FSL comes with a bunch of atlases:
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 AMDear 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,AlexanderOn 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, andJust 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 SPM8results? 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 workwith SPM results?And another easy answer for Miro: in MRIcron, when you load the AALatlas, click on a region you are interested in. MRIcron then displaysthe label, the index and the MNI coordinate.Thanks for your insights,BasOn 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-SubjectBrain. N. Tzourio-Mazoyer, B. Landeau, D. Papathanassiou, F. Crivello,
O. Etard, N. Delcroix, B. Mazoyer, and M. Joliot. NeuroImage 2002. 15:273-2892. 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 20012 Precentral_R 20023 Frontal_Sup_L 21014 Frontal_Sup_R 21025 Frontal_Sup_Orb_L 21116 Frontal_Sup_Orb_R 21127 Frontal_Mid_L 22018 Frontal_Mid_R 22029 Frontal_Mid_Orb_L 2211
10 Frontal_Mid_Orb_R 221211 Frontal_Inf_Oper_L 230112 Frontal_Inf_Oper_R 230213 Frontal_Inf_Tri_L 231114 Frontal_Inf_Tri_R 231215 Frontal_Inf_Orb_L 232116 Frontal_Inf_Orb_R 232217 Rolandic_Oper_L 233118 Rolandic_Oper_R 2332
19 Supp_Motor_Area_L 240120 Supp_Motor_Area_R 240221 Olfactory_L 250122 Olfactory_R 250223 Frontal_Sup_Medial_L 2601
24 Frontal_Sup_Medial_R 260225 Frontal_Med_Orb_L 261126 Frontal_Med_Orb_R 261227 Rectus_L 270128 Rectus_R 270229 Insula_L 300130 Insula_R 3002
31 Cingulum_Ant_L 400132 Cingulum_Ant_R 400233 Cingulum_Mid_L 401134 Cingulum_Mid_R 401235 Cingulum_Post_L 402136 Cingulum_Post_R 402237 Hippocampus_L 410138 Hippocampus_R 410239 ParaHippocampal_L 4111
40 ParaHippocampal_R 411241 Amygdala_L 420142 Amygdala_R 420243 Calcarine_L 500144 Calcarine_R 500245 Cuneus_L 501146 Cuneus_R 501247 Lingual_L 502148 Lingual_R 502249 Occipital_Sup_L 510150 Occipital_Sup_R 510251 Occipital_Mid_L 520152 Occipital_Mid_R 520253 Occipital_Inf_L 530154 Occipital_Inf_R 530255 Fusiform_L 540156 Fusiform_R 540257 Postcentral_L 6001
58 Postcentral_R 600259 Parietal_Sup_L 610160 Parietal_Sup_R 610261 Parietal_Inf_L 620162 Parietal_Inf_R 620263 SupraMarginal_L 621164 SupraMarginal_R 621265 Angular_L 622166 Angular_R 622267 Precuneus_L 630168 Precuneus_R 630269 Paracentral_Lobule_L 640170 Paracentral_Lobule_R 640271 Caudate_L 700172 Caudate_R 700273 Putamen_L 701174 Putamen_R 701275 Pallidum_L 702176 Pallidum_R 702277 Thalamus_L 710178 Thalamus_R 7102
79 Heschl_L 810180 Heschl_R 810281 Temporal_Sup_L 811182 Temporal_Sup_R 811283 Temporal_Pole_Sup_L 812184 Temporal_Pole_Sup_R 812285 Temporal_Mid_L 8201
86 Temporal_Mid_R 820287 Temporal_Pole_Mid_L 821188 Temporal_Pole_Mid_R 821289 Temporal_Inf_L 830190 Temporal_Inf_R 830291 Cerebelum_Crus1_L 900192 Cerebelum_Crus1_R 900293 Cerebelum_Crus2_L 901194 Cerebelum_Crus2_R 901295 Cerebelum_3_L 902196 Cerebelum_3_R 902297 Cerebelum_4_5_L 903198 Cerebelum_4_5_R 9032
99 Cerebelum_6_L 9041100 Cerebelum_6_R 9042101 Cerebelum_7b_L 9051102 Cerebelum_7b_R 9052103 Cerebelum_8_L 9061104 Cerebelum_8_R 9062105 Cerebelum_9_L 9071106 Cerebelum_9_R 9072107 Cerebelum_10_L 9081
108 Cerebelum_10_R 9082109 Vermis_1_2 9100110 Vermis_3 9110111 Vermis_4_5 9120112 Vermis_6 9130113 Vermis_7 9140114 Vermis_8 9150115 Vermis_9 9160116 Vermis_10 9170Khader M Hasan, PhDAssociate Professor of RadiologyMSE 168, Tel 713 500 7690 (FAX 713 500 7684)
University of Texas Health Science Center at HoustonMedical School
Diagnostic and Interventional ImagingMagnetic Resonance Imaging Research Division
Diffusion Tensor Imaging Lab, Tel 713 500 7683http://www.uth.tmc.edu/radiology/faculty/khader-m-hasan/index.html
________________________________________From: SPM (Statistical Parametric Mapping) [[log in to unmask]" target="_blank">[log in to unmask]] On
Behalf Of Miro Drahos [[log in to unmask]" target="_blank">[log in to unmask]]Sent: Tuesday, November 13, 2012 7:47 PMTo: [log in to unmask]" target="_blank">[log in to unmask]
Subject: [SPM] AAL atlas labelsHi,where can I find the labels for the AAL atlas ROIs? A legend that mapsthe 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
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http://www.medizin.uni-tuebingen.de/kinder/epn/
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