Thanks a lot!
Date: Fri, 15 Mar 2013 13:09:41 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem just: mri_convert <full path to minc file> volume.mgz cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: > Sorry, I am also a beginner in Linux environment. Now it works. > I try : > ------------- > esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA > total 13892 > -rwxr--r-- 1 esther esther 14224696 12 mar 23:33 > t1_icbm_normal_1mm_pn3_rf20.mnc > [esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc > -rwxr--r-- 1 esther esther 14224696 12 mar > 23:33/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. > mnc > ---------------- > And this > ---------- > Volume information > for/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. > mnc > type: MINC > dimensions: 181 x 217 x 181 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: SHORT (4) > fov: 217.000 > dof: 0 > xstart: -90.5, xend: 90.5 > ystart: -108.5, yend: 108.5 > zstart: -90.5, zend: 90.5 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = > 0.5000 > : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = > -17.5000 > : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = > 18.5000 > Orientation : RAS > Primary Slice Direction: axial > > voxel to ras transform: > 1.0000 0.0000 0.0000 -90.0000 > 0.0000 1.0000 0.0000 -126.0000 > 0.0000 0.0000 1.0000 -72.0000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant 1 > > ras to voxel transform: > 1.0000 -0.0000 -0.0000 90.0000 > -0.0000 1.0000 -0.0000 126.0000 > -0.0000 -0.0000 1.0000 72.0000 > 0.0000 0.0000 0.0000 1.0000 > ------------------- > > which command shoul I use for convert direct from MNC to mgz^ > > Thanks > > > Date: Fri, 15 Mar 2013 10:00:04 -0400 > From: fis...@nmr.mgh.harvard.edu > To: pval...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert problem > > can you run ls -l and mri_info on it? > On Fri, 15 Mar 2013, Valtina Pouegue > wrote: > > > I get this error------------- > > esther@m3012-04 ~]$ mri_info > > $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc > > mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t > 1_icbm_normal_1mm_pn3_rf20.m > > nc > > -------I check in the directory enad the file is right there, > > > > > Date: Fri, 15 Mar 2013 09:24:22 -0400 > > > From: fis...@nmr.mgh.harvard.edu > > > To: pval...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] mri_convert problem > > > > > > Hi Valtina > > > > > > you can convert directly without going through nii. What happens when yo > u > > > run ls -l on that file? Or mri_info? > > > > > > cheers > > > Bruce > > > > > > On Fri, 15 Mar 2013, Valtina Pouegue wrote: > > > > > > > Hi, > > > > > > > > I have a problem of conversion. I would like to convert mnc file to mg > z. > > But I think I shoul first convert mnc to nii then > > > > nii to mgz. , > > > > so I try the command mri_convert and I have this error; > > > > ------------- > > > > [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc > > Folder1.nii.gz > > > > mri_convert > > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc > > Folder1.nii.gz > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > > > reading from > > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... > > > > mincRead(): can't find file > > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc > > > > [esther@m3012-04 ~]$ > > > > -------------------- > > > > I look up, and the file is at the rith place.... Could you help me.. > > > > Thanks > > > > > > > > VP] > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom i > t > > 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 i > n > > 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 > 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 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 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.
