Hi Freesurfers,
I'm wondering if you can help with the following error that occurred when
trying to create a reconstruction:
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
RedHat release: CentOS release 6.5 (Final)
Kerne
PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error
Hi Mia
can you send us the recon-all.log? I don't think you included the error
message in your email so there isn't much for us to go on.
thanks
Bruce
On Thu, 8 Jan 2015, Borzello, Mia wrote:
>
> Hi Free
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, January 08, 2015 4:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error
did you look in
/autofs/space/huygens_001/users/mia/subjects
Can you send us the screen output of recon-all?
On Thu, 8 Jan 2015, Borzello,
Mia wrote:
> I looked
Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia
> Sent: Friday, January 09, 2015 5:30 PM
> To: Freesurfer support list
>
urfer support list
Subject: Re: [Freesurfer] recon-all error
does that dicom exist? Can you run ls -l on it?
On Sat, 10 Jan 2015,
Borzello, Mia wrote:
> I just fixed that but I'm still getting an error. I attached a screenshot.
>
> Thanks,
> Mia
> __
rfer support list
Subject: Re: [Freesurfer] recon-all error
Hi Mia
you need to run it with the full path of the dicom you are trying to give
to recon-all
cheers
Bruce
On Tue, 13 Jan 2015,
Borzello, Mia wrote:
> Okay, just ran ls-l and don't see it- image attached.
> ___
Hi Freesurfers,
I'm looking at Freesurfer files from are from years ago trying to look at the
ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so I'm
wondering if there is a way to create it. In trying to find an answer online, I
found this:
https://mail.nmr.mgh.harvar
t: Re: [Freesurfer] converting .nii to .mgz
Hi Mia
If all you want to do is convert try
mri_convert ct.anat.nii ct.anat.mgz
Cheers
Bruce
> On Jan 19, 2015, at 10:33 PM, Borzello, Mia wrote:
>
> Hi Freesurfers,
>
> I'm looking at Freesurfer files from are from years ago trying
: Tuesday, January 20, 2015 7:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] converting .nii to .mgz
Hi Mia
can you please send us the full command line? And also do an ls -l of
that file and include it?
thanks
Bruce
On Tue, 20 Jan 2015, Borzello, Mia wrote:
> Hi Bruce,
>
&g
yes, definitely. I just tried to upload to this email:
freesurfer@nmr.mgh.harvard.edu
and it says "Server Error! User 'freesurfer' is not a valid NMR Account holder"
I have a feeling this is a user error- sorry about that.
Thanks,
m
From: freesurfer-boun
e one you have below, ie
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
On 01/20/2015 11:26 AM, Borzello, Mia wrote:
> Hi guys,
> full command line: mri_convert ct.anat.nii ct.anat.mgz
>
> command line: ls -l
> /autofs/space/huygens_00
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] converting .nii to .mgz
does
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz
exist?
On 01/20/2015 03:40 PM, Borzello, Mia wrote:
> Okay, cool, I just tried with the full path to the .nii file and it worked.
> However, when I tr
Also, i didn't attach the error I got- please see attached.
Thanks!
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Tuesday, January 20, 2015 4:21 PM
To: Freesurfer support
I'm having the same issue- any updates on this problem that Jason Naftulin
posted?
Thanks,
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Naftulin, Jason Scott
Sent: Friday, February 27, 2015 2:50 PM
To: frees
You'll have to add the # of vertices in one hemi to all the indices in the
other (so that the indices remain unique, then concatenate them into a
single surface tesselation and write it out
On Thu, 5 Mar 2015,
Borzello, Mia wrote:
> I'm having the same issue- any updates on this
Hi Freesurfers,
I'm having some trouble computing the pial layers. Below are the details.
Thanks!
Here is the output from "bugr":
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
RedHat release: CentOS release 6.5 (Final)
K
Hi Freesurfers,
Hope you're doing well! I tried creating a reconstruction yesterday but got an
error.
1)BI22
2)recon-all -autorecon1 -autorecon2 -autorecon3 -subject BI22_SurferOutput -i
/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/8961/8968/896583
3)
ERROR: talairach_afd: Talai
its a T1 and the orientation is correct, so it might
> recon.
>
> Nick
>
>
>
>
>> On Sun, 2015-05-17 at 16:33 +, Borzello, Mia wrote:
>> Hi Freesurfers,
>>
>>
>> Hope you're doing well! I tried creating a reconstruction yeste
Hi Freesurfers,
I ran recon-all and didn't initially get an error. I am not plotting the
surface in matlab and am getting an error but am not sure why. Any help would
be great! Thanks!
