[MINC-users] calculating r-squared values
Jared Rowley
jared.rowley at gmail.com
Mon Jun 11 10:25:12 EDT 2012
Hi Jason,
Everything appeared to work however I'm a little unclear how to save the
data now. (It does take a very long time to run).
Here is my code. The last line was my attempt to save the data:
gf1 <- read.csv("dti_nvm_gd.csv")
> fff <- function(x) { return(summary(lm(x ~ score, gf1))$r.squared) }
> mincApply(gf1$FA, quote(fff(x)))
Number of volumes: 91
Volume sizes: 193 229 193
In slice
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58
59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77
78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96
97 98 99 100 101 102 103 104 105 106 107 108 109 110 111
112 113 114 115 116 117 118 119 120 121 122 123 124 125 126
127 128 129 130 131 132 133 134 135 136 137 138 139 140 141
142 143 144 145 146 147 148 149 150 151 152 153 154 155 156
157 158 159 160 161 162 163 164 165 166 167 168 169 170 171
172 173 174 175 176 177 178 179 180 181 182 183 184 185 186
187 188 189 190 191 192
Done
> mincWriteVolume(fff,"rsquared_test.mnc", "score")
Error in minc.dimensions.sizes(like.filename) :
Error opening input file: score.
Thanks again,
Jared
On Fri, Jun 8, 2012 at 12:39 PM, Jason Lerch <jason at phenogenomics.ca> wrote:
> Try replacing FA with x - mincApply assigns the current voxel to the
> variable x in its loop. I.e.:
>
> library(RMINC)
> gf1 <- read.csv("dti_gd.csv")
> fff <- function(x) { return(summary(lm(x ~ score, gf1))$r.squared) }
> mincApply(gf1$FA, quote(fff(x)))
>
> Jason
>
> On 2012-06-08, at 11:32 AM, Jared Rowley wrote:
>
> > Hi Jason,
> >
> > Thanks for the response.
> >
> > I did the following and got an error do you have any suggestions:
> >
> > rm(list=ls(all=TRUE))
> >> library(RMINC)
> >> gf1 <- read.csv("dti_gd.csv")
> >> fff <- function(x) { return(summary(lm(FA ~ score, gf1))$r.squared) }
> >> mincApply(gf1$FA, quote(fff(x)))
> > Number of volumes: 91
> > Volume sizes: 193 229 193
> > In slice
> > 0 Error in storage.mode(y) <- "double" :
> > invalid to change the storage mode of a factor
> > In addition: Warning message:
> > In model.response(mf, "numeric") :
> > using type="numeric" with a factor response will be ignored
> >
> > FA is a column of minc files and score is a column of integers I want to
> > correlate with FA.
> >
> > Thanks very much,
> >
> > Jared
> >
> >
> > On Wed, Jun 6, 2012 at 1:35 PM, Jason Lerch <jason at phenogenomics.ca>
> wrote:
> >
> >> This should work, though is going to be slow:
> >>
> >> fff <- function(x) { return(summary(lm(x ~ genotype, gf))$r.squared) }
> >>
> >> mincApply(filenames, quote(fff(x)))
> >>
> >> Note: replace the formula in that function with the appropriate formula
> >> for your purposes, and filenames should be a vector of your filenames.
> >> Could be worth specifying a mask, as this will run for a few hours.
> >>
> >> And I haven't actually tested it, so it might not run at all!
> >>
> >> Jason
> >>
> >> On 2012-06-05, at 4:18 PM, Jared Rowley wrote:
> >>
> >>> Hi Minc Users,
> >>>
> >>> I was wondering if anyone knows a way calculate R-squared values on a
> >> voxel
> >>> level from a linear regression.
> >>>
> >>> I assume there is a way with either glim_image or RMINC however reading
> >>> though the documentation I could not find a solution.
> >>>
> >>> Thanks very much,
> >>>
> >>> Jared
> >>> _______________________________________________
> >>> MINC-users at bic.mni.mcgill.ca
> >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > Jared Rowley
> > Translational Neuroimaging Laboratory
> > McGill Centre for Studies in Aging
> > Douglas Hospital Research Center
> > McGill University
> > 6825 LaSalle Blvd.
> > Montreal, QC Canada
> > H4H 1R3
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
--
Jared Rowley
Translational Neuroimaging Laboratory
McGill Centre for Studies in Aging
Douglas Hospital Research Center
McGill University
6825 LaSalle Blvd.
Montreal, QC Canada
H4H 1R3
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