Navid,
Are you needing to convert the thickness.mgh file or a surface (e.g., ?h.pial,
?h.white, etc) file to .vtk? We've used mris_convert many times to create .vtk
files from FS surfaces. The command is fairly straightforward.
mris_convert /?h. /?h..vtk
I'm not sure you can convert the th
Two questions:
1. We installed the latest version of 32-bit FS on several workstations
running CentOS 5.1 in our lab. However, once we ran the CentOS updates
(~280 of them through up2date), tkmedit now fails to open and tksurfer
exhibits behavior exactly as described in this message from the mai
Nick,
Yes, our tcltktixblt directory was intact and set correctly. The reason I
thought it was a BLT lib was it came up missing when I ran fs_lib check.
At any rate, the DefaultDepth is already at 24 in our xorg.conf file and
the problem persists. Any other thoughts what might be occurring? Wo
`which tksurfer.bin`
I will be looking to see if the proper tcl/tk/tix/blt libs are being
used (those in freesurfer/lib/tcltktixblt).
Nick
On Thu, 2008-10-09 at 11:15 -0500, Derin Cobia wrote:
Nick,
Yes, our tcltktixblt directory was intact and set correctly. The reason I
thought it was a BLT li
We're running subjects under the new 4.3.0 version (CentOS 4
platform), and are experiencing the following error during the
cortical ribbon mask stage:
#...@# Cortical ribbon mask Wed Apr 8 07:12:20
I'm assuming FreeSurfer should work with the new OS given the relative
minor adjustments to it, but wasn't sure. You may not have a copy of
it yet, but was wondering if you knew of any foreseeable problems.
Thanks.
-Derin
___
Freesurfer mailing li
I would be interested in this as well.
-Derin
On Oct 16, 2009, at 11:40 AM, Doug Greve wrote:
>
> Good point (meaning that I don't know the answer). I'll see if I can
> find out.
>
> doug
>
>
>
> On Fri, 16 Oct 2009, Donna Dierker wrote:
>
>> Regardless: FDR's sensitivity appears resolution-de
FYI-
We've been experiencing much faster run times on the new Core i7
architecture (for both Mac and Linux machines), on the order of 16-18
hours for the entire recon-all ("-all') pipeline. Although your
mileage may vary (depending on scan quality, amount of RAM, etc). The
Radeon 4850 c
Posted on behalf of a colleague:
FACULTY POSITION, MEG-fMRI NEUROIMAGING
Saint Louis University, is a Jesuit, Catholic university dedicated to
teaching, research, health care and community service and is seeking a
scientist at an open rank level for a non-tenure track, grant-funded
fac
Nathan,
Here are the steps I use to create QDEC dat files on a Mac:
-Export/save your data in SPSS/Excel as a .csv file
-Open the .csv file in TextWrangler (a free text editor for Mac)
-Do a Find & Replace of the "," for " " to make it a space
separated file
-Down at the bottom of the TextWran
Doug,
I think what Emily wants to do is something like running mri_glmfit on an ROI
(i.e., surface label drawn in QDEC). Then be able to display the results in
tksurfer, showing flame-scale map results for only the ROI/label (not just
singular values for the entire ROI/label). Would this be w
(Questions for all, but maybe more directed towards Martin)
I have some questions about manual edits in regard to the longitudinal stream.
Based on the current info on the wiki page, it appears that no edits are pushed
forward from the cross-sectional (initial) runs of the subject data, as any
Bumping this back up to the list. Could someone please address?
To be more concise, during longitudinal processing, where are wm/gm edits made?
On the cross-sectional runs, to the base, or on the .long. runs themselves?
Thanks.
