[Freesurfer] Using T2 or FLAIR data to improve pial surfaces
External Email - Use Caution Dear all I want to use T2 or FLAIR data to improve pial surfaces. I wonder, which one is better? using T2pial or FLAIRpial? Is there any difference in output? Thank you so much in advance for your time and help! Hengameh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using T2 or Flair data to improve pial surfaces
You have to have a separate command line for each one, but you can always write a script to do that, eg foreach subject (subjeta subjectb ) recon-all -s $subject -qcache end On 6/19/18 10:53 AM, Heidi Lindroth wrote: I did not. Can I re-run a batch of scans with the -qcache command or do I need to do it one by one? Heidi Lindroth BSN RN PhD Candidate| School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindr...@wisc.edu *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve *Sent:* Tuesday, June 19, 2018 9:38:25 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Using T2 or Flair data to improve pial surfaces Did you run recon-all with -qcache ? On 6/19/18 9:30 AM, Heidi Lindroth wrote: External Email - Use Caution Hi there, I have used T2/Flair images to improve the pial surface reconstruction, however, when I tried to analyze these data in QDEC, I was unable to load the files because the T1/T2 processed scans do not have the following file type: lh.thickness.fwhm10.fsaverage.mgz or .mgh file. . Instead, they have this file type: lh.smoothwm.FI.crv. Is there a way to convert the crv file to a mgz/mgh file? Is there an alternate way to analyze the T1/T2 data using QDEC? Thank you, Heidi Lindroth BSN RN PhD Candidate| School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindr...@wisc.edu <mailto:hlindr...@wisc.edu> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 ___ 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] Using T2 or Flair data to improve pial surfaces
External Email - Use Caution I did not. Can I re-run a batch of scans with the -qcache command or do I need to do it one by one? Heidi Lindroth BSN RN PhD Candidate| School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindr...@wisc.edu From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve Sent: Tuesday, June 19, 2018 9:38:25 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using T2 or Flair data to improve pial surfaces Did you run recon-all with -qcache ? On 6/19/18 9:30 AM, Heidi Lindroth wrote: External Email - Use Caution Hi there, I have used T2/Flair images to improve the pial surface reconstruction, however, when I tried to analyze these data in QDEC, I was unable to load the files because the T1/T2 processed scans do not have the following file type: lh.thickness.fwhm10.fsaverage.mgz or .mgh file. . Instead, they have this file type: lh.smoothwm.FI.crv. Is there a way to convert the crv file to a mgz/mgh file? Is there an alternate way to analyze the T1/T2 data using QDEC? Thank you, Heidi Lindroth BSN RN PhD Candidate| School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindr...@wisc.edu<mailto:hlindr...@wisc.edu> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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 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] Using T2 or Flair data to improve pial surfaces
Did you run recon-all with -qcache ? On 6/19/18 9:30 AM, Heidi Lindroth wrote: External Email - Use Caution Hi there, I have used T2/Flair images to improve the pial surface reconstruction, however, when I tried to analyze these data in QDEC, I was unable to load the files because the T1/T2 processed scans do not have the following file type: lh.thickness.fwhm10.fsaverage.mgz or .mgh file. . Instead, they have this file type: lh.smoothwm.FI.crv. Is there a way to convert the crv file to a mgz/mgh file? Is there an alternate way to analyze the T1/T2 data using QDEC? Thank you, Heidi Lindroth BSN RN PhD Candidate| School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindr...@wisc.edu ___ 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 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] Using T2 or Flair data to improve pial surfaces
External Email - Use Caution Hi there, I have used T2/Flair images to improve the pial surface reconstruction, however, when I tried to analyze these data in QDEC, I was unable to load the files because the T1/T2 processed scans do not have the following file type: lh.thickness.fwhm10.fsaverage.mgz or .mgh file. . Instead, they have this file type: lh.smoothwm.FI.crv. Is there a way to convert the crv file to a mgz/mgh file? Is there an alternate way to analyze the T1/T2 data using QDEC? Thank you, Heidi Lindroth BSN RN PhD Candidate| School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindr...@wisc.edu ___ 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.
