Dear Alexander, How to get access to probabilistic atlases of human brain? Could you send any links where they can be downloaded? Thank you in advacne! Sincerely yours, Vladimir Volodymyr B. Bogdanov, PhD --- On Thu, 11/15/12, Alexander Hammers <[log in to unmask]> wrote: From: Alexander Hammers <[log in to unmask]> Subject: Re: [SPM] AAL atlas labels To: [log in to unmask] Date: Thursday, November 15, 2012, 11:51 AM Dear Bas & al., Marko's recollection is correct - AAL for all its virtues was derived from a single brain, and will therefore always be off - on average - like all single brain atlases. This has now been shown systematically and repeatedly (e.g. PubMed ID of paper / PMID: 16860573, PMID: 19261422), complete with quantification of the errors. There is, in my humble opinion, no reason left to use single-subject atlases in 2012, especially as multi-subject based atlases are readily available (e.g. PMID: 12874777 / PMID: 18234511). All the best and happy mapping, Alexander On 14 nov. 2012, at 10:40, Marko Wilke wrote: Hi Bas, how nice that others are asking this question, too :) If I remember correctly, the AAL labels (PMID: 11771995) were derived from the Colin 27 high-resolution single subject brain, meaning they fit this brain very well. They may also fit pretty well when applied to other brains out there in MNI space, but as soon as you move away with your population and/or template (you can see where I am going :) ... some years ago, I used the AAL brain to parcellate children's brains, and first matched it to my template before doing this (PMID 14527581). Also, I usually smooth and binarize such masks before applying them to a population, particularly when assessing t-maps or con images, as these are usually derived from smoothed images anyway. Also, in my personal opinion, I believe that using very small masks is problematic as it assumes your spatial registration is very good, which may or may not be the case. Not sure this answered your question, or anyone's, but I thought I'd say it anyway :) Cheers, Marko Bas Neggers wrote: Hi Hasan, Donald, Miro, all, as I am currently exploring atlas options beyond what I'm used to, and Just out of interest: are all these atlasses you mention below based on the exact same 'MNI' space? That is, can they be used directly for SPM8 results? I'm used to AAL-MRIcron/wfu_pickatlas ROIs that nicely match SPMs MNI templates. Is the same true for the atlas options 1) and 2) below? Or does one need to transform that atlas a bit for it to work with SPM results? And another easy answer for Miro: in MRIcron, when you load the AAL atlas, click on a region you are interested in. MRIcron then displays the label, the index and the MNI coordinate. Thanks for your insights, Bas On 11/14/2012 04:02 AM, Hasan, Khader M wrote: 1. http://www.cyceron.fr/web/aal__anatomical_automatic_labeling.html a. AAL toolbox (SPM99, SPM2, SPM5, SPM8) b. Paper: Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain. N. Tzourio-Mazoyer, B. Landeau, D. Papathanassiou, F. Crivello, O. Etard, N. Delcroix, B. Mazoyer, and M. Joliot. NeuroImage 2002. 15 :273-289 2. International Consortium for Brain Mapping  (ICBM) http://www.loni.ucla.edu/ICBM/Downloads/Downloads_Atlases.shtml 3. Check templates and files provided with MRIcro and Human Brain Connectome works (AAl.txt  --below) 1 Precentral_L 2001 2 Precentral_R 2002 3 Frontal_Sup_L 2101 4 Frontal_Sup_R 2102 5 Frontal_Sup_Orb_L 2111 6 Frontal_Sup_Orb_R 2112 7 Frontal_Mid_L 2201 8 Frontal_Mid_R 2202 9 Frontal_Mid_Orb_L 2211 10 Frontal_Mid_Orb_R 2212 11 Frontal_Inf_Oper_L 2301 12 Frontal_Inf_Oper_R 2302 13 Frontal_Inf_Tri_L 2311 14 Frontal_Inf_Tri_R 2312 