You have to have a separate command line for each one, but you can always write a script to do that, eg

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
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