Re: [Freesurfer] trac-all problem
Hi Qi - Is /Studies/*/DTI/dmrirc_subject a single file or multiple files? What are the contents of that file? a.y On Fri, 6 May 2016, Zeng, Qi wrote: Hi, I am running dti data with trac-all. I followed the command: trac-all -prep -c /Studies/*/DTI/dmrirc_subject but it exited with error "Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension." Before. there is another post about similar problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027802.html Dr. Yendiki suggested it could be because missing defined B0 in the dmrirc, but new version wouldn't need this (5.3, a new version?). If so, where can I obtain the B0 data? Can I compute from DICOM like nifti and bval, bvec? Best, Qi ___ 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] trac-all problem
Hi, I am running dti data with trac-all. I followed the command: trac-all -prep -c /Studies/*/DTI/dmrirc_subject but it exited with error "*Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension." * Before. there is another post about similar problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027802.html Dr. Yendiki suggested it could be because missing defined B0 in the dmrirc, but new version wouldn't need this (5.3, a new version?). If so, where can I obtain the B0 data? Can I compute from DICOM like nifti and bval, bvec? Best, Qi ___ 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] trac-all problem
hello i am trying to process the dti data with trac-all. I am new to tracula my input images are 3300 dicoms, 60 slices and 55 dti diffusions i have attached my dmrirc_single_subject file i did the following command: trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject and got the result: INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 INFO: Diffusion root is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mon Feb 11 12:41:04 CST 2013 mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... Starting DICOMRead2() dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 dcmdir = /Studies/MJMRI/MJ0012//s780 Ref Series No = 13 Found 3304 files, checking for dicoms Found 3300 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 55 nslices = 60 ndcmfiles = 3300 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032 processing
Re: [Freesurfer] trac-all problem
Hi Jon - My guess is you didn't define the nb0 variable in your configuration file, see here: http://www.freesurfer.net/fswiki/dmrirc The new version, which will come out in a few days, will be able to figure it out without you having to specify it but with the current version you have to. Hope this helps, a.y On Tue, 12 Feb 2013, Jon Wieser wrote: hello i am trying to process the dti data with trac-all. I am new to tracula my input images are 3300 dicoms, 60 slices and 55 dti diffusions i have attached my dmrirc_single_subject file i did the following command: trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject and got the result: INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 INFO: Diffusion root is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mon Feb 11 12:41:04 CST 2013 mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... Starting DICOMRead2() dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 dcmdir = /Studies/MJMRI/MJ0012//s780 Ref Series No = 13 Found 3304 files, checking for dicoms Found 3300 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 55 nslices = 60 ndcmfiles = 3300 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 processing
Re: [Freesurfer] trac-all problem
Sorry, reading stuff from the dicom header will not work for all dicom versions. It should work for Siemens dicoms though. On Tue, 12 Feb 2013, Jon Wieser wrote: according to the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula nb0 does not need to be specified when using original dicoms. , but i'll try defining the nb0 variable thanks Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 10:49:18 AM Subject: Re: [Freesurfer] trac-all problem Hi Jon - My guess is you didn't define the nb0 variable in your configuration file, see here: http://www.freesurfer.net/fswiki/dmrirc The new version, which will come out in a few days, will be able to figure it out without you having to specify it but with the current version you have to. Hope this helps, a.y On Tue, 12 Feb 2013, Jon Wieser wrote: hello i am trying to process the dti data with trac-all. I am new to tracula my input images are 3300 dicoms, 60 slices and 55 dti diffusions i have attached my dmrirc_single_subject file i did the following command: trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject and got the result: INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 INFO: Diffusion root is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mon Feb 11 12:41:04 CST 2013 mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... Starting DICOMRead2() dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 dcmdir = /Studies/MJMRI/MJ0012//s780 Ref Series No = 13 Found 3304 files, checking for dicoms Found 3300 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 55 nslices = 60 ndcmfiles = 3300 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015
