Hi Kasper,
because that is the way it is designed. Whenever recon-all runs on
longitudinal data, it needs to know where the cross and base are (just
in case that this info is needed somewhere). So the correct call is the
one with the -long telling it that this is a longituidnal run (and not
just a cross sectional run that happens to have "long" in the name).
Best, Martin
On 03/29/2016 05:58 AM, Kasper Jessen wrote:
Hi Martin,
When doing cross-sectional analysis on a longitudinal data set and the
qdec table is ordered as followed:
fsid Gender Group Age
d115a.long.d115_base 1 1 19
d120a.long.d120_base 0 1 22
Why does the presmoothing not have to be:
recon-all -s d115a.long.d115_base -qcache
recon-all -s d120a.long.d120_base -qcache
instead of
recon-all -long d115a d115_base -qcache
recon-all -long d120a d120_base -qcache
Cheers,
Kasper
2016-03-11 17:52 GMT+01:00 Martin Reuter <mreu...@nmr.mgh.harvard.edu
<mailto:mreu...@nmr.mgh.harvard.edu>>:
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
*
*
*
*
*
*
*
*
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--
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
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Phone:+1-617-724-5652 <tel:%2B1-617-724-5652>
Web :http://reuter.mit.edu
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The information in this e-mail is intended only for the
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error and the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
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but does not contain patient information, please contact the
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--
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
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-- 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
_______________________________________________
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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.
