Hi David,
Thanks for your reply.
I still have problem.
I have run thresholding on my aal-prob-2mm.nii and now I have these files in
the same directory:
aal-maxprob-thr0-2mm.nii.gz
aal-maxprob-thr25-2mm.nii.gz
aal-maxprob-thr50-2mm.nii.gz
and I have corrected xml in this way:
<?xml version="1.0" encoding="ISO-8859-1"?>
<atlas version="1.0">
<header>
<name>MRIcro 222 Atlas</name>
<type>Label</type>
<images>
<imagefile>/aai/aal-prob-2mm</imagefile>
<summaryimagefile>/aai/aal-maxprob-thr25-2mm</summaryimagefile>
</images>
</header>
<data>
<label index="1"> Precentral_L 2001</label>
<label index="2"> Precentral_R 2002</label>
<label index="3"> Frontal_Sup_L 2101</label>
<label index="4"> Frontal_Sup_R 2102</label>
.........
<label index="115"> Vermis_9 9160</label>
<label index="116"> Vermis_10 9170</label>
</data>
</atlas>
but aal atlas does not appear in "Atlas Selection" windows.
I have looked a bit in archive and I have found this post:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0910&L=FSL&D=0&1=FSL&9=A&I=-3&J=on&K=1&X=20ABF201A81057049C&Y=serenaf33%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4&P=221013
I have MAC 10.6.4 (Snow Leopard) and I am using FSL 4.1.5 I have not older
FSL version.
Could the version of my MAC be the problem?
Thanks again for your help.
Serena.
On Mon, Oct 18, 2010 at 6:32 PM, David Flitney <[log in to unmask]>wrote:
> In your XML file: the "imagefile" and "summaryimagefile" nodes need to
> exist within an "images" section. Also you've specified aal_2mm as both the
> image and it's own summary. Your image ought to be a 4D 116 volume float
> image where each volume is the probability of the corresponding region. The
> summary ought to be a 3D volume with 116 labels outlining the locations of
> the different regions. There is a script in $FSLDIR/data/atlases/bin called
> "threshold" which will do this for you although I notice it expects images
> to be named of the form aal-prob-2mm.nii.gz
>
> Hope that helps,
> Dave
>
> On 18 Oct 2010, at 15:39, sere f wrote:
>
>
>
> On Mon, Oct 18, 2010 at 4:33 PM, sere f <[log in to unmask]> wrote:
>>
>>> Hi David,
>>> thanks for your prompt reply.
>>>
>>> I don't understand where I have to write this line:
>>> name "Blah" - from <name>Blah</name>
>>>
>>> Anyway:
>>>
>>> aal.xml is in Attach and this is the output of ls -lR
>>> $FSL/data/atlases:
>>>
>>>
>>> total 360
>>> drwxr-xr-x@ 18 fabbri staff 612 Jan 26 2010 Cerebellum
>>> -rwxr-xr-x@ 1 fabbri staff 2271 Feb 26 2009
>>> Cerebellum_MNIflirt.xml
>>> -rwxr-xr-x@ 1 fabbri staff 2271 Feb 26 2009
>>> Cerebellum_MNIfnirt.xml
>>> drwxr-xr-x@ 20 fabbri staff 680 Jan 26 2010 HarvardOxford
>>> -rw-r--r-- 1 fabbri staff 4335 Aug 7 2007
>>> HarvardOxford-Cortical.xml
>>> -rw-r--r--@ 1 fabbri staff 1968 Aug 7 2007
>>> HarvardOxford-Subcortical.xml
>>> drwxr-xr-x@ 19 fabbri staff 646 Jan 26 2010 JHU
>>> -rw-r--r--@ 1 fabbri staff 4622 Aug 15 2007 JHU-labels.xml
>>> -rw-r--r--@ 1 fabbri staff 2094 Aug 6 2007 JHU-tracts.xml
>>> drwxr-xr-x@ 10 fabbri staff 340 Jan 26 2010 Juelich
>>> -rw-r--r-- 1 fabbri staff 10346 Nov 3 2009 Juelich.xml
>>> drwxr-xr-x@ 11 fabbri staff 374 Jan 26 2010 MNI
>>> -rw-r--r-- 1 fabbri staff 987 Aug 7 2007 MNI.xml
>>> drwxr-xr-x@ 4 fabbri staff 136 Jan 26 2010 Talairach
>>> -rw-r--r--@ 1 fabbri staff 121710 Aug 7 2007 Talairach.xml
>>> drwxr-xr-x@ 10 fabbri staff 340 Jan 26 2010 Thalamus
>>> -rw-r--r--@ 1 fabbri staff 985 Aug 7 2007 Thalamus.xml
>>> drwxr-xr-x 5 fabbri staff 170 Oct 18 12:33 aai
>>> -rw-r--r--@ 1 fabbri staff 5808 Oct 18 13:12 aal.xml
>>> drwxr-xr-x@ 7 fabbri staff 238 Jan 26 2010 bin
>>>
>>> ./Cerebellum:
>>> total 3608
>>> -rw-r--r--@ 1 fabbri staff 44555 Feb 27 2009
>>> Cerebellum-MNIflirt-maxprob-thr0-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 9433 Feb 27 2009
>>> Cerebellum-MNIflirt-maxprob-thr0-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 34698 Feb 27 2009
>>> Cerebellum-MNIflirt-maxprob-thr25-1mm.nii.gz
>>> -rwxr-xr-x@ 1 fabbri staff 6926 Feb 25 2009
>>> Cerebellum-MNIflirt-maxprob-thr25-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 30946 Feb 27 2009
>>> Cerebellum-MNIflirt-maxprob-thr50-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 6245 Feb 27 2009
>>> Cerebellum-MNIflirt-maxprob-thr50-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 712945 Feb 26 2009
>>> Cerebellum-MNIflirt-prob-1mm.nii.gz
