Re: [Freesurfer] error in longitudinal processing dimension mismatch

2013-05-21 Thread Qi Wu 
Dear Martin,

Thank you for your helpful information. You were right that something had
gone wrong with my preprocessing (for some unknown reasons). I re-run the
preprocessing and was able to get the long_mris_slopes command
up-and-running.

Keith


On Wed, May 8, 2013 at 4:28 PM, Martin Reuter
mreu...@nmr.mgh.harvard.eduwrote:

  Hi Keith,

 your longitudinal qdec file looks OK. Something must have gone wrong
 before (in the processing, e.g. maybe the base was reprocessed and the
 longs were not updated or things were renamed?)

 I would create a new directory with only this subject, then start from
 scratch. create both cross (kp5 and kp5b), the base (kp5_base) and both
 longs with the correct naming . Then check if the long_mris_slopes command
 still fails.

 Best, Martin


 On 05/01/2013 12:11 PM, Qi Wu wrote:

 Dear Freesurfer experts,

 I have a dataset of 2 time points. I ran into problems when I tried to use
 the two-stage approach to pull out statistics such as the rate of change in
 Freesurfer 5.1.

 I could not even get the first stage working. The error messages I got
 were “ERROR: MRISar1: Surf/Src dimension mismatch” “ERROR -11 : mri_glmfit
 did not work?”

 I did further trouble-shooting for this particular message nv1 = 140942,
 nv1 = 143525, and I found out that 143525 was in the base folder
 (kp5_base), and 140942 was for the two longitudinally registered images
 (kp5.long.kp5_base, and kp5b.long.kp5_base).

 The command line I used was : “long_mris_slopes --qdec
 ./qdec/AS_long_qdec.dat --meas thickness --hemi lh --do-avg --do-rate
 --do-pc1 --do-spc --do-stack --do-label --time weeks –nosmooth”.

 The first three lines in the qdec file:

 “fsid fsid-base weeks age sex FSS avgPain

 kp5 kp5_base 0 48 0 4.1 7

 kp5b kp5_base 20 48 0 8.6 6”

 This error was similar to what was in a previous post (
 https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024576.htmlby 
 joost janssen Jun 29, 2012). I tried to fix any similar problems, but
 still wasn’t able to get it working.

 What else could I have been doing wrong?

 The on screen error output is provided as follows

 Many thanks

 Keith

 Postdoctoral fellow
 Toronto Western Hospital
 Toronto, Ontario
 Canada

 ***

 Parsing the qdec table: ./qdec/AS_long_qdec.dat

 Working in SUBJECTS_DIR:
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old

 Subject-Template: kp5_base

 INFO: 2 TPs in kp5_base , mean age: 10.0

 ===


 SUBJECT kp5_base Intersecting Within-Subject Cortex Label

 cp
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/label/lh.cortex.label
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label


 mris_label_calc intersect
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/label/lh.cortex.label
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label


 LabelWrite: saving to
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label

 ===


 SUBJECT kp5_base Stackinbg Within-Subject Maps

 mri_concat
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/surf/lh.thickness
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/surf/lh.thickness
 --o
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh

 ninputs = 2

 Checking inputs

 nframestot = 2

 Allocing output

 Done allocing

 nframes = 2

 Writing to
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh

 ===


 SUBJECT kp5_base Running Within-Subject GLM

 Writing ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat ...

 mri_glmfit --y
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
 --X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof
 --no-contrasts-ok --surf kp5_base lh --label
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
 --glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm

 Reading source surface
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.white

 Number of vertices 143525

 Number of faces 287046

 Total area 91438.851562

 AvgVtxArea 0.637094

 AvgVtxDist 0.873064

 StdVtxDist 0.245806

 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $

 cwd /data/keith/freesurferdata/subjects_longitudinal_5.1_old

 cmdline mri_glmfit --y
 /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
 --X

Re: [Freesurfer] error in longitudinal processing dimension mismatch

2013-05-01 Thread Bruce Fischl 


Keith


On Wed, May 1, 2013 at 12:43 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
  Hi Keith

  can you cc the list so that others can answer? Like Martin!

  thanks
  Bruce
  On Wed, 1 May 2013, Qi Wu wrote:

  Hi Bruce,
  Thank you so much for your quick reply.

