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 | hlindroth@wisc.edu
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 | hlindroth@wisc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 | hlindroth@wisc.edu
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu 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 | hlindroth@wisc.edumailto:hlindroth@wisc.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 | hlindroth@wisc.edu
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu *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 | hlindroth@wisc.edu mailto:hlindroth@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@nmr.mgh.harvard.edu
-
Douglas Greve -
Heidi Lindroth