1) BW30
2) recon-all -autorecon1 -autorecon2 -autorecon3 -subject BW30_SurferOutput -i
/autofs/space/huygens_
f/lh.pial:edgecolor=red
> surf/rh.pial:edgecolor=red surf/lh.white:edgecolor=blue
> surf/rh.white:edgecolor=blue"
>
> then, to use:
>
> cd BW30_PreOp_MRI
> fv
>
> it will bring-up the major volumes and surfaces.
>
> N.
>
>
>
>> On Mon, 2015-05-18 at 20:02
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
o use:
cd BW30_PreOp_MRI
fv
it will bring-up the major volumes and surfaces.
N.
On Mon, 2015-05-18 at 20:02 +, Borzello, Mia wrote:
> Hi Freesurfers,
>
>
> I ran recon-all and didn't initially get an error. I am not plotting
> the surface in matlab and am getting an
Hi Freesurfer experts,
Does Freesurfer have a separate pipeline for registering NHP data? I am trying
to register macaque data and localize the implanted electrodes, but the normal
protocol errored. I did a google search and found this- is this what I should
be using?: https://surfer.nmr.mgh.ha
...@gmail.com]
Sent: Tuesday, August 04, 2015 9:36 AM
To: Borzello, Mia
Subject: Re: [Freesurfer] registering NHP data
Mia,
You could use the 112RM-SL atlas for normalization and then use the
Saleem-Logothetis Atlas for localization. Hopefully, by August, we'll have a
parcellation on the the MR
Hi freesurfers,
I want to localize electrode locations from a NHP CT scan, am i able to do that
with tkmedit without coregistering first? I don't need all the parcellations of
a specific atlas, just the RAS coordinates.
Also, the CT images are IMA files. Is there a way to convert from IMA to MG
Hi Freesurfers,
I'm trying to convert CT dicoms to the MGZ format, but am getting an error
saying "the pixel data cannot be loaded as it is JPEG compressed." I originally
got dicoms without the extension .dcm, but then resaved them with the
extension. Using either version didn't work. If you ca
e the dcmdjpeg to do the decompression like this
dcmdjpeg +te dicomfile dicomfile
this will overwrite the dicom file, so make a backup. You will have to
run this for all of your dicoms
doug
On 02/04/2014 10:31 AM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I'm trying to convert C
PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dicom loading difficulty
I would put the new ones into a different folder
doug
On 02/04/2014 02:35 PM, Borzello, Mia wrote:
> Hmm this didn't seem to work. I converted all 78 files. Is it okay to leave
> both versions of the
Hi Freesurfers,
I was wondering if there was a way to kind of fill in the blanks for a Surfer
Output folder. I am working with an old data set, and it seem that some of the
files are empty (0 bytes), "rh.pial" for example. Is there a way to pass the
SurferOutput folder in and recreate what's mi
31 PM, "Bruce Fischl"
> wrote:
>
> Hi Mia
>
> delete the 0 length files and run recon-all -make all -s
>
> cheers
> Bruce
>> On Mon, 10 Feb 2014, Borzello, Mia wrote:
>>
>> Hi Freesurfers,
>> I was wondering if there was a way to kind
Okay and is there a way to check if the files I currently have are sufficient
to plot with?
Thanks,
m
> On Feb 11, 2014, at 9:58 AM, "Bruce Fischl"
> wrote:
>
> if they are zero length there is nothing there now
>> On Tue, 11 Feb 2014, Borzello, Mia wrote:
&g
ischl [fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, February 11, 2014 10:51 AM
To: Borzello, Mia
Subject: Re: [Freesurfer] creating specific files
Hi Mia
can you keep ccing the list? I don't know what the "outer smoothed pial
surface" is. Is this something we create? I don't think
Another question- will I need to re-coregister if I rerun a reconstruction?
Thanks,
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Tuesday, February 11, 2014 11:05 AM
To: Bruce
Hi Freesurfers,
I get an error when using spmregister saying "Maximum variable size allowed by
the program is exceeded"- is that a problem with the number of dicoms?
I can attach a screenshot of the error if that helps.
Thanks,
Mia
___
Freesurfer maili
.edu]
Sent: Friday, February 28, 2014 11:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error at spmregister
never seen that. can you send your command line and the log file?
