That worked perfectly, thanks a lot.
Duncan.
The model used is located on the second line of the .bvars files.
You can the concatenated bvars files in a text editor and change the path.
cheers,
brian
> Hi Mark,
>
> I think I may have made some progress. It looks as if I can't reach the
> required .bmv in the FIRST directory. If i strace the first_utils command,
> this is what I get:
>
> strace -e open,access first_utils --vertexAnalysis --usebvars -i
> concatenated.bvars -d t_test.mat -o shape_analysis/con0_dis1_L_Hipp
> --useReconNative --useRigidAlign -v
> access("/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or
> directory)
> open("/etc/ld.so.cache", O_RDONLY) = 3
> open("/usr/lib/libstdc++.so.6", O_RDONLY) = 3
> open("/lib/libm.so.6", O_RDONLY) = 3
> open("/lib/libgcc_s.so.1", O_RDONLY) = 3
> open("/lib/libc.so.6", O_RDONLY) = 3
> open("concatenated.bvars", O_RDONLY|O_LARGEFILE) = 3
> read model
> open("/usr/local2/fsl/data/first/models_336_bin/intref_thal/L_Hipp.bmv",
> O_RDONLY|O_LARGEFILE) = -1 ENOENT (No such file or directory)
> Cannot open file.
> Cannot open file.
>
> Note: my .txt output file did does not contain this error -
> open("/usr/local2/fsl/data/first/models_336_bin/intref_thal/L_Hipp.bmv",
> O_RDONLY|O_LARGEFILE) = -1 ENOENT (No such file or directory)
>
> I have the correct .bmv file on this machine but cannot access it:
> $FSLDIR/data/first/models_336_bin/intref_thal/*
> /disk/scratch/download/fsl/data/first/models_336_bin/intref_thal/L_Amyg.bmv
>
> /disk/scratch/download/fsl/data/first/models_336_bin/intref_thal/R_Amyg.bmv
> /disk/scratch/download/fsl/data/first/models_336_bin/intref_thal/L_Caud.bmv
>
> /disk/scratch/download/fsl/data/first/models_336_bin/intref_thal/R_Caud.bmv
> /disk/scratch/download/fsl/data/first/models_336_bin/intref_thal/L_Hipp.bmv
>
> /disk/scratch/download/fsl/data/first/models_336_bin/intref_thal/R_Hipp.bmv
> /disk/scratch/download/fsl/data/first/models_336_bin/intref_thal/L_Late.bmv
>
> /disk/scratch/download/fsl/data/first/models_336_bin/intref_thal/R_Late.bmv
>
> I don't have root access on this university owned machine, so not sure how
> to proceed from here.... (other than finding a machine I can use and add a
> manual link..)
>
> rgds,
> Duncan.
>
>
> Hi,
>
> The only difference in the concat_bvars commands you list here is in the
> filename
> of the output, that's all.
>
> I'm not sure what the problem is. Can you upload your bvars file, the
> matrix
> file and one subject's MR image and corresponding first segmentation,
> including the vtk file. Our upload site is:
> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> and please send us the reference number for the upload.
>
> Hopefully we'll be able to figure out the problem from that.
>
> All the best,
> Mark
>
>
> On 9 Jun 2011, at 12:48, Duncan wrote:
>
>> Hello again,
>>
>> Running concat_bvars again did not solve the problem. All steps were
>> carried out on the same version of FSL (4.1.5)
>>
>> Is there any way of checking the concat command worked properly? I get a
>> 'L_Hipp_all.bvars' file and a 'con_to_dis_L_Hipp.bvars' file so I
>> assumed concat worked..
>>
>> In the documentation, two concat commands are listed but I'm unclear if
>> both or either need to be used (I've tried both together and seperately
>> but the output seems to be the same..). Can you explain the difference
>> between these commands?
>>
>> 1) concat_bvars L_Hipp_all.bvars con*_L_Hipp_first.bvars
>> dis*_L_Hipp_first.bvars
>> 2) concat_bvars con_to_dis_L_Hipp.bvars con*_L_Hipp_first.bvars
>> dis*_L_Hipp_first.bvars
>>
>> Thanks and regards,
>> Duncan.
>>
>> Hi,
>>
>> This is probably due to the concat_bvars command failing or
>> using outputs from older versions of FIRST. Try running
>> concat_bvars again and see if that fixes the problem.
>>
>> All the best,
>> Mark
>>
>>
>> On 8 Jun 2011, at 14:22, Duncan wrote:
>>
>>> Hi there,
>>>
>>> I'm trying out the vertex analysis function but cannot produce the
>>> final .vtk file.
>>>
>>> I've done the segmentation and concatenated the bvars files and
>>> produced the design matrix, seemingly without problems.
>>>
>>> I then run the 'first_utils command from my 'test' directory (which
>>> contains my bvars files and my con0_dis1.mat file):
>>>
>>> first_utils --vertexAnalysis --usebvars -i con_to_dis_L_Hipp.bvars -d
>>> con0_dis1.mat -o shape_analysis/con0_dis1_L_Hipp --useReconNative
>>> --useRigidAlign -v >& shape_analysis/con0_dis1_L_Hipp_output.txt
>>>
>>> In my shape_analysis file, the only output is the .txt file. I don't
>>> get an error in my terminal when I run the above command but the
>>> contents of the text file is:
>>>
>>> read model
>>> Cannot open file.
>>> Cannot open file.
>>>
>>> Any advice greatly appreciated,
>>>
>>> rgds,
>>> Duncan.
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