Re: [Freesurfer] trac-all problem
that it is looking for? - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 1:26:55 PM Subject: Re: [Freesurfer] trac-all problem Hi Jon - This is the same issue. The reading from the dicom part will work for the Siemens dicoms that we have here but is not guaranteed to work with other dicoms. You'll have to define bvecfile, bvalfile, and nb0. (The first two should be in columns, not rows.) Let me know if you run into any other problems, a.y On Tue, 12 Feb 2013, Jon Wieser wrote: i ran the program with the nb0 set to 2 i got the following error: it's not finding a bvec files. the document says that the bevecs are read from the DICOM headers. here's the output of the run : INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 INFO: Diffusion root is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Tue Feb 12 13:00:35 CST 2013 mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... Starting DICOMRead2() dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 dcmdir = /Studies/MJMRI/MJ0012//s780 Ref Series No = 13 Found 3304 files, checking for dicoms Found 3300 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 55 nslices = 60 ndcmfiles = 3300 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs mv: rename /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs to /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs: No such file or directory Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Feb 12 13:05:29 CST 2013 - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Sent: Tuesday, February 12, 2013 11:24:56 AM Subject: Re: [Freesurfer] trac-all problem Yeah, the tutorial should say Siemens dicoms instead of dicoms. In any case in the next version this won't be a problem b/c it'll determine the nb0 from the bvals file. On Tue, 12 Feb 2013, Jon Wieser wrote: hi our scanner is a GE Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 11:14:42 AM Subject: Re: [Freesurfer] trac-all problem Sorry, reading stuff from the dicom header will not work for all dicom versions. It should work for Siemens dicoms though. On Tue, 12 Feb 2013, Jon Wieser wrote: according to the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula nb0 does not need to be specified when using original dicoms. , but i'll try defining the nb0 variable thanks Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 10:49:18 AM Subject: Re: [Freesurfer] trac-all problem Hi Jon - My guess is you didn't define the nb0 variable in your configuration file, see here: http://www.freesurfer.net/fswiki/dmrirc The new version, which will come out in a few days, will be able to figure it out without you having to specify it but with the current version you have to. Hope this helps, a.y On Tue, 12
Re: [Freesurfer] trac-all problem
and yes, you'll need to run recon-all on your data before running tracula cheers Bruce On Tue, 12 Feb 2013, Anastasia Yendiki wrote: Hi Jon - You'll the aparc+aseg.mgz (cortical parcellation + subcortical segmentation). The basis of TRACULA is that it uses the underlying anatomy to reconstruct the tracts. a.y On Tue, 12 Feb 2013, Jon Wieser wrote: no i have not run recon-all yet on this dataset, do i need to run recon-all with -autorecon1 ,-autorecon2, and -autorecon3 before i analyze the dti data? thanks Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 3:34:19 PM Subject: Re: [Freesurfer] trac-all problem Hi Jon - Have you run freesurfer (recon-all) on your T1 data? a.y On Tue, 12 Feb 2013, Jon Wieser wrote: i got past the problem with the bvesc, and bvals, my current output has a new problem: here's the last part of the output. #@# Tensor fit Tue Feb 12 15:24:51 CST 2013 dtifit -k /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz -m /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -r /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs -b /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals -o /Studies/MJMRI/MJ0012/freesurfer/dmri/dtifit 0 256 0 256 0 60 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed 59 slices processed #- #@# Priors Tue Feb 12 15:26:36 CST 2013 /Applications/freesurfer/bin/dmri_train --outdir /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni --out lh.cst_AS_avg23_mni_flt rh.cst_AS_avg23_mni_flt lh.ilf_AS_avg23_mni_flt rh.ilf_AS_avg23_mni_flt lh.unc_AS_avg23_mni_flt rh.unc_AS_avg23_mni_flt fmajor_PP_avg23_mni_flt fminor_PP_avg23_mni_flt lh.atr_PP_avg23_mni_flt rh.atr_PP_avg23_mni_flt lh.cab_PP_avg23_mni_flt rh.cab_PP_avg23_mni_flt lh.ccg_PP_avg23_mni_flt rh.ccg_PP_avg23_mni_flt lh.slfp_PP_avg23_mni_flt rh.slfp_PP_avg23_mni_flt lh.slft_PP_avg23_mni_flt rh.slft_PP_avg23_mni_flt --slist /tmp/subj23.freesurfer.92196.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dl abel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2! .flt.nii .gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1