-Derin
Begin forwarded message:
> From: Derin Cobia
>
Martin,
Not to add more to the confusion, but what if the final longitudinal scans are
"not fine" and need some editing. Can they be rerun in the standard way to
incorporate edits (e.g., -autorecon2-cp -autorecon3 ... ), or should something
different be done? Will rerunning these edited long
Along these same lines, is it possible to overlay/display a Cartesian grid on
the surface, a la the Neuroimage '99 II paper (Fig 7)? And is it possible to
specify what the 'north pole' of this coordinate system is? For example, if I
wanted it to be at the posterior end of the STS. I'm looking
;re welcome to poke through it, but I'm not sure it works
> anymore.
>
> sorry for the unhelpful answer :<
> Bruce
>
>
> On Thu, 25 Mar 2010, Derin Cobia wrote:
>
>> Along these same lines, is it possible to overlay/display a Cartesian grid
>> on the sur
Bruce,
Sorry, I think I was confusing. Basically I was wondering how the numbers
in mris_anatomical_stats are calculated, and if I can independently verify
them. Does a paper/article address this? Thanks again for your help.
-Derin
> Hi Derin,
>
> no, they aren't quantized - they are computed
Hi again,
Two questions:
1). You said earlier that GM volumes from mris_anatomical_stats are more
accurate than from the aseg files. Would you recommend using the
surface-based GM volumes instead of the ones from the aseg.stats files? I
ask because we have ~200 subjects processed for volume, b
Hello,
I read in the archive that you were planning on releasing two new atlases
(for MP-RAGE and FLASH) last year. Were those (or even newer ones)
distributed? I have some FLASH sequences I want to run. Thanks!
-Derin
___
Freesurfer mailing list
Hello,
After having run -autorecon1 on all of my subjects I've noticed
skullstripping has edited out the cerebellum/brainstem on some, but not on
others. Because I'm not interested in these structures, can I just leave
the files as is (i.e.-not bother adjusting the wsthreshold level,
re-running,
I've been experiencing some crashes/freezing using tkmedit lately, and
have been able to reproduce it pretty reliably. It occurs when I scroll
through the slices of the subject either using the arrows keys or clicking
through on the toolbar. It happens when viewing a variety of volumes
(brainmask
t Mon Aug 28 04:00:54 CDT 2006
> Hm, I can't reproduce this.
>
> So, you load up a volume, and repeatedly press an arrow key to scroll
> through the slices? Or hold the button down?
>
> On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote:
>> I've been e
re these processed any differently? The .xdebug_tkmedit should be in pwd
> wherever you ran it from.
>
> Bruce
>
>
> On Tue, 29 Aug 2006, Derin Cobia
> wrote:
>
>> Kevin-
>> Yeah, either way. In my "infinite" wisdom I thought that scrolling
>> s
the drivers for the video card, and haven't had any
>> issues
>> (yet). I'll keep my eye on it. Thanks for your help.
>>
>> -Derin
>>
>> > were these processed any differently? The .xdebug_tkmedit should be in
>> pwd
>> > wherever yo
Bruce,
I worked my way backwards through the stream on each .mgz file. The
aseg.mgz (and aseg.auto.mgz) file came up in pieces, some parts were
there, others weren't; brain.mgz was blank, there was nothing there, as
well as the values being 0; the same for norm.mgz. However, both
brainmask & nu.
I seem to be having some difficulty in converting my flash images into FS
format for processing. After using mri_convert my orig.mgz files become
excessively bright compared to the original analyze file, thus creating
poor autorecon1 output, etc. See the attached jpgs of before and after
shots.
Bruce,
I've been getting values from around 188-255 in the wm.
-Derin
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
wrong. Thanks!
-Derin
> Hi Derin,
>
> the attachment came through fine, but I need the unconformed (e.g.
> 001.mgz) volume in order to diagnose what went wrong.
