Hello FSL Experts,
I am running into a similar problem of a former user (see below). When I attempt to run first_utils I am not generating a .vtk file in my shape_analysis directory. After looking through the listerv I was till unable to develop a solution (it seems that I do not understand what actually worked for the user listed below). I can access all bmv files and have successfully concatenated my *.bvar files but I am not able to generate the .vtk output file (just the *.nii.gz and *.txt files). Any help would be appreciated.
I am running the most recent version of FSL.
Cheers,
Re: Vertex analysis/FIRST
From:
Duncan <[log in to unmask]>
Reply-To:
FSL - FMRIB's Software Library <[log in to unmask]>
Date:
Mon, 13 Jun 2011 16:18:31 +0100
Content-Type:
text/plain
Parts/Attachments:
text/plain (147 lines)
Reply
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
>
|