Hi Freesurfers,
Apologies, I've never used this format before. Here's the error:
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)
Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: huygens
SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
For additional information: 1. Neuropace2JB 2. mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/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: [Freesurfer] problem with format of CT dicoms
Hi Freesurfers,
Apologies, I've never used this format before. Here's the error:
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)
Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: huygens
SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
For additional information: 1. Neuropace2JB 2. mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/IMG84.dcm -o ct.mgz 3. UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault (core dumped)
Thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 12:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with format of CT dicoms
Hi Mia, please follow the instructions on the web site below for submitting bug reports. thanks doug
On 08/22/2014 12:37 PM, Borzello, Mia wrote:
Right, sorry. I was running a command with mri_convert in order to convert the ct dicoms to mgz format. The error I ran into was: UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault (core dumped)
Thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 12:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] problem with format of CT dicoms
Hi Mia, do you realize that your description of the problem is too vague for us to help you? If you want help in a timely fashion, please include more detail like the problem you ran, the command-line arguments, the terminal output, etc. Please see the following web page for the types information we are looking for:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The 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)."
What can I do to remedy this?
Thanks, m
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
These dicoms are run-length encoded, which FS does not read. What you can do is the following
cd /place/where/dicoms/are
foreach dcm (*.dcm) dcmdrle $dcm $dcm end
then run mri_convert, like
mri_convert -it dicom IMG10.dcm ct.mgz
I 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. Here's the error:
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)
Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: huygens
SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
For additional information:
- Neuropace2JB
- mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/XXXXXXXXXXXXXXX/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/IMG84.dcm -o ct.mgz
- 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: [Freesurfer] problem with format of CT dicoms
Hi Freesurfers,
Apologies, I've never used this format before. Here's the error:
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)
Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: huygens
SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
For additional information:
- Neuropace2JB
- mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/XXXXXXXXXXXXXXXX/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/IMG84.dcm -o ct.mgz
- UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)
Thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 12:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with format of CT dicoms
Hi Mia, please follow the instructions on the web site below for submitting bug reports. thanks doug
On 08/22/2014 12:37 PM, Borzello, Mia wrote:
Right, sorry. I was running a command with mri_convert in order to convert the ct dicoms to mgz format. The error I ran into was: UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault (core dumped)
Thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 12:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] problem with format of CT dicoms
Hi Mia, do you realize that your description of the problem is too vague for us to help you? If you want help in a timely fashion, please include more detail like the problem you ran, the command-line arguments, the terminal output, etc. Please see the following web page for the types information we are looking for:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The 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)."
What can I do to remedy this?
Thanks, m
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Awesome! Thanks a lot for your help!
m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 2:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with format of CT dicoms
These dicoms are run-length encoded, which FS does not read. What you can do is the following
cd /place/where/dicoms/are
foreach dcm (*.dcm) dcmdrle $dcm $dcm end
then run mri_convert, like
mri_convert -it dicom IMG10.dcm ct.mgz
I 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. Here's the error:
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)
Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: huygens
SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
For additional information:
- Neuropace2JB
- mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/XXXXXXXXXXXXXXX/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/IMG84.dcm -o ct.mgz
- 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: [Freesurfer] problem with format of CT dicoms
Hi Freesurfers,
Apologies, I've never used this format before. Here's the error:
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)
Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: huygens
SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
For additional information:
- Neuropace2JB
- mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/XXXXXXXXXXXXXXXX/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/IMG84.dcm -o ct.mgz
- UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)
Thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 12:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with format of CT dicoms
Hi Mia, please follow the instructions on the web site below for submitting bug reports. thanks doug
On 08/22/2014 12:37 PM, Borzello, Mia wrote:
Right, sorry. I was running a command with mri_convert in order to convert the ct dicoms to mgz format. The error I ran into was: UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault (core dumped)
Thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 12:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] problem with format of CT dicoms
Hi Mia, do you realize that your description of the problem is too vague for us to help you? If you want help in a timely fashion, please include more detail like the problem you ran, the command-line arguments, the terminal output, etc. Please see the following web page for the types information we are looking for:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The 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)."
What can I do to remedy this?
Thanks, m
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
You can use ImageJ to read in the slices and reslice them any way you want with whatever thicknesses you want.
Regards, Don <snip>
I 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
<snip>
freesurfer@nmr.mgh.harvard.edu
-
Borzello, Mia -
Douglas N Greve -
Krieger, Donald N.