Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
1. Why can not I successully unpack images for run10?
2. I got the DTI.nii image, the bvecs and bvals for run4 now. Can I use them for my analyses? Seems this run has an error. Does this error matter?
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015 ------------------------------------------ 1 localizer ok 512 512 3 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii} ----------------------------------- --------------------------------------------------------- Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf -ot mgz --nspmzeropad 3 --in_type siemens_dicom --------------------------------------------------------- Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom --------------------------------------------------------- Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
- Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
- I got the DTI.nii image, the bvecs and bvals for run4 now. Can I
use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
1 localizer ok 512 512 3 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf -ot mgz --nspmzeropad 3 --in_type siemens_dicom
Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Douglas,
Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir.
Best wishes, Baojuan
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, November 09, 2015 11:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote: Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
1. Why can not I successully unpack images for run10? Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
2. I got the DTI.nii image, the bvecs and bvals for run4 now. Can I use them for my analyses? Seems this run has an error. Does this error matter? The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015 ------------------------------------------ 1 localizer ok 512 512 3 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii} ----------------------------------- --------------------------------------------------------- Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf -ot mgz --nspmzeropad 3 --in_type siemens_dicom --------------------------------------------------------- Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom --------------------------------------------------------- Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version
On 11/10/2015 01:51 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir.
Best wishes, Baojuan
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Monday, November 09, 2015 11:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
- Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
- I got the DTI.nii image, the bvecs and bvals for run4 now. Can I
use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
1 localizer ok 512 512 3 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf
-ot mgz --nspmzeropad 3 --in_type siemens_dicom
Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
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
Dear Douglas,
Thank you!
I am using a desktop of the Martinos Center. Seems I am not allowed to replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is there another way to use it?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version
On 11/10/2015 01:51 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir.
Best wishes, Baojuan
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Monday, November 09, 2015 11:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
- Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
- I got the DTI.nii image, the bvecs and bvals for run4 now. Can I
use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
1 localizer ok 512 512 3 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf
-ot mgz --nspmzeropad 3 --in_type siemens_dicom
Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
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
Use the development environment (but only for unpacking)
source /usr/local/freesurfer/nmr-dev-env
On 11/10/2015 02:31 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you!
I am using a desktop of the Martinos Center. Seems I am not allowed to replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is there another way to use it?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version
On 11/10/2015 01:51 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir.
Best wishes, Baojuan
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Monday, November 09, 2015 11:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
- Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
- I got the DTI.nii image, the bvecs and bvals for run4 now. Can I
use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
1 localizer ok 512 512 3 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf
-ot mgz --nspmzeropad 3 --in_type siemens_dicom
Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
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
Dear Douglas,
This works great with our old dataset. But for our new dataset collected using a new protocol, I ran into another error:
The command was: unpacksdcmdir -src /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 \ -targ /autofs/space/quadra_001/users/baojuan/MRI -fsfast \ -run 13 FSL nii DTI.nii
The error was: Scanning directory Tue Nov 10 15:24:52 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 100 ERROR: parsing /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 See logfile /autofs/space/quadra_001/users/baojuan/MRI/unpack.log for more details
However, when I used the old version of mri_convert, there was not such error but I could not get the bvecs and bvals files: Scanning directory Tue Nov 10 15:41:57 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Tue Nov 10 15:49:52 EST 2015
Finally, I tried to run mri_convert directly: ./mri_convert /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii
It worked: reading from /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173... Getting Series No Scanning Directory INFO: Found 1633 files in /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 INFO: Scanning for Series Number 13 INFO: found 65 files in series INFO: loading series header info. INFO: sorting. RunNo = 12 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 ... writing to /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii... Saving bvals and bvecs
I checked the DTI.nii, bvecs, bvals files, seems they were correct.
So what may be the reason for this error? Can I still use the images obtained by running mri_convert directly?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
Use the development environment (but only for unpacking)
source /usr/local/freesurfer/nmr-dev-env
On 11/10/2015 02:31 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you!
I am using a desktop of the Martinos Center. Seems I am not allowed to replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is there another way to use it?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version
On 11/10/2015 01:51 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir.
Best wishes, Baojuan
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Monday, November 09, 2015 11:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
- Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
- I got the DTI.nii image, the bvecs and bvals for run4 now. Can I
use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
1 localizer ok 512 512 3 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf
-ot mgz --nspmzeropad 3 --in_type siemens_dicom
Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
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
how do you know that it is mri_convert that is causing the problem? It could be that unpacksdcmdir does not work. I've noticed that many data sets are coming off the scanner with each run in a separate folder, which breaks unpacksdcmdir. However, dcmunpack should work.
