Re: [Freesurfer] Multiple inputs into recon-all -i
Hi Ye you only need to give it a single file from each run and it will find the rest. The only time you use -i more than once is if you acquired more than 1 T1-weighted volume. Definitely don't give it all the files that make up the same volume cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Multiple inputs into recon-all -i
Dear Bruce, Thank you very much for your suggestion, but I am afraid that I still don't quite understand you. In order to make it simple, suppose I have two files, Barba001.IMA and Barba002.IMA, coming directly from the scanner. Now if I enter *recon-all -s Barba -i Barba001.IMA* from the command line, I am only able to find *001.mgz* in the Barba/mri/orig. Aren't I supposed to to find 001.mgz and 002.mgz? Thank you so much! Sincerely, Ye On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ye you only need to give it a single file from each run and it will find the rest. The only time you use -i more than once is if you acquired more than 1 T1-weighted volume. Definitely don't give it all the files that make up the same volume cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye 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 Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Multiple inputs into recon-all -i
Hi Ye, you would never have two files, as each file represents one image, or slice from a sequence. So you might have two sequences of files, say Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima, Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once with *one* file from each series (it wouldn't matter which one). cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear Bruce, Thank you very much for your suggestion, but I am afraid that I still don't quite understand you. In order to make it simple, suppose I have two files, Barba001.IMA and Barba002.IMA, coming directly from the scanner. Now if I enter recon-all -s Barba -i Barba001.IMA from the command line, I am only able to find 001.mgz in the Barba/mri/orig. Aren't I supposed to to find 001.mgz and 002.mgz? Thank you so much! Sincerely, Ye On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ye you only need to give it a single file from each run and it will find the rest. The only time you use -i more than once is if you acquired more than 1 T1-weighted volume. Definitely don't give it all the files that make up the same volume cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Multiple inputs into recon-all -i
Dear Bruce, Thank you very much! Sincerely, Ye On Mon, Jun 24, 2013 at 7:32 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ye, you would never have two files, as each file represents one image, or slice from a sequence. So you might have two sequences of files, say Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima, Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once with *one* file from each series (it wouldn't matter which one). cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear Bruce, Thank you very much for your suggestion, but I am afraid that I still don't quite understand you. In order to make it simple, suppose I have two files, Barba001.IMA and Barba002.IMA, coming directly from the scanner. Now if I enter recon-all -s Barba -i Barba001.IMA from the command line, I am only able to find 001.mgz in the Barba/mri/orig. Aren't I supposed to to find 001.mgz and 002.mgz? Thank you so much! Sincerely, Ye On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ye you only need to give it a single file from each run and it will find the rest. The only time you use -i more than once is if you acquired more than 1 T1-weighted volume. Definitely don't give it all the files that make up the same volume cheers Bruce On Mon, 24 Jun 2013, ye tian wrote: Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye 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 Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
