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Dear Anderson, what does it mean to make executable and therefore be able to omit the sh? thanks a lot cheers, sandra 2013/2/14 Anderson M. Winkler <[log in to unmask]> > 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 >>> >>> >> >