as it?s run with the
variable values expanded, and seeing that output could help with debugging.
- R.
On Apr 1, 2021, at 20:29, zalewk <zal...@uw.edu>
wrote:External Email - Use
CautionHi Freesurfer
team, My lab recently switched over from FS6 to FS7 and I think I've
External Email - Use Caution
Hi Freesurfer team,
My lab recently switched over from FS6 to FS7 and I think I've encountered a
bug with recon-all.
I'm running subjects stepwise and editing them, running recon-all with the
-autorecon2 and -autorecon3 flags initially are no problem
dev version?
And sorry, we haven't documented the ex vivo processing stream yet as it is=
too much of a work-in-progress.
cheers
Bruce
On Thu, 14 Mar 2019, zalewk wrote:
External Email - Use Caution
Hi Bruce,
In response to your previous email,
things like -no-cerebellum, -rh-only, and see if they are
sufficient for what you are trying to do
cheers
Bruce
On Mon, 4 Mar 2019, zalewk wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer team,
>
> I am currently working processing the volumetrics of
x-uw-ex-currentlocation-365-recipient: Outside
x-microsoft-exchange-diagnostics: =?iso-8859-1?Q?1; CY4PR08MB3573;
23:4qVRtf+4Frk8+HkoSkWpxiBI3Aktx4BluHS3p5r?=
=?iso-8859-1?Q?Y9pwKqXqpNNthdH0OWUp6OBtvK1l/YV1ElGbh7XgLoXOL3hSC0itzucGip?=
=?iso-8859-1?Q?p+wDHeAm0zUT5UWpPv2w4rF
ype: text/plain; charset="iso-8859-1"
MIME-Version: 1.0
Content-Transfer-Encoding: quoted-printable
External Email - Use Caution=
Hello Freesurfer Team,
Sorry to bother you guys again, any word on what you think is the best appr=
oach going forward here?
Best,
Kody Zalews
External Email - Use Caution
Good afternoon Freesurfer team,
I want to run the longitudinal pipeline on multiple groups of subjects, the
problem is we are at the mercy of the scanners available to us at the various
time-points. We have two different Siemens 1.5 scanners (same ty
My apologies as I misstated some of the data in my first email,
The voxel sizes are relatively similar, (two of the acquisitions are 1mm vs one
with 0.9mm).
Whereas the FOV is different between the scans being 256x256x176 on one
acquisition, 224x256x176 on the second and 240x240x180 on the thir
Hello Freesurfer team,
I have the unfortunate task of performing longitudinal volumetric analysis on
subjects collected on three different scanners with different voxel
numbers/sizes. I didn't find this out until attempting to run the longitudinal
base and receiving this message:
WARNING: Im
Excellent, thank you for sharing! I have one more question.
When running the mri_cnr function I tried using a number of different .mgz
files with varying results, which would you recommend for the most accurate
gm/wm and gm/csf CNR?
Best,
KZ
-
Dear Freesurfer Team,
We would like to have a Q/A measure (or two) that would give us indication of
how well your software worked on each of our data
sets. Obviously some image sets will be noisier than others for a variety of
reasons. Could you point us towards what
options we may have for e
Dear Freesurfer experts,
I am attempting to use QAtools to retrieve QA measures for my subjects.
I can obtain WM SNR/avg/sd, but it appears the structural segmentation table is
from a previous version of freesurfer (as the file order is different) and
doesn't appear to work with my subjects pr
Dear Freesurfer experts,
My PI would like to know, when editing the ROI labels from the freesurfer color
look-up table/aparc+aseg.mgz file with freeview voxel editor (at the end of
-autorecon3), what commands need to be re-run to apply the changes to reflect
the accurate volumetric data of eac
Hi Doug,
I sincerely apologize for being unclear! I'm still relatively new to freesurfer
and learning the ropes.
I've attached the three aforementioned .stats files.
The lh.aparc.stats and DKTatlas40.stats were generated from running recon-all.
When comparing them it appears the grey matter v
Hello Freesurfer team,
When generating the .stats files for grey matter volumetric data, this
information appears in multiple places and I'm not sure which data I should be
using for my final results.
There appears to be cortical information generated in both the .stats file
based off the DK
Hello again Freesurfer team,
Is it possible to perform a motion correction with only a T1 and a T2 scan, as
my lab only has one available T1 scan per participant.
Since the intensities of T1 and T2 are opposite of one another I've had no luck
so far, but perhaps your team knows of a work-aro
Hello Freesurfer team,
I've been previously learning freesurfer by going through the individual
recon-all commands listed on the freesurfer website v5.3 table here:
http://freesurfer.net/fswiki/ReconAllTableStableV5.3 and
recently just ran through the recon-all autorecon steps 1, 2 and 3.
Runni
Dear freesurfer team,
I'm very new to freesurfer, and I am currently working my way through the
recon-all dev table functions (listed here:
http://freesurfer.net/fswiki/ReconAllDevTable) step-by-step in preparation for
processing a large amount of participant volumetric data. While doing so I'v
18 matches
Mail list logo