  I used the following script to do the first step
  cross-sectional
  preprossessing

  #!/bin/tcsh -ef
  # add 'x' to '-ef' to trace code as it is executed

  # GO_FS1 - The Easy button #
  # Usage: GO_FS-123 subjects directory name
  # Feeds multiple subjects into autorecon1, autorecon2,
  and autorecon3
  # Requires that original scan data be placed in
  $SUBJECTS_DIR/_orig_
  # (Place each subject's anat series in separate
  folders)


  echo \n  GO FreeSurfer!
   \n

  ### Check if subjects directory specified ###
  if ( $1 !=  ) then
    set subjdir = $1
  else
    echo \n ERROR: No subjects directory specified \n
    exit 1
  endif

  ### Set FREESURFER_HOME and SUBJECTS_DIR ###

  setenv FREESURFER_HOME /usr/local/freesurfer5.1

  if ( -e
  /data/keith/freesurferdata/subjects_longitudinal/$subjdir)
  then
    setenv SUBJECTS_DIR
  /data/keith/freesurferdata/subjects_longitudinal/$subjdir
  else
    echo \n ERROR: Specified subjects directory does not
  exist \n
    exit 1
  endif

  ### Check if original scan data exists ###

  if ( ! -e /$SUBJECTS_DIR/_orig_ ) then
    echo \n ERROR: Original scan data not found. \n
    exit 1
  endif

  ### disable functional tools ###

  setenv NO_FSFAST

  # (To enable functional tools, disable the above line,
  enable the
  following:)
  # (HAVE NOT TESTED THIS YET) (MAYBE BETTER IF
  NO_FSFAST ANYWAYS)
  #setenv FUNCTIONALS_DIR $FREESURFER_HOME/sessions
  # echo FUNCTIONALS_DIR = $FUNCTIONALS_DIR
  # (and add the following to ~/matlab/startup.m)
  #fsfasthome = getenv('FSFAST_HOME');
  #fsfasttoolbox = sprintf('%s/toolbox',fsfasthome');
  #path(path,fsfasttoolbox);

  ### Set up FreeSurfer ###

  setenv prompt
  source $FREESURFER_HOME/FreeSurferEnv.csh
  echo 


  ### List out directories in _orig_ , set subj array,
  prompt to continue ###

  echo Found the following subjects: \n

  set i = 0
  set subjID

  foreach d ($SUBJECTS_DIR/_orig_/*)
    @ i++
    set subjID = ($subjID $d:t)
    echo    Subject $i:  $subjID[$i]
  end
  set subjCount = $i

  set response
  while ($response != n  $response != y)
    echo -n \n Process these $subjCount subjects? [y/n]  
    set response = $
  end
  if ($response == n) then
    echo \n Program ended by user \n
    exit 1
  endif


  ### Prompt user for First Anat Filename's ### 

  set firstAnatSame
  while ($firstAnatSame != y  $firstAnatSame != n)
    echo -n \n Are all the anat series named identically?
  [y/n]:  
    set firstAnatSame = $
  end
  switch ($firstAnatSame)
    case [y]:
      echo -n \n Please enter the first filename (e.g.
  p1_000.dcm) for all
  anat series:  
      set firstAnat = $
      breaksw
    case [n]:
      echo \n Please enter the first filename (e.g.
  p1_000.dcm) in the anat
  series for:
      set i = 0
      set firstAnat
      while ($i  $subjCount)
        @ i++
        echo -n     $subjID[$i]:  
        set firstAnat = ($firstAnat $)
      end
      breaksw
  endsw


  ### Run autorecon1 for each subject ###

  cd $SUBJECTS_DIR

  switch ($firstAnatSame)
    case [y]:
      set i = 0
      while ($i  $subjCount)
        @ i++
      echo \n| NOW PROCESSING
  $subjID[$i]
  |\n
        recon-all -i
  $SUBJECTS_DIR/_orig_/$subjID[$i]/$firstAnat -all -s
  $subjID[$i]
      end
      breaksw
    case [n]:
      set i = 0
      while ($i  $subjCount)
        @ i++
      echo \n| NOW PROCESSING
  $subjID[$i]
  |\n
        recon-all -i
  $SUBJECTS_DIR/_orig_/$subjID[$i]/$firstAnat[$i] -all -s
  $subjID[$i]
      end
      breaksw
  endsw


  echo 
  date +Finished $0 without error at %T on %a %b %d %Y
  echo 
  exit 0

  ###
  ### Simple working loop
  #set i = 0
  #while ($i  10)
  # echo $i
  # @ i++
  #end
  ###

  #
  ### TO DO ###
  #
  # why don't env's remain 'set' after running this? (they
  do after running
  SetUpFreeSurfer.csh or FreeSurferEnv.csh)
  # why can't FS_FAST be set up?


  Then I did the base step and the long step with the
  following 

  recon-all -base kp5_base -tp kp5 -tp