Using aparcstats2table program in Freesurfer to extract the stats data for multiple subjects

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1

Hi all
I’m trying to extract the statical data for multiple subjects using the aparcstats2table program in freesurfer.
I used this command to extract the statical data for one subject.

aparcstats2table --subjects /fefs1/fcit/ezahamalyoubi/freesurfer/subjects/MCI_Female_Subjects/I4688/ --hemi lh --meas volume --parc=aparc --tablefile=I4688_lh_volume.txt

how can I edit this command to work for many subjects and store the statical data in one txt file?

Any clarification will help

-Esraa

2

Hi Esraa,

The --subjects argument of the command can take multiple subjects, delimited by spaces, e.g. --subject SUB01 SUB02...

As long as your Freesurfer subjects directory is pointed to your Freesurfer outputs (e.g. setenv SUBJECTS_DIR (full path to subject dir), you can just supply the subject IDs in the --subjects argument.

For example,
1, Go to your freesurfer directory: cd $SUBJECTS_DIR
2. Get all subjects: subjects=$(ls sub*) - that assumes that all subject folders begin with sub, but you can change it to work with your data.
3. Run your command, with --subjects ${subjects[@]}

Best,
Steven

3

Thanks for your response, Steven.
actually, I have four folders inside my subjects directory. each folder has different subjects. and I’m aiming to extract the stats data for each folder in a single excel file.

Is there a way to do that?

4

You can make a new folder that contains symlinks/shortcuts to the subject data in the different folders (see the ln -s command). Then set the subject directory environment variable to the folder that contains these shortcuts.

5

1- I created a symbolic link of CN_Male_Subjetcs

ln -s  /fefs1/fcit/ezahamalyoubi/freesurfer/subject_two/CN_Male_Subjects CN_Male_Subjects

2- I changed the SUBJECTS_DIR to subjects_two

export SUBJECTS_DIR=/fefs1/fcit/ezahamalyoubi/freesurfer/subject_two/

3- I entered subject_two and created subjects variable to get all subjects.

subjects=$(ls ADN*)

4- when I run this command I got the below error

the command

aparcstats2table --subjects ${subjects[@]} --hemi lh --meas volume --parc=aparc --parcs-from-file= --tablefile=CN_Male_volume_lh.txt

the error i got

[ezahamalyoubi@klogin2 subject_two]$ aparcstats2table --subjects ${subjects[@]} --hemi lh --meas volume --parc=aparc --parcs-from-file= --tablefile=CN_Male_volume_lh.txt
ERROR: cannot read
SUBJECTS_DIR : /fefs1/fcit/ezahamalyoubi/freesurfer/subject_two/
Parsing the .stats files

ERROR: Cannot find stats file /fefs1/fcit/ezahamalyoubi/freesurfer/subject_two/ls/stats/lh.aparc.stats
6

It looks like $subjects is not being defined correctly, as FreeSurfer is looking for a folder called ls.

Try this subjects=($(ls ADN* -d)), then make sure it looks right with echo ${subjects[@]}

7 
[ezahamalyoubi@kcn061 subject_two]$ subjects=$(ls ADN*)
ls: cannot access ADN*: No such file or directory
[ezahamalyoubi@kcn061 subject_two]$ subjects=$(ls)
[ezahamalyoubi@kcn061 subject_two]$ echo ${subjects[@]}
CN_Female_Subjects_link CN_Male_Subjects MCI_Female_Subjects MCI_Male_Subjects
[ezahamalyoubi@kcn061 subject_two]$ subjects=$(ls CN_Female_Subjects_link*)
[ezahamalyoubi@kcn061 subject_two]$ echo ${subjects[@]}
CN_Female_Subjects_link

(those are the links for the four folders)
how can I access the subjects inside the links? I think freesurfer could not collect them in the subjects variable

8

You should create a single folder that contains the links to the subjects contained in all of those four folders. So, looking at subjects in CN_Male_Subjects, for example, you should send a shortcut of each of the subject folders to your final directory where you want to have all subjects represented, and the repeat for the other 3 bigger folders. See more about the ln command here: https://linuxize.com/post/how-to-create-symbolic-links-in-linux-using-the-ln-command/

9

thanks for your help, Steven.