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ADNI Archive

This page contains all old notes regarding downloading and processing ADNI data.

ADNI Download Notes

Notes on how to download ADNI subject data and incorporate into our local copy, which is found here:

cd /autofs/space/mreuter/ADNI

The main ADNI site is here: http://adni.loni.ucla.edu/

It is necessary to obtain an account with them in order to download data from the LONI site, which is here: https://ida.loni.ucla.edu/login.jsp?project=ADNI


T2/PD data

#\! /bin/tcsh -ef

# the adni root dir
set ADNI=(/autofs/cluster/con_002/users/ADNI)

# the month we're working with (be sure to update this var!!!!!!)
set m=(_m6)

foreach f (`ls *.xml`)

# find out which image type this .xml file describes (PD or T2)
set weighting=(`grep Weighting $f | awk 'BEGIN { FS = "[<>]" } ; {printf $3}'`)

# chop-off .xml extension
set ff=(`basename $f .xml`)

# extract subject name
set subjid=(`echo $ff | awk 'BEGIN { FS = "_" } ; {printf $4}'`)

# extract unique identifier for this file
set uid=(`echo $ff | awk 'BEGIN { FS = "_I" } ; {printf $2}'`)

# convert file, storing into main adni dir
set niifile=(`find | grep "_S_${subjid}" | grep "_I${uid}" | grep "\.nii"`)
set origdir=($ADNI/${subjid}${m}/mri/orig)
if ( -e $origdir) then
    mri_convert $niifile $origdir/${weighting}.mgz
endif

end

cd /autofs/cluster/con_002/users/ADNI
echo "#! /bin/tcsh -ef" > scripts/PD_T2_Month_6_subjs
echo "set SUBJECTS=(\\" >> scripts/PD_T2_Month_6_subjs
foreach s (`ls -d ????_m6`)
  if ( -e $s/mri/orig/PD.mgz) then
    if ( -e $s/mri/orig/T2.mgz) then
      echo $s
      echo "$s \\" >> scripts/PD_T2_Month_6_subjs
    endif
  endif
end
echo ")" >> scripts/PD_T2_Month_6_subjs
echo "echo <dollar>SUBJECTS" >> scripts/PD_T2_Month_6_subjs
echo "" >> scripts/PD_T2_Month_6_subjs
echo "echo <dollar>#SUBJECTS month_6 subjects with PD and T2 scans" >> scripts/PD_T2_Month_6_subjs


ADNI data was previously stored here:

cd /autofs/cluster/con_002/users/ADNI

AdniArchive (last edited 2021-05-03 08:49:59 by DevaniCordero)