On 02/28/2014 11:43 AM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I get an error when using
Hi Freesurfers,
In general when aligning an MR and a CT, is a 32 slices CT sufficient? I've
done a coregistration and am looking at it in tkmedit and the quality of the
image isn't so good.
Thanks,
Mia
___
Freesurfer mailing list
Freesurfer@nmr.mgh.ha
Warning: Executing startup failed in matlabrc.
> This indicates a potentially serious problem in your MATLAB setup,
> which should be resolved as soon as possible. Error detected was:
> MATLAB:UndefinedFunction
> Undefined function or variable 'mne_setup_toolbox'.
>
>
&
gister I guess. What would be the
problem when I ran spmregister
Thanks,
m
From: Douglas Greve [gr...@nmr.mgh.harvard.edu]
Sent: Saturday, March 01, 2014 10:31 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error at sp
t: Re: [Freesurfer] tkmedit contrast
does the brightness/contrast window you display not work?
On 03/14/2014 12:59 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I recently coregisered a patient and am trying to visualize the
> electrodes in tkmedit now, but I'm unable to see them
Was there any solution for this?
Thanks,
Mia
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Friday, March 14, 2014 1:17 PM
To: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
Subject
7:16 PM
To: Freesurfer support list
Cc: Douglas N Greve
Subject: Re: [Freesurfer] tkmedit contrast
does it work in freeview?
On Wed, 19 Mar 2014, Borzello, Mia wrote:
> Was there any solution for this?
>
> Thanks,
> Mia
>
>
u, 20 Mar 2014, Borzello, Mia wrote:
> I haven't checked that yet- would i still be able to pick points in freeview?
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf o
Hi Freesurfers,
I am trying to coregister with a high-res CT, but for some reason am getting a
very sheered image when I am in tkregister. Should I use another CT?
Thank you!
1) MG93
2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig
3) no error message, just a sheer
your CT probably
On 11/20/2015 12:47 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I am trying to coregister with a high-res CT, but for some reason am
> getting a very sheered image when I am in tkregister. Should I use
> another CT?
> Thank you!
>
>
> 1) MG93
>
: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] sheered CT in tkregister2
look at them in freeview
9 dof means 9 degrees of freedom in the registration, 3 translation, 3
rotation, and 3 scale. The 3 scale may account for errors in the voxels
size of the ct
On 11/20/2015 12:54 PM, Borzello, Mia
Hi Freesurfers,
I'm in the middle of coregistering a CT and MRI, and after running
spmregister --s MGXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig
I get the error that orig.mgz is not found in COR or MGZ formats, but I have an
orig.mgz file in my folder. Any help on this would be
Hi freesurfers,
I working on a coregistration right now with a few different CT scans. None of
them have looked that good with tkregister (for example when I used one CT
scan, the electrodes didn't even show up). Is there an certain CT I need to be
using?
Thanks,
m
___
Hi freesurfers,
In using tkregister, I generated an odd (see attached): the image not only
looks sheered but there is an old white box showing up. I'm not sure how to
resolve this.
Thanks a lot,
Mia
<>___
Freesurfer mailing list
Freesurfer@nmr.mgh.har
Hi freesurfers!
Great tutorial this week!
I've recently run a recon, and it's exited with errors, but I'm not completely
sure why. I've attached the error.log, but le tme know if I should attach
another file.
Thanks so much,
Mia
error.log
Description: error.log
__
d.edu
Subject: Re: [Freesurfer] Exiting with errors but not sure why
Hi Mia, I'm glad your enjoyed the course. Can you send the recon-all.log
file from the subject/scripts folder?
doug
On 05/02/2013 11:36 AM, Borzello, Mia wrote:
> Hi freesurfers!
>
> Great tutorial this week!
>
Hi freesurfers,
I recently ran a reconstruction, but it's errored. I'm not sure why thought,
but I've attached the recon log.
Thanks,
Mia
--
SUBJECT MGH009_SurferOutput
DATE Mon May 13 11:25:37 EDT 2013
USER miaborz
HOST huygens
PROCESSOR x86_64
OS Linux
Linux hu
sorry, recon-all.log attached!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Tuesday, May 14, 2013 4:23 PM
To: freesurfer
Subject: [Freesurfer] Recon-all error
Hi freesurfers,
I recently
work.
Thanks so much,
Mia
From: Nick Schmansky [ni...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 14, 2013 4:57 PM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] Recon-all error
Mia,
Hi, in looking at the mri/orig/001.mgz, the image in the sagita
Hi Freesurfers,
I'm wondering if there is a way to figure out if a ct.anat.nii file is corrupt
or not. I'm using MRICro as a viewer, and the file doesn't look right.
