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

2013-05-01 Thread Bruce Fischl 

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 a previous 
post(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/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_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.l
ong.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.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_base/surf/lh.l
ong.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.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

cmdline mri_glmfit 
--y/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.l
ong.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

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

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 
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 
  # 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 FreeSur

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

2013-05-08 Thread Martin Reuter 

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.html 
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_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 ./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


sysname Linux

hostname davissvr1.uhnres.utoronto.ca 



machine x86_64

user qwu

FixVertexAreaFlag

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
wrote:

>  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
> /dat