that's what I wondered. AFI = "Actual Flip angle Imaging" usually On Wed, 22 Jan 2014, Glasser, Matthew wrote:
AFI is a bias transmit scan, not an MPRAGE. Look for T1w.
On 1/22/14 11:44 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Al,
can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not familiar with their naming convention. I'll cc Matt Glasser who can probably help.
cheers Bruce On Wed, 22 Jan 2014, Alfred Ochs wrote:
Hello folks,
I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI structural T1 MRI from the Human Connectome Project, in particular 100307_3T_AFI.nii. Unless I am mistaken, their preprocessed data doesn't include aseg data, at least identified in a manner I am familiar with. Nevertheless, recon-all -s 100307_cs -all reports:
ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/100307_cs/mri/orig/001.mgz has 2 frames.
How do I work around this?
Thanks, Al
Alfred L. Ochs, Ph.D. Virginia Institute for Neuropsychiatry Richmond, Virginia
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.
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
BTW: If you download the structural preprocessed data, the HCP data already includes aparc+aseg.nii.gz in both "native" space and transformed to MNI152 space. If you want the data values contained in the native space aseg.stats file of FreeSurfer, you can quickly get that as part of the spreadsheet of data available for each subject at db.humanconnectome.org
cheers, -MH
-- Michael Harms, Ph.D.
----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
On 1/22/14 11:47 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
that's what I wondered. AFI = "Actual Flip angle Imaging" usually On Wed, 22 Jan 2014, Glasser, Matthew wrote:
AFI is a bias transmit scan, not an MPRAGE. Look for T1w.
On 1/22/14 11:44 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Al,
can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not familiar with their naming convention. I'll cc Matt Glasser who can probably help.
cheers Bruce On Wed, 22 Jan 2014, Alfred Ochs wrote:
Hello folks,
I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI structural T1 MRI from the Human Connectome Project, in particular 100307_3T_AFI.nii. Unless I am mistaken, their preprocessed data doesn't include aseg data, at least identified in a manner I am familiar with. Nevertheless, recon-all -s 100307_cs -all reports:
ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/100307_cs/mri/orig/001.mgz has 2 frames.
How do I work around this?
Thanks, Al
Alfred L. Ochs, Ph.D. Virginia Institute for Neuropsychiatry Richmond, Virginia
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.
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Harms, Michael