mrHOu-3l7---mohG7I9K0_C3zW0zFs2gVU41F/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2F>
Best wishes,
Malte
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Simon Jones
Sent: Monday, October 21, 2024 13:20
To
Mr P Simon Jones
Research Associate
Department of Clinical Neurosciences
University of Cambridge
Herchel Smith Building, Forvie Site
Robinson Way
Cambridge Biomedical Campus
Cambridge CB2 0SZ UK
External Email - Use Caution
Dear Freesurfer Support,
Under older versions of Freesurfer such as 7.2.0 I can split recon-all into two
stages:
recon-all -autorecon1 -noskullstrip -s sub -i sub.nii.gz
Manually create brainmask.mgz
recon-all -autorecon2 -autorecon3 -s sub
Using free
External Email - Use Caution
Dear all
I have tried using SAMSEG in 7.1.1 with 7T MP2RAGE sequence data which has an
inv1, inv2 and a uni images and I can create a denoised image which has a more
of a traditional T1-weighted appearance. I have got some good looking results
combi
take a look.
cheers
Bruce
On Tue, 11 Dec 2018, Simon Jones wrote:
>
> External Email - Use Caution
>
> Hi all,
>
>
>
> I have some participants whose recons look OK except the parcellations are
> incorrect. For instance the right precentral gyrus
External Email - Use Caution
Ah, all the ones with v.mgz used the bigventricles option… Must be something to
do with that.
Simon
From: Simon Jones
Sent: 13 November 2018 21:35
To: freesurfer@nmr.mgh.harvard.edu
Subject: QA_tools do not find v.mgz
I have run some
External Email - Use Caution
I have run some Freesurfer 6 recon-all processed data through the Freesurfer QA
analysis QA_tools_v1.2. The output looks mostly good but I repeatedly see these
errors.
ERROR: Subject a1 missing output file ../mri/v.mgz
ERROR: Subject a1 missing outp
Dear Tracula developers,
I posted a problem with tracula when I ran
trac-all -stat -c dmrirc_ind_mni_cvs_all_stats.all
I receive this error message
Loading output reference volume from
/home/spj24/app/freesurfer/subjects/cvs_avg35
corRead(): can't open file
/home/spj24/app/frees
Dear Tracula developers
I thought I had nearly reached the end of tracula processing. However, when
I perform the step,
trac-all -stat -c dmrirc_ind_mni_cvs_all_stats.all
I receive this error message
.
Base name of output files:
/work/imagingC/Rowe/p00363/freesurfer/all/subs_tract
