Hi Kasper,
short answer: yes.
long answer
1. yes
2. yes (you need to create a table in cross sectional format (no
fsid-base column) and the fsid needs to be the tp.long.base names for
baseline visit. the path should point to where these *.long.*
directories are located).
2. yes (fsaverage should be linked there anyway, right?)
3. yes
;-) Martin
On 03/09/2016 03:42 PM, Kasper Jessen wrote:
Dear FreeSurfer experts,
We have a longitudinal study design with up to 5 time points. However,
we both want to do a baseline cross-sectional analysis and later a
longitudinal analysis. All subjects have been run through the
longitudinal pipeline (only the base was edited). We want to start
analysing baseline cross-sectionally using QDEC. I have read through
the wiki guides but would like to make sure that we are doing it
correctly. We have done/plan to do the following:
1. The [CROSS], edited [BASE] and [LONG] is processed.
2. We will create a qdec table called qdec.table.dat. However, because
we want to use the improved longitudinal runs [LONG] (i.e., because
the [BASE] has been edited] the first column in the QDEC table (i.e.,
fsid) has been changed to include the longitudinal names (please see
below). In addition, we have included the line /SUBJECTS_DIR
/my/path/to/subject/data/ to let FreeSurfer know that it is the
longitudinal directories that should be used (is this the correct why
to let FreeSurfer know that it is the "longitudinal runs" which should
be used?).
SUBJECTS_DIR /my/path/to/subject/data
fsid Gender Group Age
d115a.long.d115_base 1 1 19
d120a.long.d120_base 0 1 22
...
2. We transfer the default fsaverage to the subject directory.
3. To presmooth the data onto the target we run the following command:
*recon-all -long <tpid> <baseid> -qcache*
*
*
When the above steps are done we plan to load it into QDEC.
*
*
Is the above steps correct for doing a cross-sectional group analysis
in QDEC?
Best regards,
Kasper Jessen
MD, PhD student
*
*
*
*
*
*
*
*
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
