External Email - Use Caution You are right, I see 'Found 2 unique series: 9 11' and it works with both of the numbers. I assume I have to do this with every single series in the data, am I correct? Is there a way to do this automatically avoiding specifying the series in each command execution?
Thank you so much for you help, S El lun, 3 jul 2023 a las 20:05, Huang, Yujing (<yhuan...@mgh.harvard.edu>) escribió: > External Email - Use Caution > > dcmunpack -src <dicomdir> -targ <sessionid> -fsfast -run <runno> > <subdir-under-targ> <format> <fname> > > > > 1. specify full path to your dicom directory for ‘-src <dicomdir>’ > > 2. specify full path for ‘-targ <seesionid>’, or it will be created under > the directory where you ran dcmunpack > > 3. I think you should see ‘Found 18 unique series: 1 2 …’ in the output. I > believe <runno> should be one of these series Nos. > > > > Best, > > > > Yujing > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sara Teso Cuesta > *Sent:* Friday, June 30, 2023 1:05 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] dcmunpack: Issues with the -run argument > > > > * External Email - Use Caution * > > Hello FreeSurfer Developers, > > > > I am trying to use dcmunpack to transform dicom images to a nifti format > inside a FSFAST formatted directory (*MailScanner has detected a possible > fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/10RhbaiY2D2ZY_bRli2ryVF5Xi3d8Dc24G2wkWrqQzyxALXmO4HuNbQMFtURi1_3ARLrMR2D9hBjlrK_ZsUTPfgfG_uQJGKqLp9Zw0wJjMiKapWrIZf-qbeCnbVntJgXd-9fJayIkNNn70dFG17LEjv26Wij73WYUg3xBeHYFrqQJ0JGjL6DeJ0V0uwJ8dMtilIMBpsBBy5_IiXFIigo8W49wji05ZDD0rB0CPPLwaHzj1X0CX-TmyDGgiZfOKZ1YAupILWkQ8JLNGVdultl5CALg1ReCrYEWUVGZXfGDQ_SexLNBKEbj4FWSmgLL8lKziO5apRJpCEkvBAvQTWjssQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Ffsfastrestingstatetutorial > <https://secure-web.cisco.com/1JV-FemocV4fiLoKofgFHZ2hQTt_nlpR8LAqJEXvFr3d88Y9d8_5ARW5ZwWfjra1Get0gYobq4LmRSdujguw3Lo8y_WXDV6ESU4ApxhlMZ7JD5AIUzRBJIoJyaHjAFeqrP2rw2iPUB2PkBukeZLPJKT2EKeWxFBBlaMczY6mQKlNi9vPHMD9NIGJc9AkxEeZnUBPjIbTBdnZNtPEUc1tZIW8XtTtgSk8bx2puWstu5z3lOGqpRN1veJpOZif_VOkQhd8xIs0a2I4PDLls1l2RQG9W7-RQQaPBRMBwtnvlJ1DXZY9ir7Z0sSJXxe6yIXLL0AqJvxXoBAvqTqJkhjDXOw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Ffsfastrestingstatetutorial>), > however I am having issues understanding how to use properly the -run > argument. > > > > This is the command I am trying to use: > > > > dcmunpack -src fMRI_dir -targ sessionid -fsfast -run 2 rest nii.gz > f.nii.gz > > > > I assume I am making some mistakes with the command, specially with the > run arguments since this is the error that I got in the terminal: ERROR: > could not find run 2 in data > > > My directory contains fMRIs downloaded directly from the ADNI database and > grouped in folders following this structure: > > /fMRI_dir/subject_id/Axial_rsfMRI/date/image_uid/dicom images > > I've searched the list and no similar errors have been reported. Does > anyone have any thoughts on how to solve this? > > 1) FreeSurfer version: freesurfer_ubuntu20-7.4.0_amd64.deb > 2) Platform: Ubuntu 20.04 in WSL > > > > Thanks for your help. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1_-HbeV1npfIvHldGS4MFKWKyADeEnwA7m_h6dC6l5dM4MDwb1q2mhBdZmyGxopj1JY8GLavZnKIlTKV_pIEz9x9vB4GJ0XjQPQJzWRZBPvKRum-_pvzE7rddouEvYRZL9kTsE_qwdne5er-PzVQofbuvnmkYp933dbZQcaZrR-zRqdVKIf88EDJnZiq-Ja2DVNLS1KHNxH9yLhXM21696PFWwEBc9xHXcYwV-yX48PLHpKsWw5Y3WPJVibpB_hgldaPCpcwCW27rW3s5xoyODCjBdRUXhfsnVDMxP97j2kAKzgDRtv_9VDGj7o7dzd54HpRXQAB-m_QuoF676I6COQ/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 > https://secure-web.cisco.com/1h7xmUYKT2FWsF5tnb8-ikNRW-_KhCPgml1oWMQ6ywvZQ6t9u78SG39m-DwXuG6wnbAMkc5KHfnluB9ZAz20pM1m-ypfLIf37VYapjDuV-3_p8lCrGtuG47u5s2CyZ2nQnkTFcf8_g_J2vsJvezgH0Y5SsWPGL0DfeIYQaPa7Og8d1Pg5XqpJh7c98s17ZvokGRa4esWuXr6KYhX1zKG8qMI0gYzkUJBAav2-awciiGsLmWFQmE8GG6Km-xMJmBnXTxag1fQjoVfuBFIWK_S0RnbQtL3rONbqNn6n8r9D_TxGZJE5JE1FcDwXAgkjSXsAoEuuy0CcKbarRvShhhfTOQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1h7xmUYKT2FWsF5tnb8-ikNRW-_KhCPgml1oWMQ6ywvZQ6t9u78SG39m-DwXuG6wnbAMkc5KHfnluB9ZAz20pM1m-ypfLIf37VYapjDuV-3_p8lCrGtuG47u5s2CyZ2nQnkTFcf8_g_J2vsJvezgH0Y5SsWPGL0DfeIYQaPa7Og8d1Pg5XqpJh7c98s17ZvokGRa4esWuXr6KYhX1zKG8qMI0gYzkUJBAav2-awciiGsLmWFQmE8GG6Km-xMJmBnXTxag1fQjoVfuBFIWK_S0RnbQtL3rONbqNn6n8r9D_TxGZJE5JE1FcDwXAgkjSXsAoEuuy0CcKbarRvShhhfTOQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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