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Thank you for your response. Yes, the key question is to adjust for
interscan variability through either histogram matching or ComBat before or
after longitudinal run.
Will await to see what the longitudinal freesufer experts think.
My best
AJ
On
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Thanks!!!
Kind regards,
Rosie
El mié., 7 jul. 2021 21:32, Paul Wighton escribió:
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>
> Hi Rosie,
>
> In that case, you can try running the v6 version of hippocampal subfields,
> e.g:
>
> recon-all -s sub-002_ses-
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Hi Rosie,
In that case, you can try running the v6 version of hippocampal subfields,
e.g:
recon-all -s sub-002_ses-BSL -hippocampal-subfields-T1
-Paul
On Wed, Jul 7, 2021 at 3:21 PM Rosalia Dacosta Aguayo
wrote:
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Hi Paul,
Thank you.
The think is that I already run recon-all in all the participants and I
made some corrections (control points,...). I just want the hipocampal
subfields...What should I do in this case scenario?
El mié., 7 jul. 2021 21:03, Paul
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Thanks Rosie, that explains it.
You are using version 6.0.0 of FreeSurfer. The script segmentHA_T1.sh is
not in this version.
There are two options. If you want to continue using v6.0.0, you can
refer to the instructions here:
https://secure-web.cis
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Here it is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la
$FREESURFER_HOME/bin/segmentHA_T1.sh
ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file
or directory
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-st
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Ok, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't
exist for some reason.
You should be able to confirm that by running:
ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh
Does it say something like?
ls: cannot access '/usr/local/frees
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Hi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh
$ segmentHA_T1.sh
sh: 1: segmentHA_T1.sh: not found
$
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani wrote:
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>
> Dear Rosalia,
>
> Once y
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Dear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh
after sourcing and then try running it(without closing the terminal)
hopef
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Hi Paul,
I did it:
# FREESURFER
export FREESURFER_HOME=/usr/local/freesurfer
export PATH=${FREESURFER_HOME}/bin:${PATH}
export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI
source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer b
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Sure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come
after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows,
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Hi AJ,
The longitudinal stream does not account for inter-scanner variability, but
does reduce biases related to registering subsequent timepoints to the
initial one.
Perhaps longitudinal experts could confirm, but I would run the
longitudinal stream,
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Hi Paul,
Thank you very much for answering my question. I set the subjects_dir in a
way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME
/usr/local/freesurfer
rosali
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Hi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin
directory. It looks like your PATH environment variable does not include
this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo
$FREESURFER_H
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