On 11/10/2015 04:26 PM, Li, Baojuan wrote:
Dear Douglas,
This works great with our old dataset. But for our new dataset collected using a new protocol, I ran into another error:
The command was: unpacksdcmdir -src /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 \ -targ /autofs/space/quadra_001/users/baojuan/MRI -fsfast \ -run 13 FSL nii DTI.nii
The error was: Scanning directory Tue Nov 10 15:24:52 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 100 ERROR: parsing /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 See logfile /autofs/space/quadra_001/users/baojuan/MRI/unpack.log for more details
However, when I used the old version of mri_convert, there was not such error but I could not get the bvecs and bvals files: Scanning directory Tue Nov 10 15:41:57 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Tue Nov 10 15:49:52 EST 2015
Finally, I tried to run mri_convert directly: ./mri_convert /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii
It worked: reading from /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173... Getting Series No Scanning Directory INFO: Found 1633 files in /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 INFO: Scanning for Series Number 13 INFO: found 65 files in series INFO: loading series header info. INFO: sorting. RunNo = 12 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 ... writing to /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii... Saving bvals and bvecs
I checked the DTI.nii, bvecs, bvals files, seems they were correct.
So what may be the reason for this error? Can I still use the images obtained by running mri_convert directly?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
Use the development environment (but only for unpacking)
source /usr/local/freesurfer/nmr-dev-env
On 11/10/2015 02:31 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you!
I am using a desktop of the Martinos Center. Seems I am not allowed to replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is there another way to use it?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version
On 11/10/2015 01:51 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir.
Best wishes, Baojuan
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Monday, November 09, 2015 11:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
- Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
- I got the DTI.nii image, the bvecs and bvals for run4 now. Can I
use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
1 localizer ok 512 512 3 1MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf
-ot mgz --nspmzeropad 3 --in_type siemens_dicom
Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, seems dcmunpack does not work with our new dataset. So can I still use the images obtained from running mri_convert directly? Actually, I got the filenames for run13 by running dcmunpack and then used these filenames with mri_convert directly. ________________________________________ 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: Tuesday, November 10, 2015 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
how do you know that it is mri_convert that is causing the problem? It could be that unpacksdcmdir does not work. I've noticed that many data sets are coming off the scanner with each run in a separate folder, which breaks unpacksdcmdir. However, dcmunpack should work.
On 11/10/2015 04:26 PM, Li, Baojuan wrote:
Dear Douglas,
This works great with our old dataset. But for our new dataset collected using a new protocol, I ran into another error:
The command was: unpacksdcmdir -src /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 \ -targ /autofs/space/quadra_001/users/baojuan/MRI -fsfast \ -run 13 FSL nii DTI.nii
The error was: Scanning directory Tue Nov 10 15:24:52 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 100 ERROR: parsing /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 See logfile /autofs/space/quadra_001/users/baojuan/MRI/unpack.log for more details
However, when I used the old version of mri_convert, there was not such error but I could not get the bvecs and bvals files: Scanning directory Tue Nov 10 15:41:57 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Tue Nov 10 15:49:52 EST 2015
Finally, I tried to run mri_convert directly: ./mri_convert /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii
It worked: reading from /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173... Getting Series No Scanning Directory INFO: Found 1633 files in /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 INFO: Scanning for Series Number 13 INFO: found 65 files in series INFO: loading series header info. INFO: sorting. RunNo = 12 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 ... writing to /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii... Saving bvals and bvecs
I checked the DTI.nii, bvecs, bvals files, seems they were correct.
So what may be the reason for this error? Can I still use the images obtained by running mri_convert directly?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
Use the development environment (but only for unpacking)
source /usr/local/freesurfer/nmr-dev-env
On 11/10/2015 02:31 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you!
I am using a desktop of the Martinos Center. Seems I am not allowed to replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is there another way to use it?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version
On 11/10/2015 01:51 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir.
Best wishes, Baojuan
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Monday, November 09, 2015 11:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
- Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
- I got the DTI.nii image, the bvecs and bvals for run4 now. Can I
use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
1 localizer ok 512 512 3 1MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf
-ot mgz --nspmzeropad 3 --in_type siemens_dicom
Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
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
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
yes
On 11/10/2015 04:35 PM, Li, Baojuan wrote:
Yes, seems dcmunpack does not work with our new dataset. So can I still use the images obtained from running mri_convert directly? Actually, I got the filenames for run13 by running dcmunpack and then used these filenames with mri_convert directly. ________________________________________ 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: Tuesday, November 10, 2015 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
how do you know that it is mri_convert that is causing the problem? It could be that unpacksdcmdir does not work. I've noticed that many data sets are coming off the scanner with each run in a separate folder, which breaks unpacksdcmdir. However, dcmunpack should work.
