1- if u want fwhm=10mm just across thickness, include the flag -measure thickness, this saves lot of time, unless you prefer to do across all measures
2- this is how i made command line for my multiple subject "-qcache"
for i in `cat list.txt`; do echo $i; recon-all -s $i -qcache -measure thickness -fwhm 10; done
hope this helps
kk ----- Original Message ----- From: mdkruepke@uwalumni.com To: "Kushal Kapse" kkapse@mail.med.upenn.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 20, 2012 2:57:30 PM Subject: Re: [Freesurfer] qdec analysis sequence
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 > 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 To: "Douglas N Greve" < greve@nmr.mgh.harvard.edu > Cc: "freesurfer" < 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 > 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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