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Dear Mark, I will try that and contact you if I have any incovinient. Thank you very much All the best, Sabrina > Date: Thu, 21 Jul 2011 18:30:40 +0100 > From: [log in to unmask] > Subject: Re: [FSL] design matrix for vertex analysis > To: [log in to unmask] > > Dear Sabrina, > > You cannot use only two subjects - the statistics will not work. > Please use at least 3 per group, but ideally all of them. > > All the best, > Mark > > On 21 Jul 2011, at 18:28, diagnostico imagenes wrote: > > > Dear Mark, > > As I had problems with the vertex analysis (different errors) now I am trying with only two subjects to see if it works. My research sample is 10 patients and 8 controls. Can I try with two subjects or I should do it with the whole sample?? > > > > > > > Date: Wed, 20 Jul 2011 23:17:29 +0100 > > > From: [log in to unmask] > > > Subject: Re: [FSL] design matrix for vertex analysis > > > To: [log in to unmask] > > > > > > Dear Sabrina, > > > > > > Are you really trying to do a vertex analysis between two subjects? > > > This is really not possible and I would not trust any output that you got. > > > > > > If you meant something else then please let us know. > > > You should be able to include the design matrix in the email if you > > > just copy it as text into the email itself. > > > > > > All the best, > > > Mark > > > > > > > > > > > > On 20 Jul 2011, at 20:42, diagnostico imagenes wrote: > > > > > > > Dear Mark, > > > > Now I am using only two subjects to try the vertex analisys and I want to now if there is a difference in the left hippocampus. > > > > I checked the vtk files in the 3D viewer and it looks fine. > > > > I tried to attach the design matrix and the vtk files from two left hippocampus but the files are too heavy, how can I send you those files? > > > > Thank you in advance, > > > > Best regards, > > > > Sabrina > > > > > > > > > > > > > Date: Tue, 14 Jun 2011 19:33:48 +0100 > > > > > From: [log in to unmask] > > > > > Subject: Re: [FSL] design matrix for vertex analysis > > > > > To: [log in to unmask] > > > > > > > > > > Dear Sabrina, > > > > > > > > > > By original analyses I mean the individual subject segmentations. > > > > > Have you checked these, and do they look correct? > > > > > > > > > > I suspect that the error you see here has something to do with > > > > > your design matrix. Can you show me the contents of the > > > > > file con0_dis1.mat ? Also, let me know how many subjects > > > > > you have and what sort of question(s) you are trying to ask > > > > > with this design matrix. > > > > > > > > > > All the best, > > > > > Mark > > > > > > > > > > > > > > > On 14 Jun 2011, at 19:20, diagnostico imagenes wrote: > > > > > > > > > > > Dear Mark, > > > > > > > > > > > > We use the command: > > > > > > 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 > > > > > > > > > > > > It only creates de .txt file inside the shape_analysis folder. An it says "abortado" > > > > > > and the text in the .txt is > > > > > > > > > > > > read model > > > > > > done reading model > > > > > > setting up shape/appearance model > > > > > > The shape has 732 vertices. > > > > > > 336 modes of variation are retained. > > > > > > The model was constructed from 336 training subjects. > > > > > > model loaded > > > > > > read model > > > > > > done reading model > > > > > > setting up shape/appearance model > > > > > > The shape has 732 vertices. > > > > > > 336 modes of variation are retained. > > > > > > The model was constructed from 336 training subjects. > > > > > > 1.12962 0.0220672 0.03358 -4.52313 > > > > > > -0.0133035 1.08221 -0.0541649 8.58251 > > > > > > -0.0318979 0.0605173 1.15819 -16.5332 > > > > > > 0 0 0 1 > > > > > > 1.12962 0.0220672 0.03358 -4.52313 > > > > > > -0.0133035 1.08221 -0.0541649 8.58251 > > > > > > -0.0318979 0.0605173 1.15819 -16.5332 > > > > > > 0 0 0 1 > > > > > > done recon > > > > > > done recon and reg > > > > > > new design matrix > > > > > > 1 0.5 -0.5 > > > > > > 1 -0.5 0.5 > > > > > > evs 1 > > > > > > set hsape Mesh > > > > > > 1 0 0 > > > > > > 0 0 1 > > > > > > do mvglm > > > > > > terminate called after throwing an instance of 'NEWMAT::SingularException' > > > > > > > > > > > > What do you mean by original analyses? > > > > > > > > > > > > Thank you in advance, > > > > > > Best regards, > > > > > > Sabrina > > > > > > > > > > > > > Date: Mon, 6 Jun 2011 21:49:45 +0100 > > > > > > > From: [log in to unmask] > > > > > > > Subject: Re: [FSL] design matrix for vertex analysis > > > > > > > To: [log in to unmask] > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > Can you please send us the exact commands you tried to run > > > > > > > and the exact error messages they gave. > > > > > > > > > > > > > > Also, have you checked that all the original analyses were correct? > > > > > > > > > > > > > > If it creates a log directory, please also look at the contents of > > > > > > > files there too and let us know of any errors. > > > > > > > > > > > > > > All the best, > > > > > > > Mark > > > > > > > > > > > > > > > > > > > > > On 6 Jun 2011, at 20:53, diagnostico imagenes wrote: > > > > > > > > > > > > > > > Thanks Mark, > > > > > > > > I could create the matrix but now I have a new problem. > > > > > > > > When I wrote the command to do the vertex analysis, it starts to run but the it says "abortado". It only creates the txt file inside the shape_analysis directory. > > > > > > > > I created the concatenated bvars using: concat_bvars and then I wrote all the filenames I wanted to concatenate (patients and controls). > > > > > > > > I hope you can help me > > > > > > > > Thanks a lot > > > > > > > > Best regards > > > > > > > > Sabrina > > > > > > > > > > > > > > > > > > > > > > > > > Date: Fri, 3 Jun 2011 21:05:19 +0100 > > > > > > > > > From: [log in to unmask] > > > > > > > > > Subject: Re: [FSL] design matrix for vertex analysis > > > > > > > > > To: [log in to unmask] > > > > > > > > > > > > > > > > > > Dear Sabrina, > > > > > > > > > > > > > > > > > > Open the Glm GUI. > > > > > > > > > Choose the higher-level design. > > > > > > > > > Set the number of inputs to the total number of subjects. > > > > > > > > > Select the Wizard. > > > > > > > > > Choose two groups, unpaired. > > > > > > > > > Set the number of subjects in the first group. > > > > > > > > > Press Process. > > > > > > > > > Check the image looks OK. > > > > > > > > > Go back to the original (small) window. > > > > > > > > > Select Save. > > > > > > > > > Choose the appropriate directory. > > > > > > > > > Type in a filename. > > > > > > > > > > > > > > > > > > And that's it. > > > > > > > > > > > > > > > > > > All the best, > > > > > > > > > Mark > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 3 Jun 2011, at 20:55, diagnostico imagenes wrote: > > > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > I am trying to use the vertex analysis for the hippocampus in FSL-FIRST but I am having problems to generate de design matrix. The manual says that I should use the glm in the FSL program with 1 EV and the matrix should be 0 for one group and 1 for the other. I tried to create the matrix by changing the number of inputs but then I canīt save it. > > > > > > > > > > Can you please give me more detailed instructions to create the matrix??? > > > > > > > > > > Thank you very much in advance, > > > > > > > > > > Best regards, > > > > > > > > > > Sabrina