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but i'm curious i'll ask ;) 2013/2/14 Sandra Petris <[log in to unmask]> > Ok great thanks! > > > 2013/2/14 zhang mingxia <[log in to unmask]> > >> You don't need to install that. Put in any place and use sh ./autoaq to >> run it. Anderson said the sh can be omitted if autoaq is made >> executable, but I don't know how to make autoaq executable. I always us sh >> ./ to run the script. >> >> Mingxia >> >> >> On Thu, Feb 14, 2013 at 12:48 PM, Sandra Petris <[log in to unmask]>wrote: >> >>> Hi Mingxia, >>> >>> I have a primitive question about the script..where do i have to install >>> it (which directory) to be able to run it? >>> >>> cheers, >>> sandra >>> >>> >>> 2013/2/14 zhang mingxia <[log in to unmask]> >>> >>>> Thanks, Anderson! I also think that is the function of autoaq. >>>> >>>> Mingxia >>>> >>>> >>>> On Thu, Feb 14, 2013 at 11:40 AM, Anderson M. Winkler < >>>> [log in to unmask]> wrote: >>>> >>>>> Dear Bonnie and Mingxia, >>>>> Yep, that's right. And if the "autoaq" is made executable, the "sh" at >>>>> the beginning can be omitted. >>>>> Note that the "autoaq" isn't a replacement for "atlasquery", but just >>>>> an interface to it. Both "atlasquery" and "cluster" are used behind the >>>>> scenes. >>>>> All the best, >>>>> Anderson >>>>> >>>>> >>>>> 2013/2/14 zhang mingxia <[log in to unmask]> >>>>> >>>>>> Hi Bonnie, >>>>>> >>>>>> I put it in a directory and then go into that directory. Suppose you >>>>>> want to know the name of the cluster in your x.nii.gz file based on >>>>>> " Harvard-Oxford Cortical Structural Atlas" with the threshold p>.95. Use >>>>>> the code like this: >>>>>> >>>>>> sh ./autoaq -i x.nii.gz -a "Harvard-Oxford Cortical Structural >>>>>> Atlas" -t .95 -o try.txt >>>>>> >>>>>> Open the try.txt and you will know what's this script for. I think >>>>>> this one is an improvement of >>>>>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlasquery. >>>>>> >>>>>> You should notice there are special names for atlas, you can only use >>>>>> these: >>>>>> >>>>>> Cerebellar Atlas in MNI152 space after normalization with FLIRT >>>>>> Cerebellar Atlas in MNI152 space after normalization with FNIRT >>>>>> Harvard-Oxford Cortical Structural Atlas >>>>>> Harvard-Oxford Subcortical Structural Atlas >>>>>> JHU ICBM-DTI-81 White-Matter Labels >>>>>> JHU White-Matter Tractography Atlas >>>>>> Juelich Histological Atlas >>>>>> MNI Structural Atlas >>>>>> Oxford Thalamic Connectivity Probability Atlas >>>>>> Oxford-Imanova Striatal Connectivity Atlas 3 sub-regions >>>>>> Oxford-Imanova Striatal Connectivity Atlas 7 sub-regions >>>>>> Oxford-Imanova Striatal Structural Atlas >>>>>> Subthalamic Nucleus Atlas >>>>>> Talairach Daemon Labels >>>>>> >>>>>> >>>>>> Please let me know if you have any other questions. >>>>>> >>>>>> Mingxia >>>>>> >>>>>> >>>>>> On Thu, Feb 14, 2013 at 4:10 AM, Bonnie Lam <[log in to unmask]>wrote: >>>>>> >>>>>>> Hi Mingxia, >>>>>>> >>>>>>> Thanks for your reply. >>>>>>> >>>>>>> Would you mind further explaining how to use the script? >>>>>>> >>>>>>> So I assume you will first need to replace your files in the >>>>>>> brackets: >>>>>>> >>>>>>> autoaq -i <input image> -a "<atlas