>
> Bruce
> On Fri, 13 Oct 2006,
> Derin Cobia wrote:
>
>> Here is the orig.mgz file. Been having trouble
Hi,
Currently we've been converting from .img to .mgz format using the
following syntax:
mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz
s1501p.img mri/orig/001.mgz
It came to my attention today that the values we used for TI, TE, and TR
are all actually in ms, and corresp
e's not much you can do
>
> cheers,
> Bruce
>
>
> On Mon, 6 Nov 2006, Derin
> Cobia wrote:
>
>> Should I expect this kind of quality/resolution from my FS images based
>> on
>> the original scan (see attached images)? These are older scans that
>>
Some of the scans I work with are of the same subject, but differ only in
the length of time they were in the scanner. Obviously the scans of
longer length (everything else being equal) will yield better quality;
however, I'm interested in a kind of "bang-for-your-buck" approach. Is
there a point
> cortex)
>
> cheers,
> Bruce
> On Wed, 31 Jan 2007, Derin Cobia wrote:
>
>> I reran our subjects from "final_surfaces" on through autorecon3 using
>> 3.0.4 to correct for the pial surface crossover at the midline (as
>> recommended by Bruce). Most t
topological
>>> defect
>>> in the hippocampus. You could manually correct it in the wm.mgz volume,
>>> but we don't really care about the surfaces in this region (cerebral
>>> cortex)
>>>
>>> cheers,
>>> Bruce
>>> On Wed
I would like to calculate total brain volume (defined as: total white,
gray, and subcortical altogether). Should I take the BrainSegVol and
minus out cerebellum and ventricles, or add the white and gray matter
volumes from mris_anatomical_stats (it seems I remember hearing that white
matter from m
n-all.
>
> cheers,
> Bruce
>
>
> On Fri, 2 Feb 2007, Derin Cobia wrote:
>
>> I would like to calculate total brain volume (defined as: total white,
>> gray, and subcortical altogether). Should I take the BrainSegVol and
>> minus out cerebellum
dd in whatever subcortical components you wanted to
>> include, as they are excluded from the wm volume
>> On Fri, 2 Feb 2007, Derin Cobia wrote:
>>
>>> Bruce,
>>>
>>> So if I downloaded the dev version of the program I could use it to get
>>&g
CentOS 4 (32-bit). Thanks!
-Derin
> sure. Tell us what platform and Nick can post it for you
> On Mon, 5 Feb 2007,
> Derin Cobia wrote:
>
>> Is there any way I can get mris_wm_volume? If not, what's the next best
>> thing? Can I use the aseg.stats estimates?
>&
5 Feb 2007,
> Derin Cobia wrote:
>
>> Is there any way I can get mris_wm_volume? If not, what's the next best
>> thing? Can I use the aseg.stats estimates?
>>
>> -Derin
>>
>>>
>>> I have not implemented it in recon-all yet.
>>>
&g
Not sure if this went through the first time yesterday, here it is again.
Thanks.
I've noticed that the gray matter volume output from mris_anatomical_stats
(lh) vs. mris_volume (lh.pial) differs. Am I missing something? Do I
need to run mris_volume for a different surface? Thanks.
-Derin
!
-Derin
> you would need to subtract the ?h.white volume from the ?h.pial to get
> gm volume
>
> On Tue, 6 Feb 2007, Derin Cobia wrote:
>
>> Not sure if this went through the first time yesterday, here it is
>> again.
>> Thanks.
>>
>>
>> I
For one of our projects. We're using cortical gray matter for another
(which I wanted to clarify).
-Derin
> On Tue, 6 Feb 2007, Derin Cobia
> wrote:
>
>> Then is there a reason to use mris_volume when I can just do
>> mris_anatomical_stats and forget the math?
>&
I have a question regarding editing the pial surface. Many times it
includes bright spots, such as fat or vessels. Should I be editing this
out? I'm pretty clear on getting rid of included dura, but if I spent the
time to edit out every little bright spot, it would be pretty time
intensive. Wou
I noticed that one of our subjects made it through the processing stream
(successfully) with the cerebellum missing, thus creating a bad aseg.mgz.
