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Hi Miao, Yes, the added EV and the new two contrasts are fine (for some reason the numbers are glued together in your email, but I believe they were entered correctly in the GLM GUI). About the error, are you sure that there is a directory called "/Downloads" and even if it exists, you have writting permissions to it? Try instead putting a tilde symbol (~) in front of the output string, like this: randomise -i GM_mod_merg_s3.nii.gz -o ~/Downloads/fsl_vbm/E_assembled -d fsl_vbm.mat -t fsl_vbm.con.txt -n 10000 -D -T It's probably not the cause of an error, but in general there's no .txt extension on these design files. It'd be good to make sure that they look ok inside (i.e., weren't screwed up by some text editor). All the best, Anderson On 1 August 2014 06:32, miao wei <[log in to unmask]> wrote: > Hi Anderson, > Thank you for getting back to me. > I just constructed the .mat and .con files as described above. And I added > another regressor which is one of my cognitive scores. > So I entered all the values for .mat file and the contrast was > C1 1000 > C2-1000 > C3 0001 > C4 000-1 > Where I am interested to test the correlations of the brain volume of each > voxel with the first and last variables. (1. learning rate, 2. age, 3. IQ, > 4. how fast subjct can subject read words) while other non-interested > variables were controlled. Am I right? > > Then I ran > randomise -i GM_mod_merg_s3.nii.gz -o /Downloads/fsl_vbm/E_assembled -d > fsl_vbm.mat -t fsl_vbm.con.txt -n 10000 -D -T > > After running for hours, it now gave me the error message: > > Starting permutation 10000 > > Error: failed to open file /Downloads/fsl_vbm/E_assembled_tstat1.nii.gz > > Image Exception : #22 :: ERROR: Could not open image > /Downloads/fsl_vbm/E_assembled_tstat1 > > ERROR: Program failed > > > An exception has been thrown > > ERROR: Could not open image /Downloads/fsl_vbm/E_assembled_tstat1Trace: > save_basic_volume4D. > > > > Exiting > > > I am not sure what went wrong. When I ls the folder it only has > fsl_vbm.con.txt, not fsl_vbm.con > > Or the problem is that I should have put -c option? I want the cluster > larger than 125 voxels to show on the image. How should I put it? But most > importantly, why this failed? > > > Please suggest. Thanks a lot. > > Miao > > > > 2014-07-31 19:41 GMT-07:00 Anderson M. Winkler <[log in to unmask]>: > > Hi, >> >> Please see below: >> >> >> On 31 July 2014 20:05, Miao Wei <[log in to unmask]> wrote: >> >>> Dear FSL experts, >>> I am doing a structural analysis using FSL and now I am at the step of >>> fslvbm_3_proc >>> It requires me to construct a design.mat and a design.con file. >>> I want to do the correlation between brain volume and a continuous >>> variable （learning rate of a foreign language） >>> and with partialing out the effect of Age and IQ scores on brain volumes. >>> >> >> I understand that by "brain volume" you mean the volume of gray matter on >> each voxel, as assessed through VBM, as opposed to an overall measurement >> of brain volume as a whole, is this right? I'll take from here that this is >> a VBM study. >> >> >> >>> 1.i understand that I need to use glm to get .mat and .con file. How >>> many EVs should I set up? 3 ? >>> >>> Do I just put a column of values of each regressor that I am interested >>> in the glm Gui? EV1 for learning rate, EV 2 for age and EV 3 for IQ. >>> >> >> Yes, exactly. >> >> >>> >>> 2. How about the contrast and F test tab? >>> >> >> It sounds that age and IQ are nuisance variables, and aren't to be >> tested. The contrasts then would be: >> >> C1: 1 0 0 >> C2: -1 0 0 >> >> An F-test isn't needed here (but if you want, you can divide the >> significance level of these tests by 2, that is, consider as significant >> p-values equal or below 0.05/2 = 0.025). >> >> >> 3. I know that there is an -D option to demean the data in the next >>> step- randomise. Should i use -D? >>> >> >> Yes, you definitely want to use the -D option here, because in the model >> you are not including an intercept (i.e., a column full of a constant >> non-zero value, such as 1). >> >> All the best, >> >> Anderson >> >> > > > -- > Miao Wei > Graduate Student, Brain and Cognitive Science > Psychology Department > University of Southern California > 3620 South McClintock Ave, SGM 501 > Los Angeles, CA 90089-1061 > http://lobes.usc.edu/ >