the subject id is something you make up. What is 001 in your example?
Maybe it is the subject ID? If so, preface it with -s. You probably also
want to specify the location of your output directory with -sd <directory
where you will put each subject>
cheers
Bruce
On Fri, 27 May 2016, Marja Caverlé wrote:
Hi Bruce,
Thank you for your response. I tried it many times and I kept getting the
same error like at the bottom of this email.
Why do you put the -s in there? and what exactly is the subject ID? FYI, I
was already in the folder where the .nii.gz is located. And by your answer
I assume I can do it only one patient at a time?
Thanks,
Marja
---
Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all
ERROR: Flag -001 unrecognized.
-001 -i AD_TM001.nii.gz -all
Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb
26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016
For more details, see the log file
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
---
On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl <[email protected]>
wrote:
Hi Marja
can you send us the actual command and screen output you ran? It
should be something like:
recon-all -all -s <subject id> -i <path to input .nii.gz file>
Depending on your hardware it will take hours to finish, but it
will do pretty much everything (segmentation, surface
reconstruction, template registration, thickness measurement,
parcellation, etc...)
cheers
Bruce
On Thu, 26 May 2016, Marja Caverlé wrote:
Hi All,
I am new to Freesurfer and I would like to use it
for a project I am working
on right now. For this project I have two patient
groups of which I have
structural MRI scans and a lot of other measures. I
hope to get cortical
thickness numbers from the scans and compare these
with the other measures.
Anyway, I am trying to get something done in
Freesurfer and it does not
really seem to work. I assume I have to do a
recon-all -all, but when I try
this, I get an error saying that the flag is
unrecognised. It probably is a
small error, easy to solve, but I already get stuck
on it since I am totally
new to Freesurfer.
Could anyone help me out?
Some of my questions are;
- Am I correct that recon-all -all already
coregisters the scans to
template?
- What will be the outcome? Will I get pictures, or
a table with numbers,
and if it is a table, which area's are specified? I
have a list of ROIs, but
how do I let Freesurfer know I am interested in
those areas?
- Can I do recon-all -all on a folder with all my
patients, or do I have to
do it one by one? (There not that much,
approximately 12 scans)
- Can I do recon-all -all on .nii.gz files? The
originals are DICOM, but the
problem is that there is just one large DICOM
folder, which does not specify
which files are part of which scan. I have converted
them to .nii.gz since I
am a bit familiar with FSL, but I do not know
whether this actually works in
Freesurfer.
- Why do I get the unrecognised flag error?
I apologise for these questions, they are probably
very easy to answer, but
I just don't have a clue yet.
Thank you guys.
Best,
Marja
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