>>> -rwxr-xr-x@ 1 fabbri staff 96399 Feb 24 2009
>>> Cerebellum-MNIflirt-prob-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 41376 Feb 27 2009
>>> Cerebellum-MNIfnirt-maxprob-thr0-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 8343 Feb 27 2009
>>> Cerebellum-MNIfnirt-maxprob-thr0-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 34221 Feb 27 2009
>>> Cerebellum-MNIfnirt-maxprob-thr25-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 6681 Feb 25 2009
>>> Cerebellum-MNIfnirt-maxprob-thr25-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 32621 Feb 27 2009
>>> Cerebellum-MNIfnirt-maxprob-thr50-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 6420 Feb 27 2009
>>> Cerebellum-MNIfnirt-maxprob-thr50-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 651100 Feb 26 2009
>>> Cerebellum-MNIfnirt-prob-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 93252 Feb 24 2009
>>> Cerebellum-MNIfnirt-prob-2mm.nii.gz
>>>
>>> ./HarvardOxford:
>>> total 16760
>>> -rw-r--r--@ 1 fabbri staff 180388 Aug 7 2007
>>> HarvardOxford-cort-maxprob-thr0-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 36850 Aug 7 2007
>>> HarvardOxford-cort-maxprob-thr0-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 146506 Aug 7 2007
>>> HarvardOxford-cort-maxprob-thr25-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 29113 Aug 7 2007
>>> HarvardOxford-cort-maxprob-thr25-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 129144 Aug 7 2007
>>> HarvardOxford-cort-maxprob-thr50-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 22629 Aug 7 2007
>>> HarvardOxford-cort-maxprob-thr50-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 3412276 Aug 7 2007
>>> HarvardOxford-cort-prob-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 513170 Aug 7 2007
>>> HarvardOxford-cort-prob-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 143394 Aug 7 2007
>>> HarvardOxford-sub-maxprob-thr0-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 28758 Aug 7 2007
>>> HarvardOxford-sub-maxprob-thr0-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 137877 Aug 7 2007
>>> HarvardOxford-sub-maxprob-thr25-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 26686 Aug 7 2007
>>> HarvardOxford-sub-maxprob-thr25-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 164702 Aug 7 2007
>>> HarvardOxford-sub-maxprob-thr50-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 31694 Aug 7 2007
>>> HarvardOxford-sub-maxprob-thr50-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 3097063 Aug 7 2007
>>> HarvardOxford-sub-prob-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 430411 Aug 7 2007
>>> HarvardOxford-sub-prob-2mm.nii.gz
>>> -rw-r--r-- 1 fabbri staff 60 May 22 2007 labels
>>> -rwxr-xr-x@ 1 fabbri staff 209 May 22 2007 relabel
>>>
>>> ./JHU:
>>> total 27168
>>> -rw-r--r--@ 1 fabbri staff 1127989 Aug 12 2007
>>> JHU-ICBM-DWI-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 206277 Aug 12 2007
>>> JHU-ICBM-DWI-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 6748509 Aug 6 2007 JHU-ICBM-FA-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 922943 Aug 6 2007 JHU-ICBM-FA-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 2685506 Aug 12 2007 JHU-ICBM-T2-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 434038 Aug 12 2007 JHU-ICBM-T2-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 0 Aug 6 2007
>>> JHU-ICBM-WhiteMatter-labels-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 286344 Aug 6 2007
>>> JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 34985 Aug 6 2007
>>> JHU-ICBM-tracts-maxprob-thr0-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 53988 Aug 6 2007
>>> JHU-ICBM-tracts-maxprob-thr25-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 7161 Aug 6 2007
>>> JHU-ICBM-tracts-maxprob-thr25-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 26051 Aug 6 2007
>>> JHU-ICBM-tracts-maxprob-thr50-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 2787 Aug 6 2007
>>> JHU-ICBM-tracts-maxprob-thr50-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 1097811 Aug 6 2007
>>> JHU-ICBM-tracts-prob-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 181917 Aug 6 2007
>>> JHU-ICBM-tracts-prob-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 52093 Aug 7 2007
>>> JHU-WhiteMatter-labels-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 9611 Aug 7 2007
>>> JHU-WhiteMatter-labels-2mm.nii.gz