15 Frontal_Inf_Orb_L 2321 16 Frontal_Inf_Orb_R 2322 17 Rolandic_Oper_L 2331 18 Rolandic_Oper_R 2332 19 Supp_Motor_Area_L 2401 20 Supp_Motor_Area_R 2402 21 Olfactory_L 2501 22 Olfactory_R 2502 23 Frontal_Sup_Medial_L 2601 24 Frontal_Sup_Medial_R 2602 25 Frontal_Med_Orb_L 2611 26 Frontal_Med_Orb_R 2612 27 Rectus_L 2701 28 Rectus_R 2702 29 Insula_L 3001 30 Insula_R 3002 31 Cingulum_Ant_L 4001 32 Cingulum_Ant_R 4002 33 Cingulum_Mid_L 4011 34 Cingulum_Mid_R 4012 35 Cingulum_Post_L 4021 36 Cingulum_Post_R 4022 37 Hippocampus_L 4101 38 Hippocampus_R 4102 39 ParaHippocampal_L 4111 40 ParaHippocampal_R 4112 41 Amygdala_L 4201 42 Amygdala_R 4202 43 Calcarine_L 5001 44 Calcarine_R 5002 45 Cuneus_L 5011 46 Cuneus_R 5012 47 Lingual_L 5021 48 Lingual_R 5022 49 Occipital_Sup_L 5101 50 Occipital_Sup_R 5102 51 Occipital_Mid_L 5201 52 Occipital_Mid_R 5202 53 Occipital_Inf_L 5301 54 Occipital_Inf_R 5302 55 Fusiform_L 5401 56 Fusiform_R 5402 57 Postcentral_L 6001 58 Postcentral_R 6002 59 Parietal_Sup_L 6101 60 Parietal_Sup_R 6102 61 Parietal_Inf_L 6201 62 Parietal_Inf_R 6202 63 SupraMarginal_L 6211 64 SupraMarginal_R 6212 65 Angular_L 6221 66 Angular_R 6222 67 Precuneus_L 6301 68 Precuneus_R 6302 69 Paracentral_Lobule_L 6401 70 Paracentral_Lobule_R 6402 71 Caudate_L 7001 72 Caudate_R 7002 73 Putamen_L 7011 74 Putamen_R 7012 75 Pallidum_L 7021 76 Pallidum_R 7022 77 Thalamus_L 7101 78 Thalamus_R 7102 79 Heschl_L 8101 80 Heschl_R 8102 81 Temporal_Sup_L 8111 82 Temporal_Sup_R 8112 83 Temporal_Pole_Sup_L 8121 84 Temporal_Pole_Sup_R 8122 85 Temporal_Mid_L 8201 86 Temporal_Mid_R 8202 87 Temporal_Pole_Mid_L 8211 88 Temporal_Pole_Mid_R 8212 89 Temporal_Inf_L 8301 90 Temporal_Inf_R 8302 91 Cerebelum_Crus1_L 9001 92 Cerebelum_Crus1_R 9002 93 Cerebelum_Crus2_L 9011 94 Cerebelum_Crus2_R 9012 95 Cerebelum_3_L 9021 96 Cerebelum_3_R 9022 97 Cerebelum_4_5_L 9031 98 Cerebelum_4_5_R 9032 99 Cerebelum_6_L 9041 100 Cerebelum_6_R 9042 101 Cerebelum_7b_L 9051 102 Cerebelum_7b_R 9052 103 Cerebelum_8_L 9061 104 Cerebelum_8_R 9062 105 Cerebelum_9_L 9071 106 Cerebelum_9_R 9072 107 Cerebelum_10_L 9081 108 Cerebelum_10_R 9082 109 Vermis_1_2 9100 110 Vermis_3 9110 111 Vermis_4_5 9120 112 Vermis_6 9130 113 Vermis_7 9140 114 Vermis_8 9150 115 Vermis_9 9160 116 Vermis_10 9170 Khader M Hasan, PhD Associate Professor of Radiology MSE 168, Tel 713 500 7690 (FAX 713 500 7684) University of Texas Health Science Center at Houston Medical School Diagnostic and Interventional Imaging Magnetic Resonance Imaging Research Division Diffusion Tensor Imaging Lab,  Tel 713 500 7683 http://www.uth.tmc.edu/radiology/faculty/khader-m-hasan/index.html ________________________________________ From: SPM (Statistical Parametric Mapping) [[log in to unmask]">[log in to unmask]] On Behalf Of Miro Drahos [[log in to unmask]">[log in to unmask]] Sent: Tuesday, November 13, 2012 7:47 PM To: [log in to unmask]">[log in to unmask] Subject: [SPM] AAL atlas labels Hi, where can I find the labels for the AAL atlas ROIs? A legend that maps the intensity in aal atlas to an anatomical description. Thank you, Miro -- ____________________________________________________ PD Dr. med. Marko Wilke Facharzt für Kinder- und Jugendmedizin Leiter, Experimentelle Pädiatrische Neurobildgebung Universitäts-Kinderklinik Abt. III (Neuropädiatrie) Marko Wilke, MD, PhD Pediatrician Head, Experimental Pediatric Neuroimaging University Children's Hospital Dept. III (Pediatric Neurology) Hoppe-Seyler-Str. 1 D - 72076 Tübingen, Germany Tel. +49 7071 29-83416 Fax  +49 7071 29-5473 [log in to unmask]">[log in to unmask] http://www.medizin.uni-tuebingen.de/kinder/epn/ ____________________________________________________