Dear freesurfers,
currently the freesurfer single tfl protocol for the segmentation of the cortex
surface was implemented at our scanner.
Siemens Verio 3T MRT
NumarisVersyngo MR B17
Gradientensystem (Tim 102x8) VQ-Engine
Unfortunately the echo-time (te) could not be set to the
Hi all,
I've got an error while running mri_glmfit-sim. I ran this for several
measures, and only for 'volume' and 'area' the function complained about
missing CSD files stating ERROR: cannot find any csd files
I don't know if this is a known issue. I saw several threads posted
regarding this
Hi Jörg
T1-weighted image contrast decreases with increasing TE so you want to
minimize it. Can you really not change it at all? I've never heard of that.
Whas is the default TE?
cheers
Bruce
On Mon, 14 May 2012, Jörg Pfannmöller wrote:
Dear freesurfers,
currently the freesurfer single
Hi Jorg,
I think the Siemens tfl (MPRAGE) sequence automatically sets the TE to
the lowest possible value consistent with the choosen bandwidth,
gradient mode, and performance of your gradient set.
In all likelihood, I'm guessing that the value was still less than 4 ms
on your system, right?
I don't know what that means. It is not an FS issue, it is something
wrong on your system.
doug
On 05/14/2012 06:17 AM, Long wrote:
Hi Douglas,
I used the command:
tkmedit fslt1mnifs orig.mgz ./lh.zmap.mgh
but it said: Resource temporarily unavailable.
Best,
Xiangyu
On Tue, Apr 24,
Can you send your command line and terminal output?
On 05/14/2012 09:26 AM, Juke Cha wrote:
Hi all,
I've got an error while running mri_glmfit-sim. I ran this for several
measures, and only for 'volume' and 'area' the function complained
about missing CSD files stating ERROR: cannot find
Is there a way to adjust the grey and white matter of the aseg automatically
based on the surfaces?
Thanks,
Matt.
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The
mri_edit_segmentation_with_surfaces
usage: mri_edit_segmentation_with_surfaces [options] aseg name surface
dir norm volume output volume
This program edits an aseg with the surface
valid options are:
-l label file - limit calculations to specified label
-hypo 1|0
How do I check this? (Apologies for my ignorance.) So I might need to just use
a different set of dicoms then?
thanks,
Mia
From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 1:02 PM
To: Borzello, Mia
Cc:
Hi Hanah, I found another bug with the way that tNullMin was being
implemented which causes this problem. You can get the new version from
here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2.linux
doug
On 05/14/2012 08:47 AM, Hanah Chapman wrote:
Dear Doug,
Thank you
You can do:
tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
When you downloaded FreeSurfer, you would have also received the subject
bert who is a good example to compare to. He will likely be located in:
$FREESURFER_HOME/subjects/bert
If you do the same command above for
It says that it couldn't open rh.orig.nofix and lh.orig.nofix. On the popup
image, it doesn't look like the skull is present, but it does look like the
cerebellum is.
From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012
(1) Version: optseq2.c,v 2.21.2.1
(2) Computer operating system: Mac OS X Version 10.7.3
(3) Command line: Not relavant here
(4) Description of the problem: A trial in my experiment involves a
countdown (duration 2 seconds) followed by the event of interest (0.5
seconds) followed by a blank
In this case, the event will be 7 sec. The way it is set up, it assumes
that you will use an FIR model to analyze the results (ie, not assuming
a shape to the HRF), making it difficult to separate the various
subevents to the event (though you can assume a shape to the HRF). It is
appropriate
would it be worth it at this point, to use another set of dicoms?
thanks,
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Monday, May 14, 2012 1:37 PM
To: Allison Stevens Player
Cc:
If you happen to have another MPRAGE for this subject, sure, you can try
it.
