Hola Gonzalo,
field strength affects T1, so different field strengths (e.g., 1.5T vs
3.0T) give somewhat different T1 contrast, which Freesurfer uses to
estimate surfaces and boundaries to then thickness and volumes. You
would have probably found also morphometric differences even if you
would
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
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Thank you! I will try this.
On Tue, May 19, 2015 at 2:30 PM, Z K 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). Or you will need to upd
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 o
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 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 mesh_vertex_nea
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 s
Hello,
I have a general design question about variation in the duration of null
intervals.
After running optseq with tnullmin set to 4 and tnullmax set to 10, the
null intervals were nearly all 4 seconds in duration, with a few of 5
seconds. Is it generally a problem to have mostly identical null
um-White-Matter (12652-14902), right Cerebellum-Cortex
> (48812-51935), etc... And a similar situation occurs in left
> hemisphere...
> The Intracranial volumen in both cases is: 1348899,976 and
> 1332590,755197... Why is the difference in volumen in the structures in
> bot
ight cerebral white matter (151164-172448), right
> Cerebellum-White-Matter (12652-14902), right Cerebellum-Cortex
> (48812-51935), etc... And a similar situation occurs in left hemisphere...
> The Intracranial volumen in both cases is: 1348899,976 and
> 1
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 take
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
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
b
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
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
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 can
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 is:
Hi Amolie
you only want a single -i 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,
Greatly appr
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 res
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 -mcex
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.
T
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