Dear Douglas, Thank you!
I am using a desktop of the Martinos Center. Seems I am not allowed to replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is there another way to use it? Best wishes, Baojuan ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, November 10, 2015 2:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir It will be distributed with version 6. For now, you can just replace the current version in $FREESURFER_HOME/bin (just make backup of it before you do). After that, all programs will use the new version On 11/10/2015 01:51 PM, Li, Baojuan wrote: > Dear Douglas, > > Thank you so much for your help. I have tried the new version of > mri_convert and it works very well, giving me the bvecs and bvals > correctly! > > Is the new mri_convert available from the latest version of > Freesurfer? Because we will need to unpack data from a directory, I > think it will be great if we can use the new version of mri_convert > through unpacksdcmdir. > > Best wishes, > Baojuan > > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > *Sent:* Monday, November 09, 2015 11:04 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] unpacksdcmdir > > > > On 11/9/15 7:41 PM, Li, Baojuan wrote: >> Hi all, >> >> I am using unpacksdcmdir to unpack our data (collected using a >> Siemens scanner) but running into an error. >> >> I have two questions and hope someone can kindly help me with them: >> >> 1. Why can not I successully unpack images for run10? > Looks like the dicom file is missing a tag (28 30). This is the voxel > size, which is weird to not be there. Is this a special output from > the scanner? Some kind of derived data? >> >> 2. I got the DTI.nii image, the bvecs and bvals for run4 now. Can I >> use them for my analyses? Seems this run has an error. Does this >> error matter? > The err does not matter. Off hand, I don't know for sure that the > bvals and bvecs are correct for 5.3. You can try the new version of > mri_convert in which I have a lot more confidence. > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert >> >> Thank you so much for your help! >> >> Best wishes, >> Baojuan >> >> The logfile is as follows: >> >> Done scanning Mon Nov 9 19:10:43 EST 2015 >> ------------------------------------------ >> 1 localizer ok 512 512 3 1 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714 >> 2 AAScout ok 128 128 128 2 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763 >> 3 T1_MPRAGE_sag ok 256 256 128 1 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 >> 4 DIFFUSION_HighRes err 128 128 64 70 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 >> 5 DIFFUSION_HighRes ok 128 128 64 1 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428 >> 6 DIFFUSION_HighRes ok 128 128 64 1 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429 >> 7 DIFFUSION_HighRes ok 128 128 64 1 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430 >> 8 DIFFUSION_HighRes ok 128 128 64 1 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431 >> 9 DIFFUSION_HighRes ok 128 128 64 1 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432 >> 10 DIFFUSION_HighRes ok 128 128 1 64 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 >> 11 ge_functionals ok 64 64 33 150 >> MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918 >> unpacking config ------------------ >> {3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii} >> ----------------------------------- >> --------------------------------------------------------- >> Run 3 ----------------------------------------- >> Mon Nov 9 19:10:43 EST 2015 >> 3 T1 mgz T1.mgz >> mri_convert >> /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 >> /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz >> --sdcmlist >> /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf >> -ot mgz --nspmzeropad 3 --in_type siemens_dicom >> --------------------------------------------------------- >> Run 4 ----------------------------------------- >> Mon Nov 9 19:10:56 EST 2015 >> 4 DTI nii DTI.nii >> INFO: this run has an error, but trying anyway >> mri_convert >> /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 >> /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii >> --sdcmlist >> /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf >> -ot nii --nspmzeropad 3 --in_type siemens_dicom >> --------------------------------------------------------- >> Run 10 ----------------------------------------- >> Mon Nov 9 19:11:19 EST 2015 >> 10 DTI nii DTI.nii >> ERROR: reading >> /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 >> tag 28 30 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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 _______________________________________________ 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 . 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