Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

Preprocessing error: 'GLIBCXX_3.4.9 not found'
by Joseph Andreano 04 May '13

04 May '13

Hello, I was attempting to preprocess a scan earlier and I got an error which seems to indicate a problem with the version of FSL: >From this command: preproc-sess -s nmasa_016_130111 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run I get this error: #----------Using FSL's BET to Extract Brain--------------# /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_016_130111/bold bet.fsl /tmp/mkbrainmask_32456/in.nii /tmp/mkbrainmask_32456/brain -m -f 0.1 /usr/pubsw/packages/fsl/current/bin/bet2: /usr/lib64/libstdc++.so.6: version 'GLIBCXX_3.4.9' not found (required by /usr/pubsw/packages/fsl/current/bin/bet2) Looking through the archive, I see others have had similar problems, and the answers generally referred to updating the version of FSL. Anybody know what to do about this? Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

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version 5.3 coming out soon
by Bruce Fischl 04 May '13

04 May '13

Hi All, We have recently uncovered problems with version 5.2. Based on these problems, we are recommending that people stop using 5.2, mainly in regards to usage of the surface data. A new version, 5.3, will be released within two weeks, and a beta version for each platform will be available within a couple days. There were two main problems that were uncovered. First, a change was made that was only meant to affect the white surface placement in high-resolution data sets, but unfortunately is being applied to all data sets. This causes the white surface to contract a small amount. This causes the surface area to be smaller and cortex to be measured as thicker relative to version 5.1. Visually, the surfaces do not necessarily look less accurate, but we feel that the systematic differences with previous versions are ill-advised without a clear reason for the change. Second, a change made to the placement of the pial surface in order to improve the positioning based on T2/FLAIR that caused it to extend too far in some data sets during the T1-based pial surface deformation. This unfortunately became the default behavior, which was not intended. None of the dozens of test data sets we ran displayed this problem. The behavior was reported by other users which led us to the bug. In general, we rigorously test each version. However, our systematic comparison of a new version with previous versions which would have caught these problems was conducted prior to these changes. We are now tightening and regimenting our testing procedures to ensure this doesnt happen again. Note that there are no problems with the volumetric segmentation (aseg) in version 5.2. We realize that this will cause a substantial inconvenience for users. We have isolated and fixed the problems and have run two rounds of alpha testing and have one more to go, after which we will release a beta version in a couple of days to anyone that wants it. sorry for the problems. Bruce

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Using mri_cor2label
by jwaugh＠nmr.mgh.harvard.edu 03 May '13

03 May '13

Hello Freesurfers, I would like to use mri_cor2label for areas of the cortext defined in the FreeSurferColorLUT.txt. There are many ROIs whose IDs are >255, the numerical limit imposed on mri_cor2label. How can I define labels using these larger-numbered ROIs? I am specifically interested in using LUT IDs such as 1024 and 2024, the L and R precentral gyrus segmentation. Thank you! Jeff

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[Release] - iSurf BrainView 4.1.0
by Pedro Paulo de Magalhães Oliveira Junior 03 May '13

03 May '13

Today it was released the version 4.1.0 of iSurf BrainView for iPad, iPhone and iPod Touch. Major changes: - Color scheme has been changed to match Windows 8 Version. - Icon has been redesigned as suggested by many users. - Now it supports the new resolution. 1136x640 - 3D engine has been redesigned to take advantage of new iOS device GPU - Aseg from FreeSurfer 5.2 As usual suggestions and feedback are welcome. The link for download is: http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8 --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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Re: [Freesurfer] epi correction of fmri data
by Douglas N Greve 03 May '13

