The subject name is the FreeSurfer subject name assigned when you ran recon-all to analyze the T1 anatomical MRI images. BTW, you need everything in native space to run the pipeline. doug
On 06/30/2016 12:25 AM, Lee Subin Kristine wrote: > Dear FreeSurfer experts, > > Hello, > I am trying to use Freesurfer's (developmental version) PVE correction > tool and I haveone question. > > The data to be PVE-corrected are some preprocessed PET data downloaded > from the Alzheimer's DIsease Neuroimaging Initiative (ADNI) database. > Basiclly, the dynamic PET images have been co-registered to one > another, averaged, and spatially normalized to a common space. Now I > am trying to apply PVE-correction. > It seems from your answers here > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html) > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html>that > > you run the following commands: > (1) gtmseg > (2) bbregister > (3) mri_gtmpvc > (4) mri_glmfit > > When I enter gtmseg --s subject such as below ('Desktop/forFSsubin_2' > is location of the subject MRI and '019_S_4835_N3m_cub_ACPC.nii' is > the filename) > > /~/Desktop/forFSsubin_2$ gtmseg --s 019_S_4835_N3m_cub_ACPC.nii/ > > I get: / > > ERROR: cannot find //019_S_4835_N3m_cub_ACPC.nii/ > > I have changed directory to the folder where the subject MRI file is, > and I have typed the subject's filename correctly, but it keeps saying > the subject file cannot be found. Any ideas on what is wrong here? > > Any help would be appreciated. > Thank you in advance. > > Regards, > Subin > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
