Dear experts,
I tried to process our data with the dev version of freesurfer. Unfortunately
the problem with FLAIR pial surface correction still persists. I have uploaded
the data to your ftp server (
anonym...@surfer.nmr.mgh.harvard.edu/transfer/incoming ) that you can inspect
the results.
Hi list,
I'm configuring mkanalysis-sess to configure an analysis for FC data by
FS-FAST.
No problem for cortical label:
mkanalysis-sess -analysis fc.lthalseed.surf.lh -surface fsaverage lh -fwhm 5
-notask -taskreg L_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5
-polyfit 5 -nskip 4
Dear Lee,Greatly appreciate for your advice. But I not sure whether it is the
reason for the comand killed. Actually, I had used the method, useing the
-i flag for each .dcm file for your training data of “014-anon” and then
running the comand “recon-all -s 014-anon -all”, to get a final
Hi Amolie
you only want a single -i dicom file for each entire T1-weighted run that
you acquired, NOT for every file in that run. Thus if you got a single
8-minute scan you should only have one -i on your recon-all command line
cheers
Bruce
On Tue, 19 May 2015, nellie wrote:
Dear Lee,
Hi FS experts,
I had a quick silly question about QDEC - I'm trying to run a group morphometry
analysis of cortical volume between two groups (patient and control). I want to
use ICV as a nuisance covariate and noticed you need to demean the ICV values
in order for QDEC to work. My question
Hello
I'm a new to FreeSurfer.
I'm looking for a matlab function for segmentation of 3D matrix.
I have a brain image in .mgz format with different labels, which I loaded
into matlab by load_mgh.m
I want to divide it into segments according to specified labels.
Will be very thankful if someone
Hi:
We have GE 1.5T MRI fspgr volumetric acquisition of a MS patient (39 years
old) and a Siemens 3T MRI mprage acquisition of the same patient three
years after (42 years old)... we processed that images to got the volume of
some structures that we need and compare... but, we found that multiple
Hello,
I just wanted to give this message a bump. Thanks!
Anthony
On 5/15/15 9:49 AM, Anthony Dick wrote:
Hello,
I have been stumped by this error I keep getting using the
rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas,
so I am wondering if the problem is with the
Hello,
Unfortunately Xquartz version 2.7.7 will not work with the version of
OSX that you are running.
You will either need to downgrade to version 2.7.5 (via the link I
provided below). Or you will need to update to the most reason version
of OSX.
Installing XQuartz 2.7.5 is by far the easier
Hi,
I am trying to run the tkmedit command (tkmedit subject_name brainmask.mgz
-aux T1.mgz) and keep getting the following error message:
ERROR: A segfault has occurred. This is not your fault,
: but is most likely an unrecoverable error and has
: made the program unstable.
:
: Please
Dear Sir/Madam,
I tried to run Tracula in the C2B2 server at Columbia University.
However, I got the following error message after submitted my job using
qsub to the sever. I'd greatly appreciate it if you could help me resolve
this problem.
*WARN: Running FSL's bedbost locally - this might
Hello,
If you've already installed XQuartz, can you provide me with the version
number? To get the version number double click the XQuartz icon located
in Applications - Utlities - XQuartz, then in the upper left hand
corner of your screen click X11 - About X11.
If you dont have Xquartz
Hi!
Has anyone tried to use ridge regression on fMRI data (instead of the
regular GLM) and would be willing to give some tips?
Thanks, Caspar
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
?... Any technical problem ?... We got a similar difference
by normalizing with ICV...
Sincerely,
Gonzalo Rojas Costa
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Message: 3
Date: Tue, 19 May 2015 14:39:45 -0400
From: Anthony Dick ad...@fiu.edu mailto:ad...@fiu.edu
Subject: Re: [Freesurfer] error in atlas creation
Hi Freesurfers,
I was just running the right and left outer pial layers for a subject and came
up with an error.
1) MG84
2) mris_compute_lgi --i rh.pial --close_sphere_size 30 --smooth_iters 60
3) Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));
Error in
Thank you! I will try this.
On Tue, May 19, 2015 at 2:30 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:
Hello,
Unfortunately Xquartz version 2.7.7 will not work with the version of
OSX that you are running.
You will either need to downgrade to version 2.7.5 (via the link I
provided below).
Hi Freesurfer users,
I'm trying to run the bbregister command on the brain.mgz file.
Here is the command line and resulting error:
[12239012@psych2 ~/001ER]$ bbregister --s 001ER --mov mri/brain.mgz --reg
register.dat
ERROR: cannot find 001ER in /usr/local/apps/freesurfer/5.1.0/subjects
I need
It looks like the SUBJECTS_DIR environment variable is probably set
incorrectly.
Does /usr/local/apps/freesurfer/5.1.0/subject/001ER exist? What is
SUBJECTS_DIR set to?
SUBJECTS_DIR should be set to the directory containing 001ER.
-Zeke
On 05/19/2015 11:48 AM, Stefani O'Donoghue wrote:
Hi
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