from:"Christopher Finuf"

[Freesurfer] Segmentation fault in mri_convert

2016-06-13 Thread Christopher Finuf

I'm trying to convert the dicom to the original 001.mgz file using the
following command on a Mac OSX Yosemite version 10.10.5. My
SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/
. My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/
. The following is the output and error that I get. I'm running the latest
version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What
is strange that it works with half my data set but the other has this
error. I've run this command in the exact way many times before and have
never had this issue.





bash-3.2$ recon-all -i
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
-subjid Bigler_Repeatability_0005Ad_M1


Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects

Actual FREESURFER_HOME /Applications/freesurfer

Darwin NS112201PSY2.byu.edu  14.5.0 Darwin
Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015;
root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1

\n mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz
\n

mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm...

Getting Series No

INFO: Found 178 files in
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1

INFO: Scanning for Series Number 2

Scanning Directory

INFO: found 176 files in series

INFO: loading series header info.


RunNo = 1

INFO: sorting.

INFO: (224 256 176), nframes = 1, ismosaic=0

PE Dir ROW ROW

AutoAlign matrix detected

AutoAlign Matrix -

 1.000   0.000   0.000   0.000;

 0.000   1.000   0.000   0.000;

 0.000   0.000   1.000   0.000;

 0.000   0.000   0.000   1.000;


FileName
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm

Identification

NumarisVersyngo MR B17

ScannerModel  TrioTim

PatientName   Bigler_Repeatability_AD_M

Date and time

StudyDate 20160512

StudyTime 075942.531000

SeriesTime081401.859000

AcqTime   080647.62

Acquisition parameters

PulseSeq  *tfl3d1_ns

Protocol  t1_mpr_sag_iso_ave2_ipat2_(mprage)

PhEncDir  ROW

EchoNo1

FlipAngle 9

EchoTime  2.26

InversionTime 900

RepetitionTime1900

PhEncFOV  218.75

ReadoutFOV250

Image information

RunNo 1

SeriesNo  2

ImageNo   1

NImageRows256

NImageCols224

NFrames   1

SliceArraylSize   1

IsMosaic  0

ImgPos 75.8389 136.8499 125.

VolRes  0.9766   0.9766   1.

VolDim224  256  176

Vc  0.0767  -0.9971   0.

Vr -0.   0.  -1.

Vs -0.9971  -0.0767   0.

VolCenter  -3.5106  21.0460   0.

TransferSyntaxUID 1.2.840.10008.1.2.1

UseSliceScaleFactor 0 (slice 0: 1)

Segmentation fault

Darwin NS112201PSY2.byu.edu  14.5.0 Darwin
Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015;
root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64


recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun
8 13:39:08 MDT 2016


For more details, see the log file
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Segmentation Fault with mri_convert

2016-06-09 Thread Christopher Finuf

I'm trying to convert the dicom to the original 001.mgz file using the
following command on a Mac OSX Yosemite version 10.10.5. My
SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/
. My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/
. The following is the output and error that I get. I'm running the latest
version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What
is strange that it works with half my data set but the other has this
error. I've run this command in the exact way many times before and have
never had this issue.





bash-3.2$ recon-all -i
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
-subjid Bigler_Repeatability_0005Ad_M1


Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects

Actual FREESURFER_HOME /Applications/freesurfer

Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1

\n mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz
\n

mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm...

Getting Series No

INFO: Found 178 files in
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1

INFO: Scanning for Series Number 2

Scanning Directory

INFO: found 176 files in series

INFO: loading series header info.


RunNo = 1

INFO: sorting.

INFO: (224 256 176), nframes = 1, ismosaic=0

PE Dir ROW ROW

AutoAlign matrix detected

AutoAlign Matrix -

 1.000   0.000   0.000   0.000;

 0.000   1.000   0.000   0.000;

 0.000   0.000   1.000   0.000;

 0.000   0.000   0.000   1.000;


FileName
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm

Identification

NumarisVersyngo MR B17

ScannerModel  TrioTim

PatientName   Bigler_Repeatability_AD_M

Date and time

StudyDate 20160512

StudyTime 075942.531000

SeriesTime081401.859000

AcqTime   080647.62

Acquisition parameters

PulseSeq  *tfl3d1_ns

Protocol  t1_mpr_sag_iso_ave2_ipat2_(mprage)

PhEncDir  ROW

EchoNo1

FlipAngle 9

EchoTime  2.26

InversionTime 900

RepetitionTime1900

PhEncFOV  218.75

ReadoutFOV250

Image information

RunNo 1

SeriesNo  2

ImageNo   1

NImageRows256

NImageCols224

NFrames   1

SliceArraylSize   1

IsMosaic  0

ImgPos 75.8389 136.8499 125.

VolRes  0.9766   0.9766   1.

VolDim224  256  176

Vc  0.0767  -0.9971   0.

Vr -0.   0.  -1.

Vs -0.9971  -0.0767   0.

VolCenter  -3.5106  21.0460   0.

TransferSyntaxUID 1.2.840.10008.1.2.1

UseSliceScaleFactor 0 (slice 0: 1)

Segmentation fault

Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64


recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun
8 13:39:08 MDT 2016


For more details, see the log file
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Segmentation fault in mri_convert

[Freesurfer] Segmentation Fault with mri_convert

2 matches

Site Navigation

Mail list logo

Footer information