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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