External Email - Use Caution
Hello FreeSurfer Developers,
I,m attempting to convert my dicom files to *.mgz, with command line in below: $ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo
but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?
where did you get the dicom files? It looks like something is wrong with it since the ras2vox in the dicom header is singular (which should never be the case for a valid transform) On Tue, 19 Mar 2019, Z Hessam wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I,m attempting to convert my dicom files to *.mgz, with command line in below: $ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo
but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?
p.s. you can see this in the log file:
Image information RunNo 0 SeriesNo 1 ImageNo 2 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 3 IsMosaic 0 ImgPos 130.0000 -0.0000 130.0000 VolRes 0.5078 0.5078 9.6000 VolDim 512 512 3 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -14.4000 -0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
syou should never have a column (or row) of all 0s
On Tue, 19 Mar 2019, Z Hessam wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I,m attempting to convert my dicom files to *.mgz, with command line in below: $ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo
but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?
External Email - Use Caution
Soory , why this error has been occured? How the column of all zero is made?
On Tuesday, March 19, 2019, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. you can see this in the log file:
Image information RunNo 0 SeriesNo 1 ImageNo 2 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 3 IsMosaic 0 ImgPos 130.0000 -0.0000 130.0000 VolRes 0.5078 0.5078 9.6000 VolDim 512 512 3 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -14.4000 -0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
syou should never have a column (or row) of all 0s
On Tue, 19 Mar 2019, Z Hessam wrote:
External Email - Use CautionHello FreeSurfer Developers,
I,m attempting to convert my dicom files to *.mgz, with command line in
below:
$ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo
but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?
where did you get the dicoms? On Thu, 28 Mar 2019, Z Hessam wrote:
External Email - Use Caution
Soory , why this error has been occured? How the column of all zero is made?
On Tuesday, March 19, 2019, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. you can see this in the log file:
Image information RunNo 0 SeriesNo 1 ImageNo 2 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 3 IsMosaic 0 ImgPos 130.0000 -0.0000 130.0000 VolRes 0.5078 0.5078 9.6000 VolDim 512 512 3 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -14.4000 -0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
syou should never have a column (or row) of all 0s
On Tue, 19 Mar 2019, Z Hessam wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I,m attempting to convert my dicom files to *.mgz, with command line in below: $ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo
but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?
External Email - Use Caution
I get them from a mri center
On Thursday, March 28, 2019, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
where did you get the dicoms? On Thu, 28 Mar 2019, Z Hessam wrote:
External Email - Use CautionSoory , why this error has been occured? How the column of all zero is
made?
On Tuesday, March 19, 2019, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
p.s. you can see this in the log file:
Image information RunNo 0 SeriesNo 1 ImageNo 2 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 3 IsMosaic 0 ImgPos 130.0000 -0.0000 130.0000 VolRes 0.5078 0.5078 9.6000 VolDim 512 512 3 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -14.4000 -0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
syou should never have a column (or row) of all 0s
On Tue, 19 Mar 2019, Z Hessam wrote:
External Email - Use CautionHello FreeSurfer Developers,
I,m attempting to convert my dicom files to *.mgz, with command line
in below:
$ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo
but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?
External Email - Use Caution
They are sagital T1 mpr mri.
On Thursday, March 28, 2019, Z Hessam z.hessam@gmail.com wrote:
I get them from a mri center
On Thursday, March 28, 2019, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
where did you get the dicoms? On Thu, 28 Mar 2019, Z Hessam wrote:
External Email - Use CautionSoory , why this error has been occured? How the column of all zero is
made?
On Tuesday, March 19, 2019, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
p.s. you can see this in the log file:
Image information RunNo 0 SeriesNo 1 ImageNo 2 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 3 IsMosaic 0 ImgPos 130.0000 -0.0000 130.0000 VolRes 0.5078 0.5078 9.6000 VolDim 512 512 3 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -14.4000 -0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
syou should never have a column (or row) of all 0s
On Tue, 19 Mar 2019, Z Hessam wrote:
External Email - Use CautionHello FreeSurfer Developers,
I,m attempting to convert my dicom files to *.mgz, with command line
in below:
$ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo
but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?
It looks like the dicom file is the localizer/scout. It is not the anatomical (eg, only 3 slices). You can try running dcmunpack to get a list of runs in the dicom folder. Then pass one of the dicoms from the anatomical to recon-all
On 3/27/19 4:50 PM, Z Hessam wrote:
External Email - Use Caution
I get them from a mri center
On Thursday, March 28, 2019, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
where did you get the dicoms? On Thu, 28 Mar 2019, Z Hessam wrote:
External Email - Use Caution
Soory , why this error has been occured? How the column of all zero
is made?
On Tuesday, March 19, 2019, Bruce Fischl
<fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
p.s. you can see this in the log file:
Image information RunNo 0 SeriesNo 1 ImageNo 2 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 3 IsMosaic 0 ImgPos 130.0000 -0.0000 130.0000 VolRes 0.5078 0.5078 9.6000 VolDim 512 512 3 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -14.4000 -0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1
syou should never have a column (or row) of all 0s
On Tue, 19 Mar 2019, Z Hessam wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I,m attempting to convert my dicom files to *.mgz, with command
line in below:
$ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo
but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Z Hessam