name>" -t <threshold> -o >>>>>>> <output.txt> >>>>>>> >>>>>>> And also add your files here : >>>>>>> >>>>>>> IN="" >>>>>>> ATLAS="" >>>>>>> OUT="" >>>>>>> >>>>>>> Then in your working directory, type in: sh autoaq.sh ? >>>>>>> >>>>>>> Thanks for your reply in advance! >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Bonnie >>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> *From: *"zhang mingxia" <[log in to unmask]> >>>>>>> *To: *[log in to unmask] >>>>>>> *Sent: *Thursday, February 14, 2013 8:42:59 PM >>>>>>> *Subject: *Re: [FSL] Reporting p-value, cluster size and percentage >>>>>>> of tract involved all in one >>>>>>> >>>>>>> >>>>>>> Here is a script. Please see the one mail in the mail list today >>>>>>> about the atlasquesry. >>>>>>> >>>>>>> >>>>>>> On Wed, Feb 13, 2013 at 9:09 PM, Bonnie Y K Lam <[log in to unmask]>wrote: >>>>>>> >>>>>>>> Dear FSL users, >>>>>>>> >>>>>>>> I have been following post from other FSL users in regards to using >>>>>>>> the cluster and altasquery command. However, the question remains as to >>>>>>>> whether there is a way to report p-value, cluster size and tract info in >>>>>>>> the same txt file? >>>>>>>> >>>>>>>> In the cluster command we can get the cluster size, t-value, MNI >>>>>>>> coordinates, etc and output as follow: >>>>>>>> >>>>>>>> Cluster Index Voxels MAX MAX X (mm) MAX Y (mm) MAX >>>>>>>> Z (mm) COG X (mm) COG Y (mm) COG Z (mm) >>>>>>>> 2 1106 0.961 6 4 24 -1.01 -4.29 25.6 >>>>>>>> 1 28 0.951 -6 -35 20 -8.18 -34.4 21.4 >>>>>>>> >>>>>>>> >>>>>>>> And in the atlasquery command we get the tract and percentage >>>>>>>> involved (in the case, the JHU White-Matter atlas is used) >>>>>>>> >>>>>>>> Anterior thalamic radiation L:1.18646 >>>>>>>> Anterior thalamic radiation R:1.01869 >>>>>>>> Corticospinal tract L:0.759451 >>>>>>>> Corticospinal tract R:0.373157 >>>>>>>> Cingulum (cingulate gyrus) L:0.259725 >>>>>>>> Cingulum (cingulate gyrus) R:0.104708 >>>>>>>> Cingulum (hippocampus) L:0.0153588 >>>>>>>> Cingulum (hippocampus) R:0.0297155 >>>>>>>> Forceps major:1.02095 >>>>>>>> Forceps minor:2.68633 >>>>>>>> Inferior fronto-occipital fasciculus L:1.72625 >>>>>>>> Inferior fronto-occipital fasciculus R:1.5613 >>>>>>>> Inferior longitudinal fasciculus L:1.51863 >>>>>>>> Inferior longitudinal fasciculus R:0.703462 >>>>>>>> Superior longitudinal fasciculus L:2.59552 >>>>>>>> Superior longitudinal fasciculus R:1.42251 >>>>>>>> Uncinate fasciculus L:0.566331 >>>>>>>> Uncinate fasciculus R:0.211678 >>>>>>>> Superior longitudinal fasciculus (temporal part) L:1.14275 >>>>>>>> Superior longitudinal fasciculus (temporal part) R:0.46396 >>>>>>>> >>>>>>>> If I would like to report on >>>>>>>> >>>>>>>> Tract name, percentage involved, cluster size and p-value PER TRACT >>>>>>>> >>>>>>>> what would be the best way to do it? >>>>>>>> >>>>>>>> Thank you very much, >>>>>>>> >>>>>>>> Bonnie >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Bonnie Yin Ka Lam >>>>>>> PhD Candidate >>>>>>> >>>>>>> >>>>>>> www.NeuRA.edu.au <http://neura.edu.au/> >>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>> PO Box 1165 Randwick Sydney NSW 2031 Australia >>>>>>> *T* +61 2 9399 1803 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >