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Dear Freesurfer, I have ASL DICOM data from a Siemens scanner in mosaic format. For each subject, there are 64 DICOM files, which consist of both tags and controls. I would like to convert each individual DICOM into a separate NIfTI file or a single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert. However, when I use the command mri_convert input_dicom output_nifti, the output does not seem right, as it only displays one slice in the sagittal and coronal views. Could you please provide guidance on how to properly convert these DICOM files using mri_convert?
Thanks very much John
Hi John,
I’m assuming all 64 DICOM files are in the same directory.
Which Freesurfer version are you using? If you are using 7.3.2, can you try mri_convert -dcm2niix to convert those DICOMs? It will use dcm2niix to convert.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of John Anderson Sent: Wednesday, March 15, 2023 1:46 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_convert mosaic data
External Email - Use Caution Dear Freesurfer, I have ASL DICOM data from a Siemens scanner in mosaic format. For each subject, there are 64 DICOM files, which consist of both tags and controls. I would like to convert each individual DICOM into a separate NIfTI file or a single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert. However, when I use the command mri_convert input_dicom output_nifti, the output does not seem right, as it only displays one slice in the sagittal and coronal views. Could you please provide guidance on how to properly convert these DICOM files using mri_convert?
Thanks very much John
External Email - Use Caution
Thank you. I would appreciate feedback from developers on two issues. 1) mri_convert in FS v6 is unable to convert any mosaic DICOMs to Nifti format. In FS 7.3.2, mri_convert was able to convert mosaic DICOMs to Nifti in some subjects but failed for many others. All subjects were scanned on the same MRI scanner with the same acquisition parameters, and I am unable to determine the cause of the issue. 2) I have 8 ASL mosaic volumes (36 slices) for each participant in my data. When attempting to convert the DICOMs to Nifti using the simple mri_convert <input.dcm> <output.nii> command, it fails. Is it correct to apply the following steps?
n=({-1..6}) unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log for i in $(cat dicomdir.sumfile | awk '{print $2}'); do n=$(($n + 1)) mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n done
Thank for guidance, John
On Wed, Mar 15, 2023 at 3:07 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
Hi John,
I’m assuming all 64 DICOM files are in the same directory.
Which Freesurfer version are you using? If you are using 7.3.2, can you try mri_convert -dcm2niix to convert those DICOMs? It will use dcm2niix to convert.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *John Anderson *Sent:* Wednesday, March 15, 2023 1:46 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mri_convert mosaic data
External Email - Use Caution *Dear Freesurfer,
I have ASL DICOM data from a Siemens scanner in mosaic format.
For each subject, there are 64 DICOM files, which consist of both tags and controls.
I would like to convert each individual DICOM into a separate NIfTI file or a single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert. However, when I use the command mri_convert input_dicom output_nifti, the output does not seem right, as it only displays one slice in the sagittal and coronal views. Could you please provide guidance on how to properly convert these DICOM files using mri_convert?
Thanks very much
John _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1exV1cafBqzzm8rkYpj9ZN1GDcQCnsNnWlSpMZ0pJeCSrmO... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1bS_r7x5d5hARMp38OKVr578uECWvno1sIuXjsvMdCyKx8I... < https://secure-web.cisco.com/1bS_r7x5d5hARMp38OKVr578uECWvno1sIuXjsvMdCyKx8I... .
Hi John,
Can you try dcmunpack (https://surfer.nmr.mgh.harvard.edu/fswiki/dcmunpack) instead?