03 May '13

If they don't match, then this is beyond the scope of the tools as they currently exist. On 05/03/2013 04:40 PM, Corinna Bauer wrote: > volume sizes don't match. > > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x1.mat file for direction > cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped > (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x1.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > volume sizes do not match > > fieldmap/20130409_153340FieldMappings011a001x1.img: (width, height, > depth, frames) = (256, 256, 52, 1) > > bold/005/f.nii: (width, height, depth, frames) = (64, 64, 36, 245) > > > > On Fri, May 3, 2013 at 4:36 PM, Corinna Bauer <corinnab83(a)gmail.com > <mailto:corinnab83@gmail.com>> wrote: > > It did run all the way through using the .img files. > > Should I try that mri_convert on all 4 real/imaginary files? > > > On Fri, May 3, 2013 at 4:30 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > It should actually run all the way through. If your field maps > have the same geometry as your fmri volumes, and your fmri > runs have correct geometry, then you can run > > mri_convert imag_fmap2300.nii imag_fmap2300.geo.nii --in_like > fmri.nii > > Also note that you are just creating a voxel shift map with > the epidewarp command, not applying it to the fmri. The > application is done in a more complicated way during preproc-sess > > doug > > > > On 05/03/2013 04:10 PM, Corinna Bauer wrote: > > hmm. can anything be done to fix it? > > Work the preproc-sess and mkanalysis-sess steps work if I > used B0 corrected images right from the get-go instead of > raw fmri runs? > > > On Fri, May 3, 2013 at 4:04 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > yep, it is basically the same error > > > On 05/03/2013 03:57 PM, Corinna Bauer wrote: > > I would imagine so. I tried it with the img files. > > > /usr/local/freesurfer/subjects/symmetry/functional/antonio> > epidewarp.fsl --complex > fieldmap/20130409_153340FieldMappings011a001x1.img > fieldmap/20130409_153340FieldMappings011a001x3.img > fieldmap/20130409_153340FieldMappings011a001x2.img > fieldmap/20130409_153340FieldMappings011a001x4.img > --tediff > 2.3 --esp 0.59278 --epi bold/005/f.nii --vsm > bold/b0dcmap.nii.gz > FSLVersion 5.0.2 > FSLVerMaj 5 > Logfile is bold/b0dcmap.nii.gz.log > FSLOUTPUTTYPE NIFTI_GZ > Extension is nii.gz > nframes = 245, nmidframe = 122 > fslroi > > /usr/local/freesurfer/subjects/symmetry/functional/antonio/bold/005/f.nii > bold/tmp-epidewarp.19423.fsl/exf.nii.gz 122 1 > mri_convert > fieldmap/20130409_153340FieldMappings011a001x1.img > bold/tmp-epidewarp.19423.fsl/real1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > mreuter Exp $ > reading from > fieldmap/20130409_153340FieldMappings011a001x1.img... > > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x1.mat > file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, > transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x1.mat > file > > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/real1.nii... > mri_convert > fieldmap/20130409_153340FieldMappings011a001x3.img > bold/tmp-epidewarp.19423.fsl/imag1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > mreuter Exp $ > reading from > fieldmap/20130409_153340FieldMappings011a001x3.img... > > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x3.mat > file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, > transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x3.mat > file > > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/imag1.nii... > mri_convert > fieldmap/20130409_153340FieldMappings011a001x2.img > bold/tmp-epidewarp.19423.fsl/real2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > mreuter Exp $ > reading from > fieldmap/20130409_153340FieldMappings011a001x2.img... > > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x2.mat > file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, > transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x2.mat > file > > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/real2.nii... > mri_convert > fieldmap/20130409_153340FieldMappings011a001x4.img > bold/tmp-epidewarp.19423.fsl/imag2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > mreuter Exp $ > reading from > fieldmap/20130409_153340FieldMappings011a001x4.img... > > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x4.mat > file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, > transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x4.mat > file > > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/imag2.nii... > > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x1.mat > file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, > transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x1.mat > file > > ----------------------------------------------------------------- > > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x3.mat > file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, > transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x3.mat > file > > ----------------------------------------------------------------- > Saving result to > 'bold/tmp-epidewarp.19423.fsl/mag.nii.gz' > (type = nii ) [ ok ] > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > bet bold/tmp-epidewarp.19423.fsl/mag.nii.gz > bold/tmp-epidewarp.19423.fsl/brain.nii.gz > fslmaths bold/tmp-epidewarp.19423.fsl/brain.nii.gz > -bin > bold/tmp-epidewarp.19423.fsl/brain.nii.gz > fslmaths bold/tmp-epidewarp.19423.fsl/brain.nii.gz > -dilM > bold/tmp-epidewarp.19423.fsl/head.nii.gz > ^C > > > > On Fri, May 3, 2013 at 3:52 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > yes, it should take img files. At some point, > the lack of > valid > geometry might mess things up > > > On 05/03/2013 03:47 PM, Corinna Bauer wrote: > > Oh I see. I have the raw par rec files, > should I try > converting it again? I used dcm2nii to > convert it to > hdr/img > files and then fslchfiletype to get it > into nifti. for > some > reason just converting it to nifti right > away doesn't > look right. > > Will epidewarp take img files? > > > On Fri, May 3, 2013 at 3:43 PM, Douglas N > Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > nope, the qform errors mean thatthere > is something > going > on with > your data. It means that the geometry > is not in > the nifti > file. > > > On 05/03/2013 03:41 PM, Corinna Bauer > wrote: > > do they need to be nii.gz? > > > On Fri, May 3, 2013 at 3:38 PM, > Corinna Bauer > <corinnab83(a)gmail.com > <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>> > <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>> > <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>>>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>>> > <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>>>>>> > > wrote: > > I still get funny warnings > about the > nifti-1 qform > or sform > > /usr/local/freesurfer/subjects/symmetry/functional/antonio> > epidewarp.fsl --complex > fieldmap/real_fmap2300.nii > fieldmap/imag_fmap2300.nii > fieldmap/real_fmap4600.nii > fieldmap/imag_fmap4600.nii --tediff 2.3 --esp > 0.59278 --epi > bold/005/f.nii --vsm > bold/b0dcmap.nii.gz > > FSLVersion 5.0.2 > FSLVerMaj 5 > Logfile is bold/b0dcmap.nii.gz.log > FSLOUTPUTTYPE NIFTI_GZ > Extension is nii.gz > nframes = 245, nmidframe = 122 > fslroi > > /usr/local/freesurfer/subjects/symmetry/functional/antonio/bold/005/f.nii > bold/tmp-epidewarp.19137.fsl/exf.nii.gz 122 1 > mri_convert > fieldmap/real_fmap2300.nii > bold/tmp-epidewarp.19137.fsl/real1.nii > $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from > fieldmap/real_fmap2300.nii... > WARNING: neither NIfTI-1 qform > or sform > are valid > WARNING: your volume will > probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, > flip angle=0.00 > WARNING: it does not appear > that there was > sufficient > information > in the input to assign > orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/real1.nii... > mri_convert > fieldmap/imag_fmap2300.nii > bold/tmp-epidewarp.19137.fsl/imag1.nii > $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from > fieldmap/imag_fmap2300.nii... > WARNING: neither NIfTI-1 qform > or sform > are valid > WARNING: your volume will > probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, > flip angle=0.00 > WARNING: it does not appear > that there was > sufficient > information > in the input to assign > orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/imag1.nii... > mri_convert > fieldmap/real_fmap4600.nii > bold/tmp-epidewarp.19137.fsl/real2.nii > $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from > fieldmap/real_fmap4600.nii... > WARNING: neither NIfTI-1 qform > or sform > are valid > WARNING: your volume will > probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, > flip angle=0.00 > WARNING: it does not appear > that there was > sufficient > information > in the input to assign > orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/real2.nii... > mri_convert > fieldmap/imag_fmap4600.nii > bold/tmp-epidewarp.19137.fsl/imag2.nii > $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from > fieldmap/imag_fmap4600.nii... > WARNING: neither NIfTI-1 qform > or sform > are valid > WARNING: your volume will > probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, > flip angle=0.00 > WARNING: it does not appear > that there was > sufficient > information > in the input to assign > orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/imag2.nii... > WARNING: neither NIfTI-1 qform > or sform > are valid > WARNING: your volume will > probably be > incorrectly > oriented > WARNING: neither NIfTI-1 qform > or sform > are valid > WARNING: your volume will > probably be > incorrectly > oriented > Saving result to > 'bold/tmp-epidewarp.19137.fsl/mag.nii.gz' > (type = > nii ) [ ok ] > bet > bold/tmp-epidewarp.19137.fsl/mag.nii.gz > bold/tmp-epidewarp.19137.fsl/brain.nii.gz > ^C > > > > On Fri, May 3, 2013 at 3:36 > PM, Douglas N > Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote: > > Actually, it might just be > that you > need to > give it > a--exf or > --epi > Can you try that? > > On 05/03/2013 02:59 PM, > Corinna Bauer > wrote: > > epidewarp.fsl --complex > fieldmap/real_fmap2300.nii > fieldmap/imag_fmap2300.nii > fieldmap/real_fmap4600.nii > fieldmap/imag_fmap4600.nii > --tediff 2.3 > --esp 0.59278 > --vsm bold/b0dcmap.nii.gz > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> > > Phone Number: 617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > <tel:617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> <tel:617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>>> > > Fax: 617-726-7422 > <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > <tel:617-726-7422 > <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

