That's almost right. Just specify the subject name and not the full path. Also, you will need to supply bvals and bvects dt_recon --i DTI_15.nii.gz --s NPI001 --o /usr/local/freesurfer/NPI001/DTI_15
Antonella Kis wrote: > Hi Doug, > > Thanks again for helping. So my question is then: I will pass for --i > (the input data) the .nii.gz file from the DTI data and the it is OK > to use for the --s which defines the file of the structural recon a > file called NPI001 where I have 10 files after recon-all (bem, label, > mri, surf, stats, etc)? In other words if I will set-up: > > setenv FREESURFER_HOME /usr/local/freesurfer > setenv SUBJECTS_DIR $FREESURFER_HOME > > and since my files are in /usr/local/freesurfer/NPI001 I am then doing: > > cd /usr/local/freesurfer/NPI001 > > Here I have the pre-processed files after recon-all and a file called > DTI_15 with my diffussion data and the DTI_15.nii.gz file so I can run: > > dt_recon --i DTI_15.nii.gz --s /usr/local/freesurfer/NPI001 --o > /usr/local/freesurfer/NPI001/DTI_15 > > Is this right? > > I will try by the time you answer but please let me know if you have > any objection and/or advise. > > Many thanks, > AK > > > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* Antonella Kis <ator...@yahoo.com>; freesurfer > <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Wednesday, August 31, 2011 1:49 PM > *Subject:* Re: [Freesurfer]: Error with dt_recon > > If you pass it dicom, it will try to extract the bvalues, which is > where it is failing. > doug > > Antonella Kis wrote: > > Dear Doug, > > > > Sorry but I still have a question about this error: > > I understood that dt_recon it takes original dicom images as input > and it generates multiple NIFTI volumes that will be used in later > steps.So why I need to use the NIFTI as input? > > > > Thnak you. > > AK > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <ator...@yahoo.com <mailto:ator...@yahoo.com>> > > *Cc:* "fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>" <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>; "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Tuesday, August 30, 2011 3:51 PM > > *Subject:* Re: [Freesurfer] Fw: Error with dt_recon > > > > It's looking for the values in the dicom file (which apparently does > not have them). Convert the dicom to nifit, then use the nifti as > input, then pass files with bvals and bvects on the command line. > > doug > > > > Antonella Kis wrote: > > > > > > > > > Dear Bruce: > > > > > > I am running the dt_recon: > > > # setenv FREESURFER_HOME /usr/local/freesurfer # setenv > SUBJECTS_DIR $FREESURFER_HOME > > > # cd /usr/local/freesurfer/NPI001 > > > # dt_recon --i > /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm > > --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti > > > > > > > > > and I am getting the following error: > > > > > > ERROR: cannot extract sDiffusion.alBValue[1] from > /usr/local/freesurfer/NPI001/dti/dwi-infodump.dat > > > > > > Can you please give me a hint? > > > > > > Thank you. > > > AK > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
