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Dear Dr Doug Greeve, For each participant in my dataset, I have 8 mosaic volumes with 36 slices each. I am trying to convert the DICOM files to Nifti format using the mri_convert command in FreeSurfer version 7.3.2. However, the conversion process fails even when using this latest dev version. To resolve this issue, I attempted to use the --nslices-override option. It seems working, however, I am unsure if I used it correctly, and I was not able to find any relevant examples or guidance on how to use this option in the FreeSurfer documentation or other websites.
n=({-1..7}) 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
Thanks for guidance, John
Can you try it with --dcm2niix ?
On 3/25/2023 9:43 AM, John Anderson wrote:
External Email - Use Caution
Dear Dr Doug Greeve, For each participant in my dataset, I have 8 mosaic volumes with 36 slices each. I am trying to convert the DICOM files to Nifti format using the mri_convert command in FreeSurfer version 7.3.2. However, the conversion process fails even when using this latest dev version. To resolve this issue, I attempted to use the --nslices-override option. It seems working, however, I am unsure if I used it correctly, and I was not able to find any relevant examples or guidance on how to use this option in the FreeSurfer documentation or other websites.
n=({-1..7}) 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
Thanks for guidance, John
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Thank you, Dr Greve. I tried it, but it didn't work. By 'didn't work,' I mean that when I visualized the NIfTI file, I saw a line on the coronal and sagittal planes, and the whole brain on the axial view. I was able to generate a NIfTI image with multiple volumes as expected by using the mri_convert command with the --nslices-override argument, but I'm not sure if I'm using it correctly.
On Mon, Mar 27, 2023 at 11:19 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you try it with --dcm2niix ?
On 3/25/2023 9:43 AM, John Anderson wrote:
External Email - Use CautionDear Dr Doug Greeve, For each participant in my dataset, I have 8 mosaic volumes with 36 slices each. I am trying to convert the DICOM files to Nifti format using the mri_convert command in FreeSurfer version 7.3.2. However, the conversion process fails even when using this latest dev version. To resolve this issue, I attempted to use the --nslices-override option. It seems working, however, I am unsure if I used it correctly, and I was not able to find any relevant examples or guidance on how to use this option in the FreeSurfer documentation or other websites.
n=({-1..7}) 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
Thanks for guidance, John
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it might be. That override was for a particular experimental case, but if it works, it works
On 3/27/2023 2:06 PM, John Anderson wrote:
External Email - Use Caution
Thank you, Dr Greve. I tried it, but it didn't work. By 'didn't work,' I mean that when I visualized the NIfTI file, I saw a line on the coronal and sagittal planes, and the whole brain on the axial view. I was able to generate a NIfTI image with multiple volumes as expected by using the mri_convert command with the --nslices-override argument, but I'm not sure if I'm using it correctly.
On Mon, Mar 27, 2023 at 11:19 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you try it with --dcm2niix ? On 3/25/2023 9:43 AM, John Anderson wrote:External Email - Use Caution Dear Dr Doug Greeve, For each participant in my dataset, I have 8 mosaic volumes with 36 slices each. I am trying to convert the DICOM files to Nifti format using the mri_convert command in FreeSurfer version 7.3.2. However, the conversion process fails even when using this latest dev version. To resolve this issue, I attempted to use the --nslices-override option. It seems working, however, I am unsure if I used it correctly, and I was not able to find any relevant examples or guidance on how to use this option in the FreeSurfer documentation or other websites. n=({-1..7}) 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 Thanks for guidance, John _______________________________________________ Freesurfer mailing list 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/freesurfer <https://secure-web.cisco.com/1zR7tdD7AFirzXdRA5dmq7yP8f9Cnqq4RfP7hn5XsC2hNeLOX4jmUQt2R7sOQ_6uN2qz3ahYAjIcbFQ-PLwaMOx7y3tUCeH3u3W0Es8xDhBgBunD8yo78fazoSZjNeD8e5vKPsfD9Ac3byrXST8yT96qatE6rPR8JA7baLwo-W-e-hfR2XJsKMzmD4cFPk2RSrPyrdCK40I0feLDa4ngEzk_5I-xkXp4RHsXR0pWXSOtF2lY9fDX2ZoFQ19Z8PHYSAspTXhPuQ32lzkN_eb_zLXQg2ACI0GSnaUFnpycA_nnTCX8M_bAmM2Y3lRDYx5ZhFSws_w9PmN11g06HxVbvVg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list 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/freesurfer <https://secure-web.cisco.com/1zR7tdD7AFirzXdRA5dmq7yP8f9Cnqq4RfP7hn5XsC2hNeLOX4jmUQt2R7sOQ_6uN2qz3ahYAjIcbFQ-PLwaMOx7y3tUCeH3u3W0Es8xDhBgBunD8yo78fazoSZjNeD8e5vKPsfD9Ac3byrXST8yT96qatE6rPR8JA7baLwo-W-e-hfR2XJsKMzmD4cFPk2RSrPyrdCK40I0feLDa4ngEzk_5I-xkXp4RHsXR0pWXSOtF2lY9fDX2ZoFQ19Z8PHYSAspTXhPuQ32lzkN_eb_zLXQg2ACI0GSnaUFnpycA_nnTCX8M_bAmM2Y3lRDYx5ZhFSws_w9PmN11g06HxVbvVg/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/complianceline <https://secure-web.cisco.com/1_XAyGfsbPBqIzk-FXWXCyIDY_7-lfDnWzqol34dnRKEvDas55bk4clygRY8wWNFoYC5kCpaM1hXeXYPfWPuXhO58dq1eFbhJvwUhJgQSFz6Vv9IgMN3avr8QwkSOvJ7Uu5hoe1jvixg38Cj-TlZBvcbnQjUnAsrrTe0T8nW4jrzr9-YI_p0uS4jX32qKIEuxAMWR_iHBzP_t6vri5R5KGcEIfuNVf6NxVvicBWl764WNJ6w5AhTxo3gGeB3Z8h9M0XnFbijmE4R_bM_4eUlUdl1HxPODX0dqLzkHz4uzL1BkiT1wB54Exb2SAtBZEBCsOtezqtRRFTZjBCxO0eYSmA/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/complianceline <https://secure-web.cisco.com/1_XAyGfsbPBqIzk-FXWXCyIDY_7-lfDnWzqol34dnRKEvDas55bk4clygRY8wWNFoYC5kCpaM1hXeXYPfWPuXhO58dq1eFbhJvwUhJgQSFz6Vv9IgMN3avr8QwkSOvJ7Uu5hoe1jvixg38Cj-TlZBvcbnQjUnAsrrTe0T8nW4jrzr9-YI_p0uS4jX32qKIEuxAMWR_iHBzP_t6vri5R5KGcEIfuNVf6NxVvicBWl764WNJ6w5AhTxo3gGeB3Z8h9M0XnFbijmE4R_bM_4eUlUdl1HxPODX0dqLzkHz4uzL1BkiT1wB54Exb2SAtBZEBCsOtezqtRRFTZjBCxO0eYSmA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
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