Thanks,
Mia
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nm
Hi,
I'm trying to run a recon, but I keep getting the error: too many arguments for
the following command:
econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i
[path to dicom]
Any help on this would be excellent!
Thanks,
M
___
Yes! I attached a screen shot. Thanks!
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, June 15, 2012 11:33 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon error- too many arguments?
Hi Mia
can you
: [Freesurfer] recon error- too many arguments?
Hi Mia, I think the problem is that you have a space in the path to the
dicom. Even though you put a backslash there, I think it is still
causing the problem
doug
On 06/15/2012 01:13 PM, Borzello, Mia wrote:
> Yes! I attached a screen shot. Tha
Hi all,
Is there a way to edit the pial files (e.g. lh.pial)? I want to delete a few
vertices we think are causing errors for a 3D printing we are trying to do.
Thanks,
m
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.
[gr...@nmr.mgh.harvard.edu]
Sent: Sunday, July 01, 2012 11:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] axial sheer
Can you give more info? Command line, description of data, where you got it
from etc
doug
On 7/1/12 9:58 PM, Borzello, Mia wrote:
Hi freesurfers,
Is there a w
line, description of data, where you got it
from etc
doug
On 7/1/12 9:58 PM, Borzello, Mia wrote:
Hi freesurfers,
Is there a way to fix sheering. The views are good on both coronal and sagittal
slices, but the horizonal view is pretty skewed. I've attached a screen shot.
Thanks for the h
Will he be back today? Upload it in an e-mail?
Thanks,
m
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 11, 2012 12:21 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] slanted
Hi Mia,
you&#x
schl
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 11, 2012 1:24 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] slanted
Hi Mia,
no, there are instructions on the wiki for uploading your data using
either ftp or the filedrop. And no, I think it will be another couple of
oh i'm trying to do the e-mail file drop though, that's fine too right? i'm
just not sure what e-mail to use for the recipient e-mail.
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 11, 2012 1:58 PM
To: Borzello, Mia
can i just send it to freesurfer@nmr.mgh.harvard.edu?
thanks
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 11, 2012 1:58 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] slanted
when you say ftp
Hi freesurfer family,
I am trying to create the inner skull boundary and ran: mri_watershed -atlas -
surf -useSRAS mri.nii brain
However, after it finished running it said it was saving "brain", but "brain"
was an unknown file type. Am i supposed to specify that somewhere?
Thanks in advance,
m
e [vi...@nmr.mgh.harvard.edu]
Sent: Friday, August 31, 2012 10:29 AM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] creating a skull
Hi,
You need to add an extension onto the file name, something like brain.mgz
or brain.nii. The extension will tell it what format to save the output
in.
-Louis
On Fr
holas Vinke [vi...@nmr.mgh.harvard.edu]
Sent: Friday, August 31, 2012 10:29 AM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] creating a skull
Hi,
You need to add an extension onto the file name, something like brain.mgz
or brain.nii. The extension will tell it what format to save the o
Also, is there a way to create a skull from a CT scan?
From: Borzello, Mia
Sent: Friday, August 31, 2012 12:17 PM
To: freesurfer
Subject: RE: [Freesurfer] creating a skull
I've been referred to the following link on the freesurfer site to handle this,
I'm using Unix. Should I try something else?
Thanks,
m
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 03, 2012 2:45 PM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] creating a skull
Hi Mia
what platform ar
Hi,
I'm picking points for a coregistration using tkmedit, but oddly all of the R
coordinates have been 0. For example, one point is [0 -14 73.5]. Does this seem
right?
Thanks in advance,
Mia
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
:59 PM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] picking peculiar points
definitely not.
On Wed, 12 Sep 2012, Borzello, Mia wrote:
> Hi,
> I'm picking points for a coregistration using tkmedit, but oddly all of the R
> coordinates have been 0. For example, one point
Hi Freesurfers,
I just ran a recon, and it seems that only the lh.pial computed, but not the
rh.pial. What would be the cause of this?
Thanks,
m
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listin
1:30 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer
and you rerun and it should be all set. You probably should take a look
at the ?h.orig.nofix to make sure it's reas
Cool, it's running. Hopefully I did that right.
Thanks for your help!
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, January 18, 2013 11:28 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not comp
Hi Freesurfers,
I was wondering if the SurferOutput files for the average subject's brain were
somewhere tobe downloaded on the wiki or within the toolbox?