>>>
>>> ./Juelich:
>>> total 9296
>>> -rw-r--r--@ 1 fabbri staff 208007 Oct 27 2009
>>> Juelich-maxprob-thr0-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 38194 Oct 27 2009
>>> Juelich-maxprob-thr0-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 162725 Oct 27 2009
>>> Juelich-maxprob-thr25-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 28787 Oct 27 2009
>>> Juelich-maxprob-thr25-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 126683 Oct 27 2009
>>> Juelich-maxprob-thr50-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 20766 Oct 27 2009
>>> Juelich-maxprob-thr50-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 3573573 Oct 27 2009
>>> Juelich-prob-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 581690 Nov 3 2009
>>> Juelich-prob-2mm.nii.gz
>>>
>>> ./MNI:
>>> total 5384
>>> -rw-r--r-- 1 fabbri staff 473 Aug 7 2007 DO
>>> -rw-r--r--@ 1 fabbri staff 127787 Aug 7 2007
>>> MNI-maxprob-thr0-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 26638 Aug 7 2007
>>> MNI-maxprob-thr0-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 139095 Aug 7 2007
>>> MNI-maxprob-thr25-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 29427 Jun 6 2007
>>> MNI-maxprob-thr25-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 147027 Aug 7 2007
>>> MNI-maxprob-thr50-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 31077 Jun 6 2007
>>> MNI-maxprob-thr50-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 1948363 Aug 7 2007 MNI-prob-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 289044 Jun 6 2007 MNI-prob-2mm.nii.gz
>>>
>>> ./Talairach:
>>> total 968
>>> -rw-r--r--@ 1 fabbri staff 430529 Aug 8 2007
>>> Talairach-labels-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 60463 Aug 3 2007
>>> Talairach-labels-2mm.nii.gz
>>>
>>> ./Thalamus:
>>> total 600
>>> -rw-r--r--@ 1 fabbri staff 19605 Aug 7 2007
>>> Thalamus-maxprob-thr0-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 3384 Aug 7 2007
>>> Thalamus-maxprob-thr0-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 14945 Aug 7 2007
>>> Thalamus-maxprob-thr25-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 2396 Aug 7 2007
>>> Thalamus-maxprob-thr25-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 13296 Aug 7 2007
>>> Thalamus-maxprob-thr50-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 2024 Aug 7 2007
>>> Thalamus-maxprob-thr50-2mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 207512 Aug 7 2007
>>> Thalamus-prob-1mm.nii.gz
>>> -rw-r--r--@ 1 fabbri staff 31649 Aug 7 2007
>>> Thalamus-prob-2mm.nii.gz
>>>
>>> ./aai:
>>> total 7064
>>> -rw-r--r--@ 1 fabbri staff 2713 Oct 17 12:11 aal.nii.txt
>>> -rw-r--r-- 1 fabbri staff 3610868 Oct 18 11:57 aal_2mm.nii
>>>
>>> ./bin:
>>> total 40
>>> -rwxr-xr-x@ 1 fabbri staff 235 Aug 5 2007 addlut
>>> -rw-r--r--@ 1 fabbri staff 33 Jul 10 2007 eye.mat
>>> -rwxr-xr-x@ 1 fabbri staff 654 Aug 5 2007 locate-centres
>>> -rwxr-xr-x@ 1 fabbri staff 627 Aug 6 2007 locate-label-centres
>>> -rwxr-xr-x@ 1 fabbri staff 650 Mar 17 2008 threshold
>>>
>>>
>>>
>>> Thank you for your help.
>>>
>>> Serena.
>>>
>>>
>>
>>
>>
>>
>> On Mon, Oct 18, 2010 at 4:09 PM, David Flitney <[log in to unmask]>wrote:
>>
>>> Hi
>>>
>>> On 18 Oct 2010, at 12:25, sere f wrote:
>>>
>>> Dear FSL users,
>>>
>>> I am trying to add an atlas (and xml file ) in $FSL/data/atlases.
>>> I have followed the instructions in
>>> http://www.fmrib.ox.ac.uk/fsl/data/atlas-reference.html to create xlm
>>> file, but FSL viewer does not find labels.
>>>
>>>
>>> Could you send me the output of:
>>>
>>> ls -lR $FSL/data/atlases
>>>
>>> along with a listing of your XML file.
>>>
>>> In fact in "the atlas selection dialog" window this file does not
>>> appear.
>>> Where do I wrong? Could you give me some help please?
>>>
>>>
>>> If the XML file is in the atlases directory then the name "Blah" - from
>>> <name>Blah</name> - should appear in the selection dialog.
>>>
>>>
>>> Thank you.
>>>
>>> Serena.
>>>
>>>
>>> --
>>> Dave Flitney, IT Manager
>>> Oxford Centre for Functional MRI of the Brain
>>> E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
>>> URL: http://www.fmrib.ox.ac.uk/~flitney
>>>
>>>
>>>
>>>
>>
> <aal.xml>
>
>
> --
> Dave Flitney, IT Manager
> Oxford Centre for Functional MRI of the Brain
> E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
> URL: http://www.fmrib.ox.ac.uk/~flitney
>
>
>
>
