Hi Janosch,
there is no fixed naming convention for subjectids from our side, only
recommendations. If you like you can call the first time point of
subject1 'mike' and the second time point of the same subject 'peter' ,
we don't care, but it would be confusing.
We recommend a convention where you have
subjectid_tp1
subjectid_tp2
or
subjectid01
...
or
subjectidA
subjectidB
etc.
that makes things easier, but is not necessary.
For cross sectional processing you can place these wherever you want and
process a subject_tp at a time in a different location if you like. For
longitudinal processing you need to create a single directory where all
of these are symlinked (we only need read access). You can do this on a
per-subject-basis or for all subjects which is often simpler. The -base
run then creates additional directories that may look like
subjectid
or
subjectid_base
or
subjectid_template
(depending on how you name it).
The -long runs finally create additional directories that look like
subjectid_tp1.base.subjectid
(or ...base.subjectid_tempalte again depending on how you named the base).
If you want (for further postprocessing scripts) you can create a
different directory structure similar to what you did for the cross
sectional runs and symlinking the *.long.* into that structure, but any
processing needs to be done in the single directory that has all time
points and base and long runs.
Hope that helps,
Best, Martin
On 01/15/2014 01:40 PM, Bruce Fischl wrote:
I'll leave this for Martin
Bruce
On Wed, 15 Jan 2014, Janosch Linkersdörfer wrote:
Hi Bruce,
thank you very much for your answer!
Am 15.01.2014 um 14:33 schrieb Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Janosch
it will certainly make your life easier if you don't change the names.
So the subject names are saved in other places/files than the folder
name?
Symlinking is fine if you keep the same name, but particularly for
the longitudinal runs the names have meaning and are stored in files
like the tps one which stores the timepoints that went into the base.
OK, so if I understand you correctly, the folder structure for the
initial processing does not matter as I can collect different
subjects from different places in one $SUBJECTS_DIR for doing
(cross-sectional or longitudinal) stats by either copying or
symlinking their subject folders.
But the name of the symlink has to be the same as the one used in the
initial processing, so I would have to include the time point in the
subject name even in the initial processing?
BTW, does one have to use your naming scheme, i.e., "tp1SUBJECTID" or
is this flexible, e.g., "tp0_SUBJECTID", "SUBJECTID_tp1",
"2011__SUBJECTID", etc.?
Thanks a lot,
Janosch
cheers
Bruce
On Wed, 15 Jan 2014, Janosch Linkersdörfer wrote:
Hi,
sorry if my question was to basic, but I would really appreciate if
somebody could give me some insight into whether the folder
organization and the subject name used in the first run of
recon-all have to be stable over all all following processing steps
or if one can, e.g., change the names of the subject folders and/or
symlink them to another location (with another name) and continue
with further processing.
Thanks,
Janosch
Am 13.01.2014 um 13:34 schrieb Janosch Linkersdörfer
<notes4ja...@googlemail.com>:
Hi all,
I have 4 years of structural scans from children and 2 from
adults. I would like to analyze the data both cross-sectionally
and longitudinally. In the recommendations for the longitudinal
analysis, it says one should process all images in one folder with
the time point in the subjectID/subject folder, e.g.,
.../data/tp1_subj001
.../data/tp2_subj001
.../data/tp3_subj001
.../data/tp4_subj001
.../data/tp1_subj002
...
For the cross-sectional analyses, I would like to organize the
analyses in folders for subject age and year, e.g.,
.../data/children/tp1/subj001
.../data/children/tp1/subj002
.../data/children/tp2/subj001
.../data/children/tp2/subj002
...
.../data/adults/tp1/adult_subj001
.../data/adults/tp1/adult_subj002
.../data/adults/tp2/adult_subj001
.../data/adults/tp2/adult_subj001
Is it possible to organize the data this way and to symlink the
individual folders into another folder for the longitudinal
analysis, i.e.,
.../longitudinal_analysis/tp1_subj001 ->
.../data/children/tp1/subj001
.../longitudinal_analysis/tp2_subj001 ->
.../data/children/tp2/subj001
...
Additionally, are there any considerations regarding
renaming/moving subject folders (as long as anything inside a
subject folder remains unchanged), i.e. are there any hard links
or similar that would break further processing?
Thanks a lot!
Janosch
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--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
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reu...@mit.edu
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
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