What happens if you remove -parallel? That flag does not do much any
more but cause trouble (we have removed it in recent versions)
On 5/3/2022 2:58 PM, FONG, manson CM [CBS] wrote:
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Hello Experts,
I'm attempting to run the longitudinal pipeline, as descri
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Thank you! Yup, this helps!
On Tue, Jun 9, 2020 at 11:06 Hoopes, Andrew wrote:
> As for the --preserve=timestamps error, this is a bug on osx. This will be
> fixed in the next 7.1 patch, but in the meantime, you can fix this manually
> via:
>
> cd $F
As for the --preserve=timestamps error, this is a bug on osx. This will be
fixed in the next 7.1 patch, but in the meantime, you can fix this manually via:
cd $FREESURFER_HOME/bin
sudo rm rca-long-tp-init
sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-
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Dear FreeSurfer experts,
I am running longitudinal processing with FreeSurfer 7.1.0 on MacOX
Catalina.
The dataset is 5 time points with T1 data. I tried to run a single subject.
So far it succeeded on Step 1 (recon-all at each time point), and Step 2
Hi Jürgen,
mainly you are right. As there is no change in the first processing
steps between the cross sectional and the longitudinal stream, it is
sufficient, to simply copy that data from the cross sectional
directories, instead of rerunning it.
The -long stream starts being different in the sku
Dear FS experts
Am I right that the input for step 3 in recon-all -long are the already
cross-sectionally processed images from step 1 and not the raw images that I
used to create these cross-sectionally images?
Thanks for clarification
Regards
Jürgen
Hi,
I have a couple questions regarding the -long option.
1) The longitudinal instructions listed in recon-all -help all use
recon-all -all -long. If I am only interested in the subcortical
segmentation, will the longitudinal processing still work if I only
use recon-all -subcortseg ?
2) How long
Hi Juergen,
we're trying to minimize technology-induced differences. In the case
where tp1 and tp2 are the same scan, you will then have applied a
different procedure to tp2 then tp1 (it will have been processes
longitudinally twice), so you will find differences where none exist.
This is why
Dear FS experts
Is there any difference or problem when running tp2 on the "longitudinally
adjusted" tp1 instead on the recommended cross-sectionaly processed tp1?
Thanks in advance
Regards
Juergen
---
Juergen Haenggi
Ph.D. (Dr. des.)
Divis
yes, you can certainly do multiple time points. Just do we one in the
same way.
A low # of topological defects is probably a good thing, but computing
CNR would be a better direct measure of sequence quality.
cheers,
Bruce
On Thu, 11 Sep
2008, Juergen Haenggi wrote:
Dear FS experts
Thank
Dear FS experts
Thanks a lot for the beta version of recon-all -long. It works fine. Is it
possible to use more than two time points in the recon-all -long pipeline.
If yes, can I add the third and forth time point of each subject with
additional -i options (-i tp3.nii -i tp4.nii)?
If no, is there
Hi Juergen,
this is being replaced by recon-all -long ...
which we're close to being ready to release. Our local tests indicate it
works pretty well, we'd just like to try it out a little more before
distributing it.
cheers,
Bruce
On Thu, 4 Sep 2008, Juergen Haenggi wrote:
Dear FS experts
Dear FS experts
I tried to run recon-all-long, but there is no such command. I use FS 4.0.5
on a MacIntel.
Where can I find this command and is there any documentation about a
longitudinal FS analysis?
Thanks in advance
Best regards
Juergen
-
Chacko,
Attached is the file 'AsegStatsLUT.txt'
I'm not sure about the other messages.
Nick
On Fri, 2007-01-26 at 16:55 -0800, Chacko Cherian wrote:
> Hello users,
>
> I was running longitudinal analysis for a couple of
> scans and recon-all exited with this error.
>
> CTABread(/usr/local/fre
Hello users,
I was running longitudinal analysis for a couple of
scans and recon-all exited with this error.
CTABread(/usr/local/freesurfer/ASegStatsLUT.txt):
could not open file
No such file or directory
atlas_icv = 1.74537e+06
Loading mri/aseg.mgz
Loading mri/norm.mgz
Loading mri/norm.mgz
Loadi
Hi HweeLing,
you can recon the first timepoint with the cross-sectional tools, as
recon-all-long expects it.
Bruce
On Thu, 4 May 2006, Lee HL wrote:
Hi,
I was wondering where would I be able to find information regarding the
longitudinal tools for freesurfer.
I'm working on a dataset that wa
The longitudinal tools are still somewhat experimental and we are not
distributing them yet. Check back in July.
doug
Lee HL wrote:
Hi,
I was wondering where would I be able to find information regarding the
longitudinal tools for freesurfer.
I'm working on a dataset that was meant for a l
Hi,
I was wondering where would I be able to find information regarding the
longitudinal tools for freesurfer.
I'm working on a dataset that was meant for a longitudinal study. For the
first pass, we intend to report the cross-sectional results first. Would it
be a good idea to start using the lo
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