Here is an example usage:
dcmunpack -auto-runseq <format> -src <dicom-dir> -trg <output-dir> -no-exit-on-error -dcm2niix
You will find the converted images in <output-dir>.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of John Anderson Sent: Thursday, March 23, 2023 12:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert mosaic data
External Email - Use Caution Thank you. I would appreciate feedback from developers on two issues. 1) mri_convert in FS v6 is unable to convert any mosaic DICOMs to Nifti format. In FS 7.3.2, mri_convert was able to convert mosaic DICOMs to Nifti in some subjects but failed for many others. All subjects were scanned on the same MRI scanner with the same acquisition parameters, and I am unable to determine the cause of the issue. 2) I have 8 ASL mosaic volumes (36 slices) for each participant in my data. When attempting to convert the DICOMs to Nifti using the simple mri_convert <input.dcm> <output.nii> command, it fails. Is it correct to apply the following steps?
n=({-1..6}) unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log for i in $(cat dicomdir.sumfile | awk '{print $2}'); do n=$(($n + 1)) mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n done
Thank for guidance, John
On Wed, Mar 15, 2023 at 3:07 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi John,
I’m assuming all 64 DICOM files are in the same directory.
Which Freesurfer version are you using? If you are using 7.3.2, can you try mri_convert -dcm2niix to convert those DICOMs? It will use dcm2niix to convert.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of John Anderson Sent: Wednesday, March 15, 2023 1:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_convert mosaic data
External Email - Use Caution Dear Freesurfer, I have ASL DICOM data from a Siemens scanner in mosaic format. For each subject, there are 64 DICOM files, which consist of both tags and controls. I would like to convert each individual DICOM into a separate NIfTI file or a single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert. However, when I use the command mri_convert input_dicom output_nifti, the output does not seem right, as it only displays one slice in the sagittal and coronal views. Could you please provide guidance on how to properly convert these DICOM files using mri_convert?
Thanks very much John _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1exV1cafBqzzm8rkYpj9ZN1GDcQCnsNnWlSpMZ0pJeCSrmOhdnqGURVulfItnCi6Ik0q3zfFKHPmfIn6gzla29VDhA5cU_V3i3BooMZLq7_19a5GjvIzPH9JdI4XyjiSZaKtC4Fx8LrNpFtAgNF4arJciaiMxiuhn3aDJqJ-YNetdTt1ZPYSKnbzMWot_T_HQGDOdYv6E-paWOQIqjapzv23k3JulXnBE1qo2pk_4XlWVyPsQD7feO7jwGcznf8z4MvzyMR63pAzWpFf6m3r9lIkzs5Cj0En2-vtCENXTmHIACSXoU7d12J_8krtoPHFR33OFR9iNBM35NRl9JoDAyA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1bS_r7x5d5hARMp38OKVr578uECWvno1sIuXjsvMdCyKx8Izw4ectJDqcZrFYs8l7hyaF-kogGHnkRnh_I3S08KRJi3oH94EY22jVfDitccUj0nAt1ZHYctjjnSd6cbwjY9VqiO1jFGiHTrYP-sLTSy0EDKu7G_Mq-bVra71ZM8n6sOmcAvJgE7Gs2MXfAqlDQwJ6NX2yQ9hWBVt-uai_vLxq_Kd3rS9j9_dxokAcPVTt0zc16K9NXuiugAaFwmwKMyCLPHrFPnkCGDOqctYh1st7rVNaxcfhuhLuVCrJPyKTL57UOaD_yOvJP_qYVGqrbHv2Nfa3cbyDJMKZ8Ja5qg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1bS_r7x5d5hARMp38OKVr578uECWvno1sIuXjsvMdCyKx8Izw4ectJDqcZrFYs8l7hyaF-kogGHnkRnh_I3S08KRJi3oH94EY22jVfDitccUj0nAt1ZHYctjjnSd6cbwjY9VqiO1jFGiHTrYP-sLTSy0EDKu7G_Mq-bVra71ZM8n6sOmcAvJgE7Gs2MXfAqlDQwJ6NX2yQ9hWBVt-uai_vLxq_Kd3rS9j9_dxokAcPVTt0zc16K9NXuiugAaFwmwKMyCLPHrFPnkCGDOqctYh1st7rVNaxcfhuhLuVCrJPyKTL57UOaD_yOvJP_qYVGqrbHv2Nfa3cbyDJMKZ8Ja5qg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
freesurfer@nmr.mgh.harvard.edu
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Huang, Yujing -
John Anderson