Hi everyone,
I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error :
WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
I tried to unpack the mosaics with gdcmtar, but I got the same error.
Thank you in advance for your help,
Ismail
Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file.
Best, a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone,
I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error :
WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
I tried to unpack the mosaics with gdcmtar, but I got the same error.
Thank you in advance for your help,
Ismail _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Anastasia,
Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more.
I run trac-all -prep -c on some DICOM files but I had the following error : WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error.
Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional space, but when the new bvecs and bvals are created, they seem messed up. I will attach you all the bvecs and bvals I used and the ones I get too.
Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space.
Thank you in advance for your help.
Best,
Ismail
P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edumailto:ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file.
Best, a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone,
I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error :
WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
I tried to unpack the mosaics with gdcmtar, but I got the same error.
Thank you in advance for your help,
Ismail _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ismail - It sounds like the error has to do with the nifti volume, not the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Thanks, a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more.
I run trac-all -prep -c on some DICOM files but I had the following error : WARNING: file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043 .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error.
Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional space, but when the new bvecs and bvals are created, they seem messed up. I will attach you all the bvecs and bvals I used and the ones I get too.
Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space.
Thank you in advance for your help.
Best,
Ismail
P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file.
Best, a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail _______________________________________________ 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
Hi Anastasia,
Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again,
Ismail
On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ismail - It sounds like the error has to do with the nifti volume, not the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Thanks, a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error : WARNING: file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043 .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional space, but when the new bvecs and bvals are created, they seem messed up. I will attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ismail - You can see from the log file that the command that causes the error is this:
mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out.
a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again,
Ismail
On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Thanks, a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error
:
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
0043
.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional
space,
but when the new bvecs and bvals are created, they seem messed up. I
will
attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote: Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone,
I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error :
WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
I tried to unpack the mosaics with gdcmtar, but I got the same error.
Thank you in advance for your help,
Ismail _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Anastasia,
This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason. Also why the DICOMs wouldn’t work at the beginning ?
Thanks, Ismail
On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ismail - You can see from the log file that the command that causes the error is this:
mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out.
a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again, Ismail
On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Thanks, a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error
:
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
0043
.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional
space,
but when the new bvecs and bvals are created, they seem messed up. I
will
attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail _______________________________________________ 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
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
I do not know why the dicoms do not work. When you run mri_info on your nifti, what is the number of frames that shows up?
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason. Also why the DICOMs wouldn’t work at the beginning ?
Thanks, Ismail
On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ismail - You can see from the log file that the command that causes the error is this:
mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out.
a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again, Ismail
On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Thanks, a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error
:
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
0043
.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional
space,
but when the new bvecs and bvals are created, they seem messed up. I
will
attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail _______________________________________________ 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
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
It says 1 … I don’t understand why I get that knowing that when I open the nifti I can go through the frames …
Ismail
On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
I do not know why the dicoms do not work. When you run mri_info on your nifti, what is the number of frames that shows up?
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason. Also why the DICOMs wouldn’t work at the beginning ?
Thanks, Ismail
On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ismail - You can see from the log file that the command that causes the error is this:
mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out.
a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again, Ismail
On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
ayendiki@nmr.mgh.harvard.edu wrote:
Hi Ismail - It sounds like the error has to do with the nifti volume, not
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Thanks, a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error
:
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
0043
.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional
space,
but when the new bvecs and bvals are created, they seem messed up. I
will
attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail _______________________________________________ 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Also when I run mir_convert on the DICOMs I get the same error as the one I got when I used DICOMs : WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea what this could be ?
Thanks,
Ismail
On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail <IKOUBIYR@BWH.HARVARD.EDUmailto:IKOUBIYR@bwh.harvard.edu> wrote:
It says 1 … I don’t understand why I get that knowing that when I open the nifti I can go through the frames …
Ismail
On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edumailto:ayendiki@nmr.mgh.harvard.edu> wrote:
I do not know why the dicoms do not work. When you run mri_info on your nifti, what is the number of frames that shows up?
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason. Also why the DICOMs wouldn’t work at the beginning ?
Thanks, Ismail
On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edumailto:ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Ismail - You can see from the log file that the command that causes the error is this:
mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out.
a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again, Ismail On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edumailto:ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Ismail - It sounds like the error has to do with the nifti volume, not the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Thanks, a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error : WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368 0043 .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional space, but when the new bvecs and bvals are created, they seem messed up. I will attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edumailto:ayendiki@nmr.mgh.harvard.edu> wrote: Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone,
I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error :
WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
I tried to unpack the mosaics with gdcmtar, but I got the same error.
Thank you in advance for your help,
Ismail _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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You get the same error as trac-all because trac-all runs mri_convert. I'd send the mri_convert error in a new email with mri_convert somewhere in the title, so that someone else can help you.
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Also when I run mir_convert on the DICOMs I get the same error as the one I got when I used DICOMs : WARNING: file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19. 45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header
Any idea what this could be ?
Thanks,
Ismail
On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail <IKOUBIYR@BWH.HARVARD.EDU> wrote:It says 1 … I don’t understand why I get that knowing that when I open the nifti I can go through the frames …
Ismail
On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: I do not know why the dicoms do not work. When you run mri_info on your nifti, what is the number of frames that shows up? On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason. Also why the DICOMs wouldn’t work at the beginning ? Thanks, Ismail On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Ismail - You can see from the log file that the command that causes the error is this: mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out. a.y On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again, Ismail On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Ismail - It sounds like the error has to do with the nifti volume, not the bvecs/bvals. Can you send the log file from scripts/trac-all.log? Thanks, a.y On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error :WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826 .0.1.368
0043 .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional space, but when the new bvecs and bvals are created, they seem messed up. I will attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used. On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote: Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail _______________________________________________ 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 _______________________________________________ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Anastasia Yendiki -
Koubiyr, Ismail