Allison
On Mon, 14 May 2012, Borzello, Mia wrote:
would it be worth it at this point, to use another set of dicoms?
thanks,
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
Hi Mia,
You may want to check your talairach to make sure that looks okay. If
that's not causing the problem, you can edit the wm.mgz to remove the
cerebellum and then rerun and this should fix the problem.
Allison
On Mon, 14 May 2012, Borzello, Mia wrote:
It says that it couldn't open
Hey Allison,
Thanks for you help. What do you mean by check your talairach? I'll hold off on
using a different set of dicoms, and make that my last resort since it takes a
day to complete.
Thanks,
m
From: Allison Stevens Player
There are instructions on how to check it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
On Mon, 14 May 2012, Borzello, Mia wrote:
Hey Allison,
Thanks for you help. What do you mean by check your talairach? I'll hold off
on using a different set of dicoms, and make
Hi Mia
can you clarify what you mean by a different set of dicoms? Did you
acquire more than 1 T1-weighted structural on this subject? And can you
send us an image of the acquisition, say in coronal view?
thanks
Bruce
On Mon, 14 May
2012, Borzello, Mia wrote:
Hey Allison,
Thanks for you
actually I wanted one from tkmedit. Can you tell us something about the
acquisition? What kind of scan is it? What resolution? And if you can
send us images from tkmedit in coronal and sagittal view that would help
too (say of the orig.mgz)
Bruce
On Mon, 14 May 2012, Borzello, Mia wrote:
I
so that's most likely the problem?
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:46 PM
To: Borzello, Mia
Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] cannot allocate memory issue
oh woops. sorry.
so both of these sets of dicoms are T2
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:46 PM
To: Borzello, Mia
Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] cannot
yes, that's the kind of thing I was worried about. You need a relatively
high resolution set of T1s (mprage, FLASH/SPGR, close to 1mm isotropic).
On Mon, 14 May 2012,
Borzello, Mia wrote:
oh woops. sorry.
so both of these sets of dicoms are T2
From:
okay, well i'll give it a try with a set of T1s. Thanks guys!
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:57 PM
To: Borzello, Mia
Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] cannot
Dear Freesurfers,
Over the last years, MR imaging technology hasimproved such that sub 1-mm
isotropic scans can be obtained with good signal to noise characteristics.
For example, our lab uses 0.7mm isotropic structural MR images. I
understand that the Freesurfer pipeline will up-sample these to
Hi Joshua
yes, we already have upgraded mris_make_surfaces to take higher res data
and refine the surfaces with it. Haven't tried it on the aseg yet, but if
you upload a sample dataset I could see how hard it is.
cheers
Bruce
On Mon, 14 May 2012,
Joshua Lee wrote:
Dear Freesurfers,
Over
I'd be interested to hear how this goes too.
Thanks,
Matt.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, May 14, 2012 4:09 PM
To: Joshua Lee
Cc: FreeSurfer
Subject: Re: [Freesurfer]
Hello all,
I am trying to create a template for longitudinal processing and am running
into some problems generating the file. I have many subjects so I am
running a batch script. I am using version 5.1.0
Any suggestions?
Thanks!
Corinna
Here is my script:
#!/bin/tcsh
setenv FREESURFER_HOME
Hi corinna,
Can you send the corresponding call to recon-all that your script generates?
Best Martin
On May 14, 2012, at 18:27, Corinna Bauer corinna...@gmail.com wrote:
Hello all,
I am trying to create a template for longitudinal processing and am running
into some problems generating the
Hi all
I have some longitudinal data ready for the group analysis but I have a doubt:
Can I simply use the following command to resample all left hemisphere
thickness maps onto the fsaverage surface (as in traditional cross-sectional
analyses)?
mris_preproc --fsgd fsgd.txt --target fsaverage
Hi Bruce,
Is there a flag for this on recon-all? Or do you need to use
mri_make_surfaces directly?
Best,
Michael
On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Joshua
yes, we already have upgraded mris_make_surfaces to take higher res data
and refine the
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