Why don't you just create a fake directory structure. Should be pretty
easy to script (if you know how to script:)
On 1/15/18 3:44 AM, Stephanos Leandrou wrote:
Dear Freesurfer Developers,
I want to use the asegstats2table and aparcstats2table for my
research. First of all, my subjects (several hundreds) are not in the
Freesurfer/Subjects directory and for each one I have run the
recon-all command.
For the asegstats2table command we know that the subjects list can be
specified in one of four ways:
1. Specify each subject after -s
* -s subject1 -s subject2 ..
2. specify all subjects after --subjects.
* --subjects does not have to be the last argument. Eg:
o --subjects subject1 subject2 ...
3. Specify each input file after -i
* -i subject1/stats/aseg.stats -i subject2/stat/aseg.stats ..
4. Specify all the input stat files after --inputs. --inputs does not
have
* to be the last argument. Eg:
o --inputs subject1/stats/aseg.stats
subject2/stats/aseg.stats ...
The first two methods assume the freesurfer directory structure.
The last two are general and can be used with any file produced
by mri_segstats regardless of whether it was created with recon-all or
not…..
According to 3 and 4 by changing –subjects to –i I was able to run the
asegstats2table command for my subjects that are not in the Freesurfer
directory structure with success.
However, (and here comes my question) I cannot do the same for the
aparcstats2table because there is no option (if I am not mistaken) to
run the command for subjects outside the Freesurfer directory
structure? In the aparcstats2table webpage mentions that the subjects
list can be specified on either of two ways:
1. Specify each subject after a -s flag
* -s subject1 -s subject2 ... --hemi lh
2. Specify all subjects after --subjects flag. --subjects does not have
* to be the last argument. Eg:
o --subject subject1 subject2 ... --hemi lh
However, when I run the command (in the path of my subjects directory
where the stats folder is) it comes with an error which says that it
cannot find the stats file in the Freesurfer/directory which is
expected…as my subjects are not in that directory.
Thank you for your help !!
Stephanos
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