1.5T Siemens Vision
Schultz et al., 2010a	54	SCZ	54	108	1.5T Siemens Vision
Shattuck et al., 2009	40	HC	0	40	1.5T GE
Strangman et al., 2010	50	TBI	0	50	1.5T Siemens Avanto
Tae et al., 2008	21	MDD	20	41	1.5T Philips
Tomasevic et al., 2013	20	RRMS	0	20	1.5T Philips	S, C
Tosun et al., 2010	171	AD and MCI	77	248	1.5T
Travis et al., 2014	17	HC (infants)	0	17	1.5T GE	C
Weier et al., 2012	15	MS	15	45	1.5T Siemens Avanto
Winkler et al., 2010	486	HC	0	486	3T Siemens Trio
Wonderlick et al., 2009	11	HC	0	11	3T Siemens Trio	S
Woodward et al., 2009	50	PTSD	47	97	1.5T GE Signa

^aThe literature review was conducted during the summer of 2013 via PubMed search of the terms “freesurfer” and “freesurfer editing,” which yielded hundreds articles largely between the years 2006 and 2013. Studies were excluded (1) if they were based on dissertations, posters, or abstracts; or (2) if they compared FreeSurfer performance between computer systems, as most did not report utilizing any manual editing protocol. The full length studies remaining had their methods section analyzed for the precise methods of editing used. Studies which definitively stated that no editing was done were included, as it showed awareness of the possibility to edit. If they failed to mention manual editing in their methods section, they were excluded on the basis of the wide variability in possible minor manual edits that could have been made and gone unreported. Additionally, if the study did mention minor manual intervention, but failed to specify precisely what was done at each stage, the study was excluded. We also looked for studies that applied homogenous editing protocols to all study scans: those in which only a subset of scans were edited were excluded due to variability in selection of the images to be edited.

AD, Alzheimer's; PTSD, post-traumatic stress disorder; ADHD, attention-deficit hyperactivity disorder; RRMS, relapsing-remitting MS; BD, bipolar disorder; SCA, schizoaffective disorder; FTD, frontotemporal dementia; SCZ, schizophrenia; HC, healthy controls; SD, semantic dementia; JME, juvenile myoclonic epilepsy; TBI, traumatic brain injury; MDD, major depressive disorder; TLE, temporal lobe epilepsy; MS, multiple sclerosis; S, data was manually skull stripped; MCI, mild cognitive impairment; C, control points were manually applied; NPH, normal pressure hydrocephalus; W, white matter edits were utilized; PD, Parkinson's disease.