Ahh, that did the trick. Thanks!
On Fri, Jul 11, 2014 at 5:30 PM, Bruce Fischl
wrote:
> Hi Mark
>
> have you tried "conforming" the inputs (making them all 256^3, 1mm iso and
> 8 bits/voxel)?
> Bruce
>
> On Fri, 11 Jul 2014, Mark Plantz wrote:
>
> Hello
Hello freesurfers,
I am running into some sort of memory allocation issue when running
mri_ca_train. I am simply using an intensity volume and a segmentation
volume to create a GCA atlas. I keep getting this "segmentation fault: 11",
which is data allocation error. I have tried using all differ
/gm means were OK for skull stripping,
but then suddenly null for the other steps.
On Mon, May 12, 2014 at 7:49 PM, Bruce Fischl wrote:
> Hi Mark
>
> did you create your own .gca file? If so, why? Does it happen for all your
> subjects?
> Bruce
>
>
>
>
>
> On Mo
previous steps? I did include the -nogcareg flag with the recon-all command.
On Mon, May 12, 2014 at 4:36 PM, Mark Plantz <
markplantz2...@u.northwestern.edu> wrote:
> Hi Freesurfers,
>
>Does anyone know if it is possible to manually set the brain centroid
> during the EM Re
Hi Freesurfers,
Does anyone know if it is possible to manually set the brain centroid
during the EM Registration step of the recon-all pipeline. I am using a
non-default atlas, and have discovered that many of my difficulties have
resulted from the brain centroid being incorrectly assigned to a
Hi freesurfers,
I am running into an error where the white matter and gray matter means
of my atlas are automatically setting to 0 during the #@# CA Normalize
pathway. I copied a code segment below to help explain better. Has anyone
else run into this problem? Is there a way to manually change t
Hello freesurfers,
I recently attempted to fix the talairach.lta file from a bad recon-all
run for one of my subjects. I originally thought that the second pass of
recon-all would automatically load this talairach file. However, it looks
like the talairach alignment keeps restarting each time
ot an option". Is
there another way to check talairach.lta?
On Fri, Jan 17, 2014 at 4:06 PM, Bruce Fischl wrote:
> see if the talairach.lta looks reasonable
>
>
> On Fri, 17 Jan 2014, Mark Plantz wrote:
>
> Hi Bruce,
>> The nu.mgz file looks OK to me (I also attache
Hello freesurfers,
I am running into a problem during the "CA Normalize" sequence of
autorecon-2. It looks like freesurfer is having a hard time creating
control points based off the atlas I am using. The output is as follows:
"finding control points in ...found 0 control
points"
Thi
Hello freesurfers,
Does anyone know the physical meaning of the "transform matrix" and
the "quasinewton matrix" outputted during "EM Registration" of auto-recon2?
For some odd reason, both of them are identity matrices (one's along the
diagonal). I am almost certain that should not be the cas
Not sure if this helps, but you can alter the output orientation using the
flag "--out_orientation" followed by LIA (for example). Maybe the input
file needs to be in a specific orientation before it can be converted
properly.
On Wed, Dec 4, 2013 at 9:56 PM, prasser wrote:
> Hi,
>
> I'm curren
Hello all,
I am experiencing an error during the mri_ca_normalize step of
auto-recon-1 using a non-default atlas (for infant brains). Essentially,
"norm.mgz" and "ctrl_pts.mgz" are both outputting as blank files
(completely black). However, brainmask.mgz looks completely fine, which
leads
Hello freesurfers,
I am currently attempting to run recon-all on infant subjects with a
newly created 'gca' atlas. I e-mailed the listserv a while back about a
strange memory allocation error that occurred right at the beginning of the
"subcortical segmentation" pipeline. For a while, we thou
PM, Z K wrote:
> I think the best way to diagnose the issue would be to run the subject
> using the standard atlas provided with freesurfer. If that runs to
> completion that the .gca is almost certainly the source of the problem.
>
> -Zeke
>
>
> On 08/19/2013 03:0
Hello all,
While running recon-all for a subject, I ran into the following error
message:
*reading aseg from
/Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/aseg.auto_noCCseg.mgz*
*reading norm from /Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/norm.mgz*
*0 voxels in left wm, 0 in right w
Hello freesurfers,
I have an image that is in RAS orientation with the axial primary slice
direction. Is there anyway to change this to LIA orientation with the
coronal primary slice direction? I am assuming mri_convert would work, but
I'm not sure which flags to use.
Thanks in advance.
MP
__
It is currently in INT format. Thank you.
MP
On Wed, Aug 7, 2013 at 11:51 AM, Bruce Fischl wrote:
> yes, mri_convert -odt float will do it. What format is it in?
>
>
> On Wed, 7 Aug 2013, Mark Plantz wrote:
>
> Hello freesurfers,
>>I am currently attempting to run
Hello freesurfers,
I am currently attempting to run mri_ca_train to create a .GCA atlas
based of off a series of subjects. I am receiving the following error:
***
processing subject CMH-3074, 1 of 10...
mri_ca_train: segme
0. 1.
