Hi Kasper,
That needs to be the cross-sectinal name (whenever you also pass a base,
it will automatically create the ..long.. names internally).
cheers, Martin
On 03/11/2016 08:51 AM, Kasper Jessen wrote:
Hi Martin,
Thanks for the answer :-)
To presmooth the data onto target, with the following command:
recon-all -long <tpid> <baseid> -qcache
*
*
The <tpdi>, does that have to be the longitudinal name
(d115a.long.d115_base) or the cross-sectional name (d115a)?
Best wishes
Kasper
2016-03-09 22:38 GMT+01:00 Martin Reuter <mreu...@nmr.mgh.harvard.edu
<mailto:mreu...@nmr.mgh.harvard.edu>>:
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
<mailto: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 <tel:%2B1-617-724-5652>
Web :http://reuter.mit.edu
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto: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.
--
Kasper Jessen,
MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR)
Mental Health Centre Glostrup
Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kaspe...@cnsr.dk <mailto:kaspe...@cnsr.dk> eller
kasper.jes...@regionh.dk <mailto:kasper.jes...@regionh.dk>
_______________________________________________
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.
