Dear FreeSurfer experts,
I am trying to perform hippocampal subfield segmentation with
FreeSurfer 6. I followed the instructions found on this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which
said that I first need to download Matlab Runtime. Which brought me to
this page:
Dear FreeSurfer experts,
in the txt files [lr]h.hippoSfVolumes-T1.v10.txt we can see the
volumes of individual hippocampal subfields - I was wondering what are
the units in which volume is given? Millimeters cubic, voxels, or
something else?
Thanks in advance!
Best,
Darko
__
Dear experts,
I would like to run a for-loop in FreeSurfer 5.1. so that I can have
multiple subjects analyzed over the holiday, without having to come to the
lab and start each of them myself. I searched the previous emails in this
list and know that I can make a file with a subject list, and then
Hi Bruce,
thanks for the reply. I only have one acquisition per subject. I guess
I can make a separate text file with a list of paths to dicoms and
then somehow try to pair the path and the subject name in the
recon-all command.
> From: Bruce Fischl
> Subject: Re: [Freesurfer] defining input ima
Dear experts,
while running recon-all on FreeSurfer 5.1.0 I encountered the following error:
mri_watershed Error: indices out of bounds
I searched the email archive and found this thread:
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Freesurfer\]+mri_watershed
Hi Bruce,
I attached the recon-all.log!
Thanks in advance for taking a look!
Darko
Message: 3
Date: Sat, 31 Mar 2018 06:47:12 -0400
From: Bruce Fischl
Subject: Re: [Freesurfer] mri_watershed Error: indices out of bounds
To: Freesurfer support list
Message-ID: <23b23889-c042-4a04-9316-4c8ed5468.
Dear experts,
I encountered a problem when trying to open freeview. I am using FreeSurfer
v.5.3.0-HCP, and after sourcing it, I tried typing simply freeview in the
terminal, as described in this link:
http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewQuickStart
but the feedbac
ated!
Thanks in advance,
Darko
On Tue, Apr 17, 2018 at 5:28 PM, Hoopes, Andrew
wrote:
> Hi Darko, how are you sourcing freesurfer? And what is the output of
> running “which freeview” and “which freeview.bin”?
>
>
>
> best,
>
> Andrew
>
>
>
> *From: * on behalf of
line right before the call to “freeview.bin $argv”:
>
>
>
> echo $PATH
>
>
>
> and send the output over.
>
>
>
> best
>
> Andrew
>
>
>
>
>
> *From: *Darko Komnenić
> *Date: *Tuesday, April 17, 2018 at 11:35 AM
> *To: *"Hoopes, And
6:36 PM, Darko Komnenić wrote:
> Hi Andrew,
> thanks for getting back so quickly.
> Here are the outputs:
> “tcsh --version” gives a "tcsh 6.18.01 (Astron) 2012-02-14
> (x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filec"
>
> I added echo $PATH right
the
> TCL package. Can you send me your tcl_setup file in $FREESURFER_HOME/bin?
>
>
>
> It would also be helpful if you add another “echo $PATH” line right below
> the “#!/bin/tcsh -ef” in the freeview script
>
>
>
> best
>
> Andrew
>
>
>
> *From: *Dar
hed errors with
> freesurfer tools? I can try to help you solve this, but I’m not quite sure
> I understand the initial problem.
>
>
>
> PS: At some point in your .bashrc is linuxbrew called? You don’t want that
> “Linuxbrew directory detected…” error in your PATH variable
te:
> Are you using a bash shell? If you are, there should be a file located at
> ~/.bashrc (it’s a hidden file in your home folder)
>
> Andrew
>
>
>
>
>
> *From: *Darko Komnenić
> *Date: *Tuesday, April 17, 2018 at 2:24 PM
>
> *To: *"Hoopes, Andrew"
An update,
in the .bash_profile file, there is a line about linuxbrew. Do you
recommend that I remove it? Sending the file attached.
Best,
Darko
On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić
wrote:
> Hi Andrew,
> sorry for the delay. Attached is the hidden bashrc file from my Home
&g
out the last two lines and rerunning freeview
> (it’s possible that the error message getting inserted into your PATH is
> the source of these issues):
>
> # export PATH="$HOME/.linuxbrew/bin:$PATH"
>
> # export PATH="$(brew --prefix)/bin:$PATH"
>
>
>
error is no longer
> present
>
> Andrew
>
>
>
> *From: *Darko Komnenić
> *Date: *Thursday, April 19, 2018 at 1:08 PM
>
> *To: *"Hoopes, Andrew"
> *Cc: *FS Help
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
>
External Email - Use Caution
Dear Freesurfer experts,
I wanted to run the Freesurfer's longitudinal processing pipeline
(described here
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a
series of MRI scans from a single patient. However, after looking at the
sc
External Email - Use Caution
Hi Douglas,
thanks for your reply. Indeed, in this particular data set they don't all
have contrast, which is unfortunate. But my question was also general, if
we assume that they all have contrast, would it be OK to use those images
as inputs in the lo
External Email - Use Caution
Thanks a lot for the reply and the suggestions, Douglas! These scans are at
3T.
Best,
Darko
> --
>
> Message: 4
> Date: Wed, 20 Nov 2019 22:45:18 +
> From: "Greve, Douglas N.,Ph.D."
> Subject: Re: [Freesurfer] Question
External Email - Use Caution
Dear Freesurfer experts,
I am using Human Connectone Project pipelines to calculate cortical myelin
levels. These pipelines use Freesurfer 6.
Since certain subjects' brain surfaces had some chunks and spikes sticking
out, I edited the brainmask.mgz file
External Email - Use Caution
Thanks Matt!
Should I also add the -autorecon3 flag, or does that get performed
automatically if I put in "autorecon2"?
Best,
Darko
> Message: 4
> Date: Mon, 30 Nov 2020 19:16:06 +
> From: "Glasser, Matthew"
> Subject: Re: [Freesurfer] arguments
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