On Mon, Aug 5, 2013 at 11:41 AM, Bruce Fischl wrote:
> can you send us the full command line and screen output of what you ran?
>
> On Mon, 5 Aug 2013, Mark Plantz wrote:
>
> For some reason, when I run that command, I get the following output:
>> Input
hanks!
MP
On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl wrote:
> yes, I think so
>
> On Mon, 5 Aug 2013, Mark Plantz wrote:
>
> thank you. Would the command simply be something like this: mri_modify
>> -tr 0 -te 0 -ti 0 -fa 0 ?
>>
>>
>> On Thu, Aug 1, 201
-- Forwarded message --
From: Mark Plantz
Date: Mon, Aug 5, 2013 at 11:32 AM
Subject: Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train
To: Bruce Fischl
thank you. Would the command simply be something like this: mri_modify -tr
0 -te 0 -ti 0 -fa 0 ?
On Thu, Aug 1
Hello freesurfers,
I currently have a series of images with various TR,TE,TI,FA values. I
would like to use mri_ca_train to create a .gca atlas based on these
segmented volumes. Unfortunately, they all have slightly different control
parameters (TR,TE,TI,FA). Is there any way around this probl
Yep, it is also down for me. Just happened recently, because it was working
less than an hour ago.
- Mark
On Mon, Jul 29, 2013 at 1:06 PM, Caspar M. Schwiedrzik <
cschwie...@mail.rockefeller.edu> wrote:
> not sure whether others are experiencing this as well, but the
> freesurfer wiki seems to
g
>
> On 07/24/2013 03:21 PM, Mark Plantz wrote:
>
>> I guess the problem is that those regions should not be out of bounds.
>> Maybe I need to create a new Lookup Table for the infant mri's? Is that
>> possible to do?
>>
>>
>> On Wed, Jul 24,
Nevermind, it turned out to be a permissions issue. Thanks!
On Wed, Jul 24, 2013 at 10:12 AM, Mark Plantz <
markplantz2...@u.northwestern.edu> wrote:
> Thanks for the reply Doug. I recently ran the bbregister command and
> attempted to view the results using tkregister2. I
roblem, but it might. In
> any case if they aren't registered it won't generate a useful atlas, even
> if it does run to completion
> Bruce
>
>
> On Tue, 23 Jul 2013, Mark Plantz wrote:
>
> Hello freesurfers,
>> I recently ran into a problem with mr
, Douglas Greve wrote:
>
> You can try using bbregister. Normally, you don't use bbregister on a
> segmentation, but the segmentation index numbers just happen to be
> "T1-weighted".
> doug
> ps. Please remember to copy the list when responding. thanks!
>
>
&g
Hello freesurfers,
I recently ran into a problem with mri_ca_train, a function that
creates a .gca atlas from a manually segmented volume and input volume(s).
My command line is:
mri_ca_train -T1 T1.mgz CMH-11460 CMH-11461 ~/Desktop/atlas.gca
The results:
processing subject CMH-11461, 1
Hello freesurfers,
I am currently trying to create a normalized .mgz file using the
mri_ca_normalize command. Instead of using a .gca atlas, I am using a
manually segmented image.
I have tried using the -seg flag. However, I keep getting an error that
I am not inputting the correct argumen
Hello,
I have a quick question about talairach transform. I know that
FreeSurfer previously used mritotal to create the linear talairach
transform. You could check the "final objective function value" in the
mritotal.log file. I think the ideal value was in the ballpark of 0.06.
Is there a
Hello freesurfers,
I am currently attempting to create a normalized .mgz file from an
input brain using mri_ca_normalize. Ultimately, I will use the norm.mgz
file to create a .gca atlas for infant MRI's.
Currently, I have three of the four required arguments. I am lacking the
talairach.lta
arguments (prefixed with a dash)
> must come before all the mandatory ones. Also, you shouldn't give it the
> mri directory - give it an input volume (like nu.mgz).
>
> cheers
> Bruce
>
>
> On Tue, 2 Jul 2013, Mark Plantz wrote:
>
> Hello,
>>I am currently
Hello,
I am currently having some difficulties with the mri_ca_normalize
command. I am attempting to create a normalized volume file using an input
brain with the following command:
mri_ca_normalize
/Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/ -seg
/Volumes/Wong_Lab/Cochle
nfant templates
(.nifti format) to work with the FreeSurfer recon-all process.
Thank you.
- Mark Plantz
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The information in this e-ma
Thanks for the help.
- Mark
On Mon, Jun 24, 2013 at 3:02 PM, Bruce Fischl wrote:
> Hi Mark
>
> can you clarify what you mean? What template are you referring to?
>
> Bruec
>
> On Mon, 24 Jun 2013, Mark Plantz wrote:
>
> Hello freesurfers,
>> I am currently
.tiff image
to use as an actual template for reconstruction with FreeSurfer?
If so, would the conversion distort/ruin the template?
Thank you!
- Mark Plantz
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:
/Applications/freesurfer/subjects: Permission denied.
Any ideas on how to solve this problem? Is it a licensing issue? I have
already created the .license file.
Best,
Mark Plantz
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