On 11/10/2015 04:26 PM, Li, Baojuan wrote:
Dear Douglas,
This works great with our old dataset. But for our new dataset collected using a new protocol, I ran into another error:
The command was: unpacksdcmdir -src /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 \ -targ /autofs/space/quadra_001/users/baojuan/MRI -fsfast \ -run 13 FSL nii DTI.nii
The error was: Scanning directory Tue Nov 10 15:24:52 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 100 ERROR: parsing /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 See logfile /autofs/space/quadra_001/users/baojuan/MRI/unpack.log for more details
However, when I used the old version of mri_convert, there was not such error but I could not get the bvecs and bvals files: Scanning directory Tue Nov 10 15:41:57 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Tue Nov 10 15:49:52 EST 2015
Finally, I tried to run mri_convert directly: ./mri_convert /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii
It worked: reading from /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173... Getting Series No Scanning Directory INFO: Found 1633 files in /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 INFO: Scanning for Series Number 13 INFO: found 65 files in series INFO: loading series header info. INFO: sorting. RunNo = 12 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 ... writing to /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii... Saving bvals and bvecs
I checked the DTI.nii, bvecs, bvals files, seems they were correct.
So what may be the reason for this error? Can I still use the images obtained by running mri_convert directly?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
Use the development environment (but only for unpacking)
source /usr/local/freesurfer/nmr-dev-env
On 11/10/2015 02:31 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you!
I am using a desktop of the Martinos Center. Seems I am not allowed to replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is there another way to use it?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version
On 11/10/2015 01:51 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir.
Best wishes, Baojuan
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Monday, November 09, 2015 11:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
- Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
- I got the DTI.nii image, the bvecs and bvals for run4 now. Can I
use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
1 localizer ok 512 512 3 1MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf
-ot mgz --nspmzeropad 3 --in_type siemens_dicom
Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
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-- 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/
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-- 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/
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-- 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/
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Good news! Thank you :) ________________________________________ 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: Tuesday, November 10, 2015 4:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
yes
On 11/10/2015 04:35 PM, Li, Baojuan wrote:
Yes, seems dcmunpack does not work with our new dataset. So can I still use the images obtained from running mri_convert directly? Actually, I got the filenames for run13 by running dcmunpack and then used these filenames with mri_convert directly. ________________________________________ 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: Tuesday, November 10, 2015 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
how do you know that it is mri_convert that is causing the problem? It could be that unpacksdcmdir does not work. I've noticed that many data sets are coming off the scanner with each run in a separate folder, which breaks unpacksdcmdir. However, dcmunpack should work.
On 11/10/2015 04:26 PM, Li, Baojuan wrote:
Dear Douglas,
This works great with our old dataset. But for our new dataset collected using a new protocol, I ran into another error:
The command was: unpacksdcmdir -src /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 \ -targ /autofs/space/quadra_001/users/baojuan/MRI -fsfast \ -run 13 FSL nii DTI.nii
The error was: Scanning directory Tue Nov 10 15:24:52 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 100 ERROR: parsing /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 See logfile /autofs/space/quadra_001/users/baojuan/MRI/unpack.log for more details
However, when I used the old version of mri_convert, there was not such error but I could not get the bvecs and bvals files: Scanning directory Tue Nov 10 15:41:57 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Tue Nov 10 15:49:52 EST 2015
Finally, I tried to run mri_convert directly: ./mri_convert /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii
It worked: reading from /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173... Getting Series No Scanning Directory INFO: Found 1633 files in /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 INFO: Scanning for Series Number 13 INFO: found 65 files in series INFO: loading series header info. INFO: sorting. RunNo = 12 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 ... writing to /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii... Saving bvals and bvecs
I checked the DTI.nii, bvecs, bvals files, seems they were correct.
So what may be the reason for this error? Can I still use the images obtained by running mri_convert directly?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
Use the development environment (but only for unpacking)
source /usr/local/freesurfer/nmr-dev-env
On 11/10/2015 02:31 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you!
I am using a desktop of the Martinos Center. Seems I am not allowed to replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is there another way to use it?
Best wishes, Baojuan ________________________________________ 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: Tuesday, November 10, 2015 2:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version
On 11/10/2015 01:51 PM, Li, Baojuan wrote:
Dear Douglas,
Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir.
Best wishes, Baojuan
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Monday, November 09, 2015 11:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] unpacksdcmdir
On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
- Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
- I got the DTI.nii image, the bvecs and bvals for run4 now. Can I
use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes, Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
1 localizer ok 512 512 3 1MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 unpacking config ------------------ {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
Run 3 ----------------------------------------- Mon Nov 9 19:10:43 EST 2015 3 T1 mgz T1.mgz mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf
-ot mgz --nspmzeropad 3 --in_type siemens_dicom
Run 4 ----------------------------------------- Mon Nov 9 19:10:56 EST 2015 4 DTI nii DTI.nii INFO: this run has an error, but trying anyway mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
Run 10 ----------------------------------------- Mon Nov 9 19:11:19 EST 2015 10 DTI nii DTI.nii ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- 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/
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-- 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/
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-- 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/
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-- 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/
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Li, Baojuan