Dear all,
I created an average subject from my dataset and I would like to use it to run
a group analysis of thickness. I am using the command:
recon-all -s subjid -qcache -target MyAverage
When looking at the terminal, I noticed that the srcsurfreg and the trgsurfreg
are both sphere.reg: shouldn
Dear Bruce
Thanks a lot
Cheers
Jürgen
---
-
Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
Hi Doug,
coming back to this once more. I am thinking that I can bypass
mkcontrast-sess entirely if I provide a contrast matrix that has
ContrastMtx_0 and WCond set to the contrast that I am interested in.
For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous
predictor and agains
I don't know whether that will work or not. If it runs, you can compare
the result to computing the contrast manually to see if there is a
difference. If there is no difference, then it works.
On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> coming back to this once more. I am t
Hi freesurfers,
I've been stuck on this problem for a while and couldn't find anything
online to help me out so I've come to the mailing list as my last resort.
I am trying to unpack my functional data into fsl format using the
unpacksdcmdir command. However, I am not successful using this comma
Are these Siemens dicoms? If not, try dcmunpack
doug
On 11/13/2014 01:06 PM, Shady El Damaty wrote:
> Hi freesurfers,
>
> I've been stuck on this problem for a while and couldn't find anything
> online to help me out so I've come to the mailing list as my last resort.
>
> I am trying to unpack m
Hi,
Sorry if this is the wrong place to put this - never used a mailing list
before - but I've been watching the FreeSurfer lectures on Youtube. The
link to download the slides in the Introduction Lecture (
https://www.youtube.com/watch?v=GywOKtfKZIU ) the only one I've watched so
far is broken. I
Hi FS Experts,
I am interested in doing a group analysis between different cohorts using
the white matter volume as the variable of interest. Would the best way to
do that be to follow the group analysis pipeline described in the wiki for
cortical thickness (but replace the --meas thickness with -
Hi all,
I have structural data that has a slice thickness of 5mm and spacing
between slices of 5mm (there are around 30 dicom images). I ran it through
recon-all but the output was bad. Is it possible to create surfaces from
such data? Or is the bad output the answer to this question...
Thanks,
W
Hi Doug,
so I made contrast matrices and stored them in mystudy, and then ran
selxavg3-sess per subject.
I defined three different contrasts (in three mat files), but selxacg3-sess
only gives me one analysis, it seems to be an F-test.
When I do isxconcat-sess after that, I get six ces files per ana
ok, so the issue is in fast_ldanaflac.m, around line 520:
flac.con(nthcon).ContrastMtx_0=[];
that effectively ignores the contrasts that are set up in mystudy.
caspar
2014-11-13 17:33 GMT-05:00 Caspar M. Schwiedrzik :
> Hi Doug,
> so I made contrast matrices and stored them in mystudy, and then r
Hi Will
not with 10mm spacing I don't think. Sorry. The aseg will probably still
give you something sensible.
cheers
Bruce
On Fri, 14 Nov 2014, will brown wrote:
> Hi all,
> I have structural data that has a slice thickness of 5mm and spacing between
> slices
> of 5mm (there are around 30 dico
Hi Anastasia,
I was wondering if there is a flag in the tractstats2table function that
extracts all the variables in the dwi_motion.txt file for all subjects and put
them into a single spreadsheet. Thanks!
Best,
Yoon
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