1 0

Re: [Freesurfer] epi correction of fmri data
by Corinna Bauer 03 May '13

03 May '13

I re-converted the par rec files using dcm2nii into spm3 3d nifti format and no longer get the errors. Previously I was using FSL 4d nifti and spm2 3d analyze formats. not sure why that makes a difference though. On Fri, May 3, 2013 at 4:40 PM, Corinna Bauer <corinnab83(a)gmail.com> wrote: > volume sizes don't match. > > > INFO: could not find fieldmap/20130409_153340FieldMappings011a001x1.mat > file for direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped > (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x1.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > volume sizes do not match > > fieldmap/20130409_153340FieldMappings011a001x1.img: (width, height, depth, > frames) = (256, 256, 52, 1) > > bold/005/f.nii: (width, height, depth, frames) = (64, 64, 36, 245) > > > > On Fri, May 3, 2013 at 4:36 PM, Corinna Bauer <corinnab83(a)gmail.com>wrote: > >> It did run all the way through using the .img files. >> >> Should I try that mri_convert on all 4 real/imaginary files? >> >> >> On Fri, May 3, 2013 at 4:30 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu> wrote: >> >>> >>> It should actually run all the way through. If your field maps have the >>> same geometry as your fmri volumes, and your fmri runs have correct >>> geometry, then you can run >>> >>> mri_convert imag_fmap2300.nii imag_fmap2300.geo.nii --in_like fmri.nii >>> >>> Also note that you are just creating a voxel shift map with the >>> epidewarp command, not applying it to the fmri. The application is done in >>> a more complicated way during preproc-sess >>> >>> doug >>> >>> >>> >>> On 05/03/2013 04:10 PM, Corinna Bauer wrote: >>> >>>> hmm. can anything be done to fix it? >>>> >>>> Work the preproc-sess and mkanalysis-sess steps work if I used B0 >>>> corrected images right from the get-go instead of raw fmri runs? >>>> >>>> >>>> On Fri, May 3, 2013 at 4:04 PM, Douglas N Greve < >>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >>>> wrote: >>>> >>>> yep, it is basically the same error >>>> >>>> >>>> On 05/03/2013 03:57 PM, Corinna Bauer wrote: >>>> >>>> I would imagine so. I tried it with the img files. >>>> >>>> /usr/local/freesurfer/**subjects/symmetry/functional/**antonio> >>>> epidewarp.fsl --complex >>>> fieldmap/20130409_**153340FieldMappings011a001x1.**img >>>> fieldmap/20130409_**153340FieldMappings011a001x3.**img >>>> fieldmap/20130409_**153340FieldMappings011a001x2.**img >>>> fieldmap/20130409_**153340FieldMappings011a001x4.**img --tediff >>>> 2.3 --esp 0.59278 --epi bold/005/f.nii --vsm bold/b0dcmap.nii.gz >>>> FSLVersion 5.0.2 >>>> FSLVerMaj 5 >>>> Logfile is bold/b0dcmap.nii.gz.log >>>> FSLOUTPUTTYPE NIFTI_GZ >>>> Extension is nii.gz >>>> nframes = 245, nmidframe = 122 >>>> fslroi >>>> /usr/local/freesurfer/**subjects/symmetry/functional/** >>>> antonio/bold/005/f.nii >>>> bold/tmp-epidewarp.19423.fsl/**exf.nii.gz 122 1 >>>> mri_convert fieldmap/20130409_**153340FieldMappings011a001x1.** >>>> img >>>> bold/tmp-epidewarp.19423.fsl/**real1.nii >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>>> reading from fieldmap/20130409_**153340FieldMappings011a001x1.* >>>> *img... >>>> ------------------------------**------------------------------* >>>> *----- >>>> INFO: could not find >>>> fieldmap/20130409_**153340FieldMappings011a001x1.**mat file for >>>> direction cosine info. >>>> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >>>> unflipped (default). >>>> INFO: if not valid, please provide the information in >>>> fieldmap/20130409_**153340FieldMappings011a001x1.**mat file >>>> ------------------------------**------------------------------* >>>> *----- >>>> analyzeRead() roi_scale 2.639800072 >>>> analyzeRead() changing type to float >>>> analyzeRead() scaling by 2.639800072 >>>> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, 1, 0) >>>> k_ras = (0, 0, 1) >>>> writing to bold/tmp-epidewarp.19423.fsl/**real1.nii... >>>> mri_convert fieldmap/20130409_**153340FieldMappings011a001x3.** >>>> img >>>> bold/tmp-epidewarp.19423.fsl/**imag1.nii >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>>> reading from fieldmap/20130409_**153340FieldMappings011a001x3.* >>>> *img... >>>> ------------------------------**------------------------------* >>>> *----- >>>> INFO: could not find >>>> fieldmap/20130409_**153340FieldMappings011a001x3.