Hi Rosalia
that you would do outside of FreeSurfer, probably with a shell script. I
typically make a scripts dir under SUBJECTS_DIR and put a file names
subjects.csh that creates an env variable listing the subjects and setting
the SUBJECTS_DIR, then write scripts that source it and run things
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Thank you a lot Bruce.
Just one more question. If I would like to run all the participants. where
should I include the subject.list?
Regards,
Rosalia
On Thu, Oct 18, 2018 at 7:56 PM Bruce Fischl
wrote:
> yes, you can do that. If you run recon-all thr
yes, you can do that. If you run recon-all through the skill stripping,
then replace the brainmask.mgz with yours generated by bet, we should
detect that and retain it for further processing
cheers
Bruce
On Thu, 18 Oct 2018,
Rosalia Dacosta Aguayo wrote:
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Yes, you are right. I saw the error.
I have been running one of the participants and here it is the report.log.
Also, because these kind of participants are special, I used some bet
parameters to run the skull-stripping. This is the main reason why I di
Hi Rosalia
-i must point to a file that you want to import, usually a single dicom
file in the correct (e.g. mprage) series.
cheers
Bruce
On Thu, 18 Oct 2018, Rosalia
Dacosta Aguayo wrote:
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Hi Bruce,
There is not recon-all.log.
The full comman
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Hi Bruce,
There is not recon-all.log.
The full command line is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ *recon-all
-sd ~/Desktop/MS_STUDY/subjects -s 001 -i
/home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1*
*ERROR
Hi Rosalia
can you send us the full command line, screen output and recon-all.log?
In the arrangement you show below it would be:
recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i -all
cheers
Bruce
On Thu, 18 Oct 2018, Rosalia
Dacosta Aguayo wrote:
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Hi Bruce,
Thank you very much for answering my questions.
This is how I have organized my subject_dir for one subject so you can see
better. It is still not working.
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls
FOLDERS S_01
Hi Rosalia
you either need to give recon-all an input file (or more than one) with the
-i switch, or create the subject directory tree under SUBJECTS_DIR for that
subject, and put a file named 001.mgz in the mri/orig subdir. Note you can
also specify SUBJECTS_DIR explicitly on the recon-all co
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Dear Free Surfer team,
Surely this is a basic question but I am having a trouble setting the
subjects_dir in my terminal and, as a result, any of the commands work.
This is how I have my Free Surfer configurated in my computer:
freesurfer-Li
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