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.MingxiaOn 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.MingxiaOn 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,
Anderson2013/2/14 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.txtOpen 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 FLIRTCerebellar Atlas in MNI152 space after normalization with FNIRTHarvard-Oxford Cortical Structural AtlasHarvard-Oxford Subcortical Structural AtlasJHU ICBM-DTI-81 White-Matter LabelsJHU White-Matter Tractography AtlasJuelich Histological AtlasMNI Structural AtlasOxford Thalamic Connectivity Probability AtlasOxford-Imanova Striatal Connectivity Atlas 3 sub-regionsOxford-Imanova Striatal Connectivity Atlas 7 sub-regionsOxford-Imanova Striatal Structural AtlasSubthalamic Nucleus AtlasTalairach Daemon Labels
Please let me know if you have any other questions.MingxiaOn 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 oneHere 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
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