Re: [Freesurfer] error in longitudinal processing "dimension mismatch" - Freesurfer

1 May 2013

      ...
Keith
On Wed, May 1, 2013 at 12:43 PM, Bruce Fischl fischl@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 k5b -all

  recon-all -long kp5 kp5_base -all
  recon-all -long kp5b kp5_base -all

  Keith

  On Wed, May 1, 2013 at 12:15 PM, Bruce Fischl
  <fischl@nmr.mgh.harvard.edu>
  wrote:
        Hi Keith

        what were the recon-all command lines you ran?
        Bruce
        On Wed, 1 May 2013, 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 apreviouspost(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-Jun
  e/024576
        .htm
        l by 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_bas
        e/

label/lh.cortex.label/data/keith/freesurferdata/subjects_longitudinal_5.1_o
        ld/kp5_base/label/lh.
        long.cortex.label

       mris_label_calcintersect/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/k
        p5_base/label/lh.
        long.cortex.label

        LabelWrite:savingto/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/l
  abel/l
        h.
        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/k
        p5b.long.kp5_base
       /surf/lh.thickness--o/data/keith/freesurferdata/subjects_longitudinal_5.1_o
  ld/kp5_base/surf/l
        h.l
  ong.thickness-stack.mgh

  ninputs = 2

  Checking inputs

  nframestot = 2

  Allocing output

  Done allocing

  nframes = 2

Writingto/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/
      surf/lh
      .l
      ong.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_b
      ase/surf/l
      h.l
      ong.thickness-stack.mgh --X
      ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat
      --allow-zero-dof --no-contrasts-ok --surf kp5_baselh--label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/
      la
      bel/lh.
      long.cortex.label --glmdir
      ./tmp-kp5_base_lh_thickness_6PR2rH/glm
  Readingsourcesurface/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_b
  ase/su
  rf/lh.w
  hite

  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

cmdlinemri_glmfit--y/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_b
ase/surf/l
h.l
ong.thickness-stack.mgh --X
./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat
--allow-zero-dof --no-contrasts-ok --surf kp5_baselh--label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/
la
bel/lh.
long.cortex.label --glmdir
./tmp-kp5_base_lh_thickness_6PR2rH/glm
sysname Linux
hostname davissvr1.uhnres.utoronto.ca
machine x86_64
user qwu
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.
l
ong.thickness-stack.mgh
logyflag 0
X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat
usedti 0
labelmask/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/
label/lh.
long.cortex.label
maskinv 0
glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory ./tmp-kp5_base_lh_thickness_6PR2rH/glm
Loadingyfrom/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf
/
lh.l
ong.thickness-stack.mgh
Saving design matrix to
./tmp-kp5_base_lh_thickness_6PR2rH/glm/Xg.dat
Normalized matrix condition is 1
Matrix condition is 10
Found 131455 points in label.
ERROR: mri_reshape: number of elements cannot change
nv1 = 143525, nv1 = 140942
Pruning voxels by thr: 0.000000
Found 134956 voxels in mask
Saving mask to ./tmp-kp5_base_lh_thickness_6PR2rH/glm/mask.mgh
Reshaping mriglm->mask...
ERROR: mri_reshape: number of elements cannot change
nv1 = 140942, nv1 = 143525
search space = 91439.090793
DOF = 0
Starting fit and test
Fit completed in 0.0042 minutes
Computing spatial AR1 on surface
ERROR: MRISar1: Surf/Src dimension mismatch.
ERROR -11 : mri_glmfit did not work?
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