Re: [Freesurfer] qdec analysis sequence

Are you using tcsh/csh as your shell? Also you type the foreach line and hit return. It will prompt you for commands, a separate one on each line, when you're done with the commands, type "end" and hit return

foreach list.txt `cat list.txt` echo $list.txt recon-all -s $list.txt -qcache -fwhm 10 end

On 06/20/2012 02:57 PM, mdkruepke@uwalumni.com wrote:

Kushal -

This helps immensely! Just have to get this working now

So my understanding is that after setting my subject dir in terminal, and creating a txt file with the list of my subject id numbers (list.txt) i would type into terminal

foreach list.txt `cat list.txt` echo $list.txt recon-all -s $list.txt -qcache -fwhm 10 end

however i keep getting an error saying that "foreach" cannot be found as a command.

michael

On Wed, Jun 20, 2012 at 12:54 PM, Kushal Kapse <kkapse@mail.med.upenn.edu mailto:kkapse@mail.med.upenn.edu> wrote:

for multiple subjects to run for -qcache, i wud suggest use this

http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/Two

substitute "-all" with "-qcache"......you can also pick specific
measure and fwhm if you dont want all others to be ran.....

hope this helps


kk

----- Original Message -----
From: mdkruepke@uwalumni.com <mailto:mdkruepke@uwalumni.com>
To: "Douglas N Greve" <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Sent: Wednesday, June 20, 2012 1:43:28 PM
Subject: Re: [Freesurfer] qdec analysis sequence


Perfect that should make things a bit easier on me, also according
to this post


http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12406.html


it is not possible to run multiple subjects with this set up
(recon-all -s (subjectid) -qcache -fwhm 10, however this was from
2009, so not sure if this is true still, but i am getting an error
when trying to run multiple subjects.


michael




On Wed, Jun 20, 2012 at 11:02 AM, Douglas N Greve <
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > wrote:


Hi Jenny, Martin will be the best person to answer your question.
Unfortunately, he is in China now. I think he's back next week.
doug



On 06/20/2012 01:37 AM, Jenny Liu wrote:
> Hello,
>
> I am attempting to use the Qdec Analysis for longitudinal data.
> Specifically, each subject has two timepoints, and belongs to one of
> two groups. Each subject has an accompanying age and
> painUnpleasantness rating. I do not have a 'time in years' variable,
> and instead listed the timepoint as baseline = 0, and post=1.
>
> Thus far, what is done is the PREPROCESSING (listed below as
step #3).
> Thus, every subject has a directory labeled
> "WB101_1.long.WB101_template", and another labeled "WB101_template".
>
> I am on the POSTPROCESSING (listed as step #4). I would like to
> confirm that this is the correct sequence of events to use the Qdec
> Analysis tool to do a mixed linear effects models analysis or mixed
> ANOVA analysis.
>
>
> #1. INITIALIZATION
>
> freesurfer
> tksurfer 005 brainmask.mgz
>
>
> #2. SET SUBJECT DIRECTORY
>
> export
SUBJECTS_DIR=/study/NCCAM/Data/MRI/processed/structural/freesurfer
> cd /study/NCCAM/Data/MRI/processed/structural/freesurfer/
>
>
> #3. PREPROCESSING LONGITUDINAL
>
> recon-all -base ${subject}_template -tp ${subject}_1 -tp
${subject}_2 -all
> recon-all -long ${subject}_1 ${subject}_template -all
> recon-all -long ${subject}_2 ${subject}_template -all
> #4. POSTPROCESSING LONGITUDINAL BY CREATING QDEC TABLE
> #Example file named: long.qdec.table.dat
>
> fsidfsid-basegroupagepainUnptp
> WB101_1WB101_templateMNP65.7211.7 0
> WB401_1WB401_templateLTM5911.6 0
> WB101_2WB101_templateMNP65.728.6 1
> WB401_2WB401_templateLTM59 1


>
>
> #5. OPEN QDEC TABLE
>
> gedit qdec/long.qdec.table.dat
>
>
> #6. CREATE a qdec/measures.Qdecrc file in the qdec directory that
> contains the following line, so that the QDEC analysi know about new
> files.
> #Example file named: measures.Qdecrc
>
> MEASURE1 = long.thickness-avg
> MEASURE2 = long.thickness-rate
> MEASURE3 = long.thickness-pc1
> MEASURE4 = long.thickness-spc
>
>
> #7. CREATE file for each discrete (categorical) factor
> #Example file named: group.levels
>
> MNP
> LTM
>
>
> #8. Pre-smooth fsaverage surfaces
> #Qdec needs each subject to have pre-computed smoothed data for the
> target surface (fsaverage is the default) for each measure
(thickness,
> sulc, area, curv, etc.). Your SUBJECTS_DIR should contain either a
> link or a copy of the 'fsaverage' subject found in your
> $FREESURFER_HOME/subjects directory. Presmoothing the data onto the
> target surface is not part of the normal recon processing
stream, but
> you can easily create this data with recon-all, using the command:
>
> recon-all -s <subject> -qcache
>
>
> #9. Shrink qdec table from a longitudinal form to a cross sectional
> form, in order to run the QDEC group analysis.
>
> long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out
> ./qdec/cross.qdec.table.dat
>
>
> #10. PREPARE DATA QCACHE
>
> long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
> --time tp --qcache fsaverage
>
>
> #11. Open pial surface of left hemi on average subject. Open
> symmetrized percent change.
> #--qcache flag of long_mris_slopes has been registered and
mapped all
> results to the average subject
>
> tksurfer fsaverage lh pial -overlay
>
$SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh
-aparc
>
>
> #12. Run the QDEC analysis on the qdec table:
>
> qdec --table ./qdec/cross.qdec.table.dat
>
>
> #13. Use GUI as indicated by
>
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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--
Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign
BA - Psych - University of Wisconsin-Madison
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The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

-- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke@gmail.com mailto:mdkruepke@gmail.com (262)-483-7449

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