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Dear FreeSurfer team,
I am experiencing an error when trying to run a subject from a different
group but with the same number.
I would much appreciate your helping here.
Regards,
Rosalia
rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects_c
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Dear FreeSurfer team,
I am trying to run recon -all -autorecon2 using the following command
line: *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i
/home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2*
It is the same command I used yesterday t
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Dear Free Surfer team,
I keep trying to run -autorecon2 but it seems that I should have run recon
-all -all instead as I am having problems with the names of my subjects and
the same error appears once and again and I do not know how I should do it
so
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Dear Rosalina,
you should run recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -autorecon2 and
everything will run nicely. You should not include the -i flag again if you
want to continue processing your data, as this flag tells FreeSurfer to create
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Dear Falk,
Thank you very much for your email and explanation. It is working now.
I wonder how I could set the smoothing for autorecon3 as to run recon -all
-all I had the options: -qcache -openmp 8
Kind regards,
Rosalia
On Fri, Oct 19, 2018 at 2:06
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Dear Rosalia,
You can specify all flags in every call of recon-all. If this flags does not
change any commands, they will simply be ignored.
In your case, to first run autorecon1, overwrite the brainmask and continue
with autorecon2 and 3, you can d
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Dear Falk,
Thank you very much.
Once last question: what would happen if I did run -autorecon1 without the
flags: *-qcache -openmp 8’ *and I use them in autorecon2 or 3?
Best regards,
Rosalia
On Fri, Oct 19, 2018 at 2:34 PM Falk Lüsebrink
wrote:
>
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Dear Rosalia,
When you use the openmp flag, you should make sure to use it always in the same
for all subjects in your study, as otherwise you may introduce a bias (in your
case either use it for autorecon1, autorecon2, and autorecon3 or use it for
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Dear Falk,
I understand. I will do exactly the same for all the participants.
Thank you very much for all your helpful and kind explanations.
Best regards,
Rosalia
On Fri, Oct 19, 2018 at 3:13 PM Falk Lüsebrink
wrote:
> External Email - Use
Hi Rosalia
the subject ID specified by -s (001C in your case) has to be unique
within a given SUBJECTS_DIR
cheers
Bruce
On Fri, 19 Oct 2018, Rosalia Dacosta Aguayo
wrote:
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Dear FreeSurfer team,
I am experiencing an error when trying to run a s
Hi Matthieu,
in LME it is OK if subjects have differently many time points in
general. You need to ask a statistician about your specific setup, but
I think it might be OK (basically less time points, means more variance
on the slope estimates, but that should be considered in LME). But I am
not
Hi Rosalia
once you have imported the data for a subject with -i , you
shouldn't specify it for subsequent analyses
cheers
Bruce
On Fri, 19 Oct 2018, Rosalia Dacosta
Aguayo wrote:
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Dear FreeSurfer team,
I am trying to run recon -all -autoreco
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Doug-
Did you have any other ideas on this? I'm using FreeSurfer 6.0.0, if that
helps any. I've tried the "mkheadsurf" command on three different subjects and
all have the same issues. The coordinates I get in matlab are nowhere near
what I see
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Hi Martin,
Do you mean that high attrition (less time points with time) would induce
more variance on the slope estimates but this effect would be compensated
by LME modeling ?
Would there be proportion of early drop outs to respect in order to
compen
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Hello. Could you point me to any recommended acquisition protocols specific to
longitudinal studies on a 3T Prisma (morphometry and fMRI)? Thanks!
Carla Ammons, M.S.
Doctoral Candidate | Medical Clinical Psychology
University of Alabama at Birmingham
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I suggest you talk to the folks at Washington university in St Louis. There
has been considerable amount of work looking at this. You should contact
the following individuals
Steve Petersen s...@wustl.edu
Avi Snyder azsny...@wustl.edu
Michael harms
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I would particularly recommend the third name on that list, as Mike has done a
lot of work on the HCP-Style acquisition protocols.
Matt.
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Aaron Tanenbaum
mailto:aaron.b.tanenb...@gm
Andre (ccd) probably also has some protocols you can use
cheers
Bruce
On Fri, 19 Oct
2018, Aaron Tanenbaum wrote:
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I suggest you talk to the folks at Washington university in St Louis. There has
been considerable
amount of work looking at this. Y
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I would not limit yourself to one person. I have designed protocols for
multiple studies. The answer will surprisingly vary depending on your
question. I would not recommend simply using a protocol that some one
gives you. I have seen very promising
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Dear FreeSurfer Developers,
I am now working on the analysis of MRI images with freesurfer. I read your
webpage about submillimeter reconstruction,
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_SubmillimeterR
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