Thanks,
m
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvar
Hi all,
I'm trying to use tkmedit to pick electrode points for a patient. For the mri,
I'm using the average brain provided by freesurfer. I realized that I have no
norm.mgz file which tkmedit calls. How do I create this?
Thanks,
Mia
___
Freesurfer ma
/2014 02:40 PM, Borzello, Mia wrote:
> Hi all,
>
> I'm trying to use tkmedit to pick electrode points for a patient. For
> the mri, I'm using the average brain provided by freesurfer. I
> realized that I have no norm.mgz file which tkmedit calls. How do I
> cr
...@nmr.mgh.harvard.edu]
Sent: Friday, May 30, 2014 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] creating norm.mgz
why not just use the orig.mgz that is there?
On 05/30/2014 02:40 PM, Borzello, Mia wrote:
> Hi all,
>
> I'm trying to use tkmedit to pick electrod
Hi Freesurfers,
I ran mris_compute_lgi to make the pial layers but they've error- I've included
a screenshot. It says it can't find that directory, but I'm pretty sure that
directly exists.
Thanks so much for your help,
Mia
___
Freesurfer mailing list
Hi Freesurfers,
I'm in the process of creating the ct.mgz file, but it is erroring and saying
there is a "segmentation fault (core dumped)."
What can I do to remedy this?
Thanks,
m
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easier you make it for us, the more likely you are to get help.
thanks
doug
On 08/22/2014 12:17 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I'm in the process of creating the ct.mgz file, but it is erroring and
> saying there is a "segmentation fault (core dumped)."
.232143365/1.3.12.2.1107.5.1.4.11060.3014081213381840600011010/IMG84.dcm
-o ct.mgz
3. UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)
Thanks so much,
m
____
From: Borzello, Mia
Sent: Friday, August 22, 2014 1:14 PM
To: Freesurfer support list
Subject: RE: [
did this and it converts, but the slice thickness looks wrong. I don't
know how to fix it because we always trust the slice thickness in the dicom
doug
On 08/22/2014 01:51 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> Apologies, I've never used this format before.
urfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Monday, October 06, 2014 11:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] skewed CT viewed in tkregister2
Hi Freesurfers
I'm having trouble viewing a CT in tkregister2. Here is the output from bugr:
FREESURFER_HOME: /usr/l
e delay. I think the problem is that the geometry
info in the CT header is incorrect. The directions are not orgthogonal,
and, when made orthogonal, the pixel sizes look wrong. How did you
create ct.mgz?
doug
On 10/12/2014 08:52 PM, Borzello, Mia wrote:
> Hi,
>
> Any insight on this problem I
Hey guys,
When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz
file. but when i use spmregister, it says that spm.reg.dat is
unrecognizable. How can i remedy this?
Thanks so much!
Mia
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fsvol orig
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 02, 2012 1:39 PM
To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] coreg error
There does not appear to be an error at the end.
doug
On 04/02/2012 12:58 PM, Borzello, Mia wrote:
>
rmats
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 02, 2012 1:45 PM
To: Borzello, Mia
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] coreg error
You need a space between ct.mgz and --reg. PE Dir unknown is ok.
On 04/02/2012 01:43 PM, Bor
Yes it's in RIH_E1_SurferOutput/mri. Would the double forward slashes before
RIH_E1_SurferOutput have effect?
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 02, 2012 1:51 PM
To: Borzello, Mia
Cc: Freesurfer@nmr.mgh.harvar
Hi,
I'm just wondering if there is something that needs to be selected using
tkmedit to get electrode coordinates. I usually don't have this issue, but
right now i'm unable to move my cursor to a new location.
Thanks so much,
Mia
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n selected.
doug
On 05/07/2012 02:05 PM, Borzello, Mia wrote:
> Hi,
>
> I'm just wondering if there is something that needs to be selected using
> tkmedit to get electrode coordinates. I usually don't have this issue, but
> right now i'm
I'm not sure what you mean by "conformed"? My input volume is that one that I
coregistered if that's what you mean?
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 07, 2012 2:57 PM
To: Borzello, Mia
Cc: Douglas
arvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 07, 2012 3:04 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inability to pick points
conformed means 1mm isotropic. What is your tkmedit cmd
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: freesurfer
y 14, 2012 1:28 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] "cannot allocate memory" issue
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
"be
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
astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:16 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] "cannot allocate memory" issue
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
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 mem
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] "c
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] &q
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