no, it's the average that we distribute. You can use make_average_subject
to create your own if you want, although usually it isn't necessary (since
the warp is so high dimensional)
On Mon, 3 Aug 2015, Lim, Lena wrote:
But is the fsaverage file the group norm for all the final 68 subjects I have
so far ?
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 03 August 2015 16:41
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
I think you should be all set. I meant don't delete fsaverage and all
On
Mon, 3 Aug 2015, Lim, Lena wrote:
Sorry, I don’t understand. Those files are now in the directory. What exactly
should I run next?
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: 03 August 2015 16:04
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
no! Don't delete those files - we need them. Just don't include them
in your for loop
cheers
Bruce
On Mon, 3 Aug 2015,
Lim, Lena wrote:
Thanks, Bruce. So do I delete that files and run recon-all -qcache -subjid $i
for all the subjects again though they have already been smoothed?
Cheers,
L
----------------------------------------------------------------
Lena Lim, PhD
Department of Child & Adolescent Psychiatry (PO 85) Institute of
Psychiatry, Psychology & Neuroscience King's College London De
Crespigny Park London SE5 8AF lena....@kcl.ac.uk
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: 03 August 2015 15:38
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
Hi Lena
those aren't files that you need to recreate - they are distributed
with FS (which is also why you don't have permission to write into
their directories). You should leave them out of the list that you
are running -qcache on
cheers
Bruce
On Mon, 3 Aug 2015, Lim, Lena wrote:
Thanks Bruce.
I managed to get the hippo files for the 3 new subjects.
However, when I ran
#! /bin/bash
for i in $ ( ls ) ; do
recon-all -qcache -subjid $i
done
The smoothing for each individual subject was alright (e.g.
recon-all -s
PAC70 finished without error) but there were these errors messages
below (please see log attached):
ERROR: you do not have write permission to
/home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage
ERROR: you do not have write permission to
/home/spjwker_PAC/Lena/CT_SA/FSL/rh.EC_average
ERROR: you do not have write permission to
/home/spjwker_PAC/Lena/CT_SA/FSL/lh.EC_average
I think the fsaverage, rh.EC_average and lh.EC_average files were
already before I ran the above commands…
How do I create the final fsaverage, rh.EC_average and lh.EC_average
files for all the 68 subjects that I want in the final analysis?
Thanks,
Lena
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: 30 July 2015 18:02
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
Hi Lena
you need to run the hippocampal subfield code. Depending on what
version you are running it could mean adding something like:
-hippocampal-subfields-<T1/T1T2/T2>
and removing the -autorecon-all
cheers
Bruce
On Thu, 30 Jul 2015, Lim, Lena wrote:
Dear Freesurfer experts,
My colleague (who has now left) told me that he has run the
preprocessing
autorecon1—3 and that I only have to run recon-all –qcache -subjid
$i
for all the subjects. However, I realised that there were 3 missing
subjects and so I tried to run the preprocessing for these 3 new
subjects with the following commands:
#!/bin/bash
files=( PAC03 PAC17 PAC57 )
for i in ${files[*]}; do
#echo $i
recon-all -autorecon-all -subjid $i
done
1) The preprocessing finished without any errors but the outputs in
the mri folders seem slightly different from the others he did
(please
see screenshots attached, my PAC17 vs his PAC01). In particular, I
don’t have the 20 posterior_* files (e.g. posterior_left_CA1.mgz
etc)
in the mri folder, the hippo-subfield.log in the scripts folder and
the hippocampal_subfield.touch in the touch folder. How and when
were
they been created? Are they needed for subsequent analyses?
2) Shall I run the following for the 3 missing subjects all over again?
#!/bin/bash
files=( PAC03 PAC17 PAC57 )
for i in ${files[*]}; do
recon-all -autorecon-all –qcache -subjid $i
done
3) Finally, do I then run the following for all the subjects as the
final preprocessing step?
#!/bin/bash
for i in $ ( ls ); do
recon-all –qcache -subjid $i
done
I am using Freesurfer v5.3.0 and have attached the recon-all log
for
PAC17 and PAC01.
Many thanks,
Lena
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