I filled it back in, and was wondering if I needed to reprocess it
completely under autorecon2 and 3 again, or just run -aseg and whatever
else it need
Two questions for two different subjects during autorecon1:
1. The initial skull strip on this subject left too much extra-cerebral
material. Subsequent attempts at using the wsatlas or manual adjustment
of the wsthresh have resulted in this error:
*WATERSHED*
r
> correct it manually with tkregister2, or remove/rename the talairach.xfm
> and talairach.auto.xfm use recon-all with -notalairach so it won't be
> rebuilt. Nick: is there a flag to ignore the tal xform even if it's there?
> Something like -badtalairach?
>
> cheers,
> Br
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary
appropriately. What should I try next?
-Derin
> this is probably a topology fixing problem. Look at the ?h.orig.nofix and
> see how it is
> On Fri, 13 Apr 2007, Derin Cobia wrote:
>
>> Did you mean wm.m
.
-Derin
> it looks like there is an (incorrect) connection in the wm.mgz from the
> temporal lobe across the insula. The data also looks really noisy - what
> is the acquisition? You'll need to erase some stuff form the wm.mgz I
> think.
>
> On Fri, 13 Apr 2007, Derin
white matter edits:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
>
> Nick
>
>
> On Fri, 2007-04-13 at 15:31 -0500, Derin Cobia wrote:
>> Here is a pic of the inflated.nofix, how do I know what to edit? I've
>> checked the wm.mgz and it
Is this something the rest of us need to worry about? I've been checking
some of my data and don't believe I'm finding the same problem as Alex.
Thanks.
-Derin
> Hi Alex,
>
> sorry, this is an unintended consequence of the code that prevents the
> surface from deforming into non-cortical struct
I'm getting the following error on several of my subjects during the
aparc2aseg stage:
_
[EMAIL PROTECTED] AParc-to-ASeg Sat Jun 9 12:19:58 EDT 2007
/disk/eli/freesurfer/conte_flash/5111
mri_aparc2aseg --s 5111 --ribbon
SUBJECTS_DIR /disk/eli/freesurfer/conte_flash
subj
How is the volume of each cortical structure (and hemisphere) calculated?
It seems I remember from somewhere that it is the thickness x average
surface area of the tesselated triangles? Is this right? What I'm most
interested in is how the cortical gray matter volume from
mris_anatomical_stats is
what is going
> on.
>
> Currently I am working on testing out the 5.0 fix and some other
> possible improvements...
>
> Best, Martin
>
> On Fri, 2010-09-03 at 13:54 -0500, Derin Cobia wrote:
>> Based on our understanding of the longitudinal pipeline for 4.5, image e
I'm experiencing this as well on my Mac OS X distribution of FS v5.0.0. Here
is terminal output when running the "Map Label to Subjects" command on the rh,
with a rh label in QDEC (below). Looks like there is a small bug in the code
where it points to the left hemi for registration instead of
So if I understand correctly, you would not recommend getting a jump start on
cross-sectional processing and editing under 5.0, rerunning everything under
5.1 once it comes out, then run (for the first time) longitudinal under 5.1?
Are there going to be some incompatibilities with 5.1, where it
All,
Just curious about the current estimated timeline for version 5.1, trying to
schedule some projects around it. Thanks!
-Derin
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf
I'm curious about the use of this method as well (thanks for the paper PPJ).
Bruce/Doug, how exactly does QDEC treat this design? Can a single-subject
comparison properly be done? Thanks.
-Derin
On Mar 23, 2011, at 4:11 PM, Pedro Paulo de Magalhães Oliveira Junior wrote:
> We have dono s
Hi Doug,
To follow up on this question, we were able to calculate effect sizes for every
vertex on the surface using the gamma(var).mgh files, as well as an average
effect size across each hemisphere surface using the equation below. In
determining alpha, would the most appropriate method be t
I received the follow error while running a set of subjects under
'long_mris_slopes,' and wasn't able to decipher the problem. It appears that
mris_calc is not able to do the division for these files (dividing by 0
perhaps?). Any help appreciated, here's the command and tail end of
output/err
58 matches
Mail list logo
