In that case, you can just do a paired analysis. Do a search for that on
the wiki and you'll find examples
doug
On 3/21/14 5:50 PM, Peggy Skelly wrote:
The actual time between tp1 & tp2 varies for subjects, *but* every
subject received the same "dose" of treatment between timepoints. To
ask
The actual time between tp1 & tp2 varies for subjects, *but* every subject
received the same "dose" of treatment between timepoints. To ask if the
treatment changed a subject's cortical thickness, I'm not using the actual
time difference, I'm using a constant 1 for the time difference. (i.e. in
lon
Is the time between tp1 and tp2 the same for all subjects? If not, are
you using that information?
On 03/21/2014 04:15 PM, Peggy Skelly wrote:
> The overall question is: did the cortical thickness of healthy
> hemispheres (of stroke subjects) change from tp1 to tp2, and does it
> correlate wit
The overall question is: did the cortical thickness of healthy hemispheres
(of stroke subjects) change from tp1 to tp2, and does it correlate with the
change in their functional measure? So I was using the long.thickness-rate
measure and qdec.
Peggy
On Fri, Mar 21, 2014 at 1:38 PM, Douglas N Gre
mri_label2label needs to be called with --surfreg fsaverage_sym.sphere.reg
Martin, can you modify long_mris_slopes to add this?
But another question is exactly what you want to do in the end. What
function of the slopes and hemisphere are you trying to compute?
doug
On 03/21/2014 01:20 PM, P
I tried your suggestion (using subjTP/xhemi in place of subjTP) in the qdec
table. I doesn't work because long_mris_slopes uses subjTP and subjBase to
create "subjTP.long.subjBase", the directory of the actual data. Extra
slashes "/" in the name create an incorrect name (i.e.
subjTP/xhemi.long.subj
I'm not sure this will work but try entering the subjectids in the qdec
table as subjectTP and subjectTP/xhemi and use subject as the base (TP
is just a shorthand for time point, use whatever you used)
doug
On 03/17/2014 01:09 PM, Peggy Skelly wrote:
> The patch works! Thank you.
>
> Now, to co
The patch works! Thank you.
Now, to compute the longitudinal measures: I don't see 'long_mris_slopes
--help' mentioning xhemi, so I suppose
it won't be able to find the flipped subjects. Is there a way to
copy/rename the /xhemi/ directory
to $SUBJECTS_DIR so I could run long_mris_slopes?
Peggy
Thanks -- (I thought I might not have understood the processing pipeline
properly.)
I'm running 5.3, I'll try the patch and let you know how it works.
Peggy
On 3/14/14, 16:07 , Douglas N Greve wrote:
> Actually, I don't think this will work. What version of FS are you running?
>
> I've created
Actually, I don't think this will work. What version of FS are you running?
I've created a patch of the 5.3 recon-all here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!)
then re-run
doug
O
You have uncovered a bug. I don't think anyone has tried to run xhemi on
a longitudinal data set before. There is a work-around. First run
xhemireg --s subject --no-tal
Then run
surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
I think this should work
doug
On 03/14/2014
Hi All,
Although the question of flipping hemispheres has come up before, I
still struggling with it.
I'm working on a longitudinal study with stroke subjects (half with lh
lesions, half with rh lesions). We want to compare only the
non-lesioned, healthy, hemispheres at 2 timepoints (pre- and
Hi Irene,
sorry, but you should probably reprocess them
Bruce
On Wed, 20 Apr 2011, Irene
Altarelli wrote:
> Dear Fs experts,
>
> I've been processing a whole group of subjects, manually correcting the
> surfaces, and I just noticed that a small part of that sample was badly
> oriented (right-le
Dear Fs experts,
I've been processing a whole group of subjects, manually correcting the
surfaces, and I just noticed that a small part of that sample was badly
oriented (right-left).
Should I flip the initial images and reprocess/recorrect them...? Would
the result of mris_reverse be as good?
T
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