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Hi Rachel,
Have you sourced Freesurfer install directory?
Here is help page on how to setup your Freesurfer environment on Linux -
https://secure-web.cisco.com/1Ub7K0QLalONiy0rW3bBM14kqwMElWC9S8wklOMGTNEoROLtbi5l-vQB0xjZDlZmXEwIz_EwWsnjfnVZZ7ljJGZLQ9
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Have you tried the latest Mac build of freeview? This has been fixed recently.
On Jul 30, 2023, at 11:02 AM, Ha Manh Luu
mailto:hal4...@med.cornell.edu>> wrote:
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From: Ha Manh Luu
Sent: Thursday, July 20, 2023
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Hi Michelangelo,
I'm wondering if you are using FS 7.3.2? 'DOCAREG' was accidentally dropped
for autonrecon2. You can fix it by adding '-careg' at the end of command line.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of
External Email - Use CautionDear Yujing,yes, I am using FS 7.3.2, so thanks I will try withrecon-all -s sub-01_recon -autorecon2 -caregshould I add the -careg also for the -autorecon3 step?Can you eventually have a look also at the questions in my first email below (at the very bott
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You don’t need ‘-careg’ if you just run autorecon3.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Michelangelo Fabbrizzi
Sent: Monday, July 31, 2023 8:55 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_watershed and improve
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I'm not sure how to force mri_watershed command to use the brainmask.mgz
already created.
Recon-all '-gcut' is achieved by running mri_gcut after mri_watershed.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mi
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Hello,
'timepoints' refers to the individual scan sessions that make up a longitudinal
dataset for a subject.
i.e. If a subject was scanned 3 times, say in 2010, 2015, and 2020, this
subject would have 3 timepoints. One from each year they were scan
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Dear Yujing,
thanks again for your help, just a last question, how can give to autorecon1
the input to use certain options at the mri_watershed step (for instance a
certain preflood height (-h 5) or use of the atlas option (-atlas))?
recon-all -s su
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Dear Freesurfer developers,
Previously, I downloaded the
freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully
analyzed some data using this version. Now, I find myself in the need to
reinstall Freesurfer, but I am unable to
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Development builds are continually updated and may not be stable, i.e., so the
March 31st development build is no longer available. I suggest using one
of the release builds listed on the release page. The 7.4.1 build from
this June is the most rec
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Hello all,
I’m getting an error as follows:
developer@developer-VirtualBox:~/freesurfer$ setenv SUBJECTS_DIR
$FREESURFER_HOME/subjects
Command 'setenv' not found, did you mean:
command 'getenv' from snap getenv (0.3.1)
See 'snap info ' for a
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It reads like you downloaded and setup the public VM
(from https://secure-web.cisco.com/1YpN3buNDQ0c9lVvFb2LEMMoXu4bGzcQrSQ6ddm7xsasVOV9uJhcsnEgL1Hc1mSNTG6VXMshwnJdqirgu2VRs15W0S-so_lVY_Zs4BzyCsjkRnrwG9WvOGP2d5Ouk04JzWWWwFTI7BGpwgkV95xP86xw6PpMlHcWLUA
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Hi FS experts,
I was just wondering about how long it takes to receive the download for
infantFS. I would like to use the program to analyze my dissertation data, so I
just want to have a timeframe in mind for about how long it will take to start
to
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Hi Doug et al,
I recently moved from Linux to MAC OS running Ventura. When I run the
recon-all, it gives me this message:
“mri_compute_overlap” cannot be opened because the developer cannot be
verified.
The help given at the FS website is for previou
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there are not options to autorecon1 specifically. You can pass some
watershed args on the command line, but it is probably easier to use an
expert options file, eg, create a text file (eg, xopts.txt) with
something like
mri_watershed -less
then run r
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there is not an easy way to do it, but there is a way
1. convert the annot to labels using mri_annotation2label
2. for each label, run mri_label2label with the --erode option to create
a new set of labels (different folder)
3. use mris_label2annot to
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Try adding --no-surfs
On 7/24/2023 12:45 PM, Viktorija Pratuseviciute wrote:
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Thank you very much! We did try the command tkregisterfv --s PI163
–fstal, however the recon-all processing fails before a surf/lh.whi
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Hello,
I am looking to cortically project onto a pial surface and am trying to use the
following code in the freeview GUI to do so:
[FreeView] -v 004/mri/wm.mgz:colormap=jet 004/mri/brainmask.mgz -f
004/surf/lh.pial:edgecolor=blue 004/surf/lh.white:
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does 004/mri/wm.mgz exist?
On 7/31/2023 6:40 PM, Rachel Wagner wrote:
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Hello,
I am looking to cortically project onto a pial surface and am trying
to use the following code in the freeview GUI to do so:
[FreeV
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Try right clicking on the .pkg installer and select “open with” and then
select “installer.app”. That should allow you to do an install of the
distribution which will go under /Applications/freesurfer/7.4.1, e.g., for the
7.4.1 release pkg obtained
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