Fabulous!!! It worked
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, May 11, 2015 5:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fcseed-sess
oh, the 1126 is for the 2005 atlas, try 11129 (ctx_lh_G_precentral) instead
On 05/11/2015 03:00 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
>
> Here is the output:
>
> cmdline mri_binarize --i aparc.a2009s+aseg.mgz --binval 1 --o
> L_G_Precentralgyrus.mgz --match 1126 sysname Linux hostname glia
> machine x86_64
> user malshikh
>
> input aparc.a2009s+aseg.mgz
> frame 0
> nErode3d 0
> nErode2d 0
> output L_G_Precentralgyrus.mgz
> Binarizing based on matching values
> nMatch 1
> 0 1126
> binval 1
> binvalnot 0
> Found 0 values in range
> Counting number of voxels
> Found 0 voxels in final mask
> mri_binarize done
>
>
> and I ran the following command line by
> changing bival to 0
>
> mri_binarize --i aparc.a2009s+aseg.mgz --binval 0 --o 111.mgz --match
> 1126
>
> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cmdline
> mri_binarize --i aparc.a2009s+aseg.mgz --binval 0 --o
> L_G_Precentralgyrus.mgz --match 1126 sysname Linux hostname glia
> machine x86_64
> user malshikh
>
> input aparc.a2009s+aseg.mgz
> frame 0
> nErode3d 0
> nErode2d 0
> output L_G_Precentralgyrus.mgz
> Binarizing based on matching values
> nMatch 1
> 0 1172
> binval 0
> binvalnot 0
> Found 0 values in range
> Counting number of voxels
> Found 16777216 voxels in final mask
> mri_binarize done
>
>
> Thank you for any advice?
>
> Mohamad
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 11, 2015 2:11 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fcseed-sess
>
> Use aparc.a2009s+aseg.mgz
>
> On 05/11/2015 02:01 PM, Alshikho, Mohamad J. wrote:
>> Hi Doug,
>>
>> I want to use the command "fcseed-config" to configure the segment 1126 (in
>> aparc+aseg) as a seed to pass it to connectivity analysis. I ran the command
>> line:
>>
>> fcseed-config -segid 1126 -fcname L_G_Precentralgyrus.dat -fsd bold
>> -mean -cfg mean.L_G_Precentralgyrus.config
>>
>> Then I ran the command fcseed-sess -s ${i} -cfg
>> mean.L_G_Precentralgyrus.config to create the FC seed for every subject.
>>
>>
>> The final message for the previous command line was "Found 0 voxels in final
>> mask"
>>
>> I changed the configuration file as the following : FillThresh I make it (0)
>> , Domean I make it (0)... and I got the same result "Found 0 voxels in
>> final mask"
>>
>> I tried to run mri_binarize --i aparc+aseg.mgz --o L_G_Precentralgyrus.mgz
>> --match 1126 I got the same result "Found 0 voxels in final mask"
>>
>> When I ran the previous command line using the flag -binval 0 I got voxels
>> in the final mask.
>>
>>
>> Regarding the command fcseed-sess how can I force it to find voxels in the
>> final mask?
>>
>> Thanks,
>> Mohamad
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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