Hi Bruce,
The dcm files are from SIMENS MAGNETOM VISION plus. The file does exist. Myriam
Siefert met same problem. She suggested me to convert the dcm to nii file.
Because Freesurfer cannot read header of the some dcm files. After converting
to nii, it seems working now. The analysis is
Nope, I have the same files as before :(
2012/7/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
The monitoring script that bedpostx runs and tells you if things have or
haven't finished properly can't always be trusted. So if that's the only
error message you see, I wouldn't worry about
Hello,
I emailed last week to ask about an error I was getting. Has anyone had a
chance to look into it?
Thank you very much.
Best wishes,
Clare
From: Gibbard, Clare
Sent: 25 July 2012 16:45
To: Bruce Fischl
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:
Try re-installing. Make sure you have enough disk space.
doug
On 07/30/2012 12:43 AM, Fidel Vila wrote:
Hi Doug.
The missing files are NOT in $FREESURFER_HOME/bin; So, I guess that's why
they are not found even though the path is set up in the system PATH variable.
Suggestions?
Fidel
Are
Hi Jeni, you should not smooth with both. If you want to smooth within a
given label with surf2surf, pass that label to surf2surf then don't
smooth with glmfit.
doug
On 07/30/2012 12:46 AM, Jeni Chen wrote:
Hi Doug,
When you say If you smooth using surf2surf, then do not smooth using
Hi Susan, if you are not doing a thickness study, then I don't think it
will matter much if you have 1 or 2 or 3 T1s. There's not an easy way to
compare the recons. You can do a paired difference using 1 T1 vs mult
T1s. That will mostly give you bias information, not accuracy or
repeatability.
where did this file come from? Can you upload it to our file drop (URL
at the end of this email)?
doug
On 07/30/2012 01:51 AM, Liu Yawu wrote:
Hi Doug,
Thanks for your reply. Here are the message:
ERROR:
/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm
is
Hi Clare, what kind of edits did you make? Can you send the terminal
output when you ran qcache?
doug
On 07/30/2012 05:50 AM, Gibbard, Clare wrote:
Hello,
I emailed last week to ask about an error I was getting. Has anyone had a
chance to look into it?
Thank you very much.
Best wishes,
glad to hear it, but I'm surprised that there are dicoms that we can't
read. Maybe it's just an old variant of the format?
good luck
Bruce
On Mon, 30 Jul 2012, Liu Yawu wrote:
Hi Bruce,
The dcm files are from SIMENS MAGNETOM VISION plus. The file does exist. Myriam
Siefert met same
Hi,
In our functional MRI studies, we co-registration the functional
images to anatomical scans (a part of preproc-sess routine in version 5)
before measuring the contrasts. But for one of our studies, a reviewer has
asked if a “non-rigid image registration” would change results when we are
It depends on what the reviewer is concerned about. You don't want to
use a fully non-rigid registration because the drop out will look like
the edge of the brain, and the non-rigid will warp it incorrectly. If
he/she is talking about using something more constrained like B0
correction, then
Dear FS Experts,
I have run recon-all on my subjects. I'm looking to convert the V1 and various
BA labels to ROIs in 3D anatomical space (orig.mgz). How would I convert my
freesufer label files to ROIs. Thank you!
Massieh Moayedi
___
Freesurfer
I am trying to import an MPRAGE structural sequence of 160 images acquired
from a Siemens Allegro. Only one of my subjects displays the following
error message when I try to import him using the recon-all -s Subject -i
function. Below is the brief error message and full log. Thanks in advance
for
try mri_label2vol (assuming by 'ROI' you mean a 3D volume)
On Mon, 30 Jul 2012, mmoay...@uhnres.utoronto.ca wrote:
Dear FS Experts,
I have run recon-all on my subjects. I'm looking to convert the V1 and
various BA labels to ROIs in 3D anatomical space (orig.mgz). How would I
convert my
it looks like someone accidentally turn on jpeg compression on the
console. Our converter does not read jpeg. You can use dcmdjpeg from the
dcmtk toolkit to create new dicoms that are uncompressed, something like
dcmdjpeg +te old.dcm new.dcm
doug
On 07/30/2012 01:00 PM, Nathan Hutcheson
Hi:
I ran trac-all -prep -c dmrirc and it finished ok... Then, when I
tried to run the command trac-all -bedp -c dmrirc, I got the error:
ln -sf
/usr/local/freesurfer/subjects/bmvf_23_7_2012/dlabel/diff/anat_brain_mask.bbr.nii.gz
Hi Sergio - Sorry, if this occurs independently of trac-all, whenever you
run bedpostx directly, you're better off asking for help on the FSL list.
We've never run into this problem with bedpostx up till now.
a.y
On Mon, 30 Jul 2012, Sergio Medina wrote:
Nope, I have the same files as
Hi Gonzalo - This has come up a few times recently. Please see here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23064.html
Hope this helps,
a.y
On Mon, 30 Jul 2012, Gonzalo Rojas Costa wrote:
Hi:
I ran trac-all -prep -c dmrirc and it finished ok... Then, when I
tried
Hi Liz,
you need more memory (see the error message: cannot allocate memory).
Best, Martin
On Mon, 2012-07-23 at 10:21 +1000, Liz Bowman wrote:
Hello,
I have several patients scans taken over multiple time points (up to
nine time points in some patients). I thought I might be able to
Hi Matthew
what shell are you using? If you type
printenv SUBJECTS_DIR
right before calling mri_segstats, what does it return? And when do you
get that output? Are you sourcing the FreeSurferEnv.csh file? Don't
execute it as otherwise it pushes a new shell, sets all that stuff, then
pops
Ok the main email is CC'd. Below is what I did and the output I received.
The goal is to get a brain volume, Subdural space and/or a CSF volume to
estimate how much room for displacement/deformation the brain has. Thanks
in advance for your help.
Matthews-MacBook-Pro-2:~] matthew% printenv
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