**mat file for >>>> direction cosine info. >>>> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >>>> unflipped (default). >>>> INFO: if not valid, please provide the information in >>>> fieldmap/20130409_**153340FieldMappings011a001x3.**mat file >>>> ------------------------------**------------------------------* >>>> *----- >>>> analyzeRead() roi_scale 2.639800072 >>>> analyzeRead() changing type to float >>>> analyzeRead() scaling by 2.639800072 >>>> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, 1, 0) >>>> k_ras = (0, 0, 1) >>>> writing to bold/tmp-epidewarp.19423.fsl/**imag1.nii... >>>> mri_convert fieldmap/20130409_**153340FieldMappings011a001x2.** >>>> img >>>> bold/tmp-epidewarp.19423.fsl/**real2.nii >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>>> reading from fieldmap/20130409_**153340FieldMappings011a001x2.* >>>> *img... >>>> ------------------------------**------------------------------* >>>> *----- >>>> INFO: could not find >>>> fieldmap/20130409_**153340FieldMappings011a001x2.**mat file for >>>> direction cosine info. >>>> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >>>> unflipped (default). >>>> INFO: if not valid, please provide the information in >>>> fieldmap/20130409_**153340FieldMappings011a001x2.**mat file >>>> ------------------------------**------------------------------* >>>> *----- >>>> analyzeRead() roi_scale 2.639800072 >>>> analyzeRead() changing type to float >>>> analyzeRead() scaling by 2.639800072 >>>> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, 1, 0) >>>> k_ras = (0, 0, 1) >>>> writing to bold/tmp-epidewarp.19423.fsl/**real2.nii... >>>> mri_convert fieldmap/20130409_**153340FieldMappings011a001x4.** >>>> img >>>> bold/tmp-epidewarp.19423.fsl/**imag2.nii >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>>> reading from fieldmap/20130409_**153340FieldMappings011a001x4.* >>>> *img... >>>> ------------------------------**------------------------------* >>>> *----- >>>> INFO: could not find >>>> fieldmap/20130409_**153340FieldMappings011a001x4.**mat file for >>>> direction cosine info. >>>> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >>>> unflipped (default). >>>> INFO: if not valid, please provide the information in >>>> fieldmap/20130409_**153340FieldMappings011a001x4.**mat file >>>> ------------------------------**------------------------------* >>>> *----- >>>> analyzeRead() roi_scale 2.639800072 >>>> analyzeRead() changing type to float >>>> analyzeRead() scaling by 2.639800072 >>>> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, 1, 0) >>>> k_ras = (0, 0, 1) >>>> writing to bold/tmp-epidewarp.19423.fsl/**imag2.nii... >>>> ------------------------------**------------------------------* >>>> *----- >>>> INFO: could not find >>>> fieldmap/20130409_**153340FieldMappings011a001x1.**mat file for >>>> direction cosine info. >>>> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >>>> unflipped (default). >>>> INFO: if not valid, please provide the information in >>>> fieldmap/20130409_**153340FieldMappings011a001x1.**mat file >>>> ------------------------------**------------------------------* >>>> *----- >>>> ------------------------------**------------------------------* >>>> *----- >>>> INFO: could not find >>>> fieldmap/20130409_**153340FieldMappings011a001x3.**mat file for >>>> direction cosine info. >>>> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse >>>> unflipped (default). >>>> INFO: if not valid, please provide the information in >>>> fieldmap/20130409_**153340FieldMappings011a001x3.**mat file >>>> ------------------------------**------------------------------* >>>> *----- >>>> Saving result to 'bold/tmp-epidewarp.19423.fsl/**mag.nii.gz' >>>> (type = nii ) [ ok ] >>>> analyzeRead() roi_scale 2.639800072 >>>> analyzeRead() changing type to float >>>> analyzeRead() scaling by 2.639800072 >>>> analyzeRead() roi_scale 2.639800072 >>>> analyzeRead() changing type to float >>>> analyzeRead() scaling by 2.639800072 >>>> bet bold/tmp-epidewarp.19423.fsl/**mag.nii.gz >>>> bold/tmp-epidewarp.19423.fsl/**brain.nii.gz >>>> fslmaths bold/tmp-epidewarp.19423.fsl/**brain.nii.gz -bin >>>> bold/tmp-epidewarp.19423.fsl/**brain.nii.gz >>>> fslmaths bold/tmp-epidewarp.19423.fsl/**brain.nii.gz -dilM >>>> bold/tmp-epidewarp.19423.fsl/**head.nii.gz >>>> ^C >>>> >>>> >>>> >>>> On Fri, May 3, 2013 at 3:52 PM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> >>>> wrote: >>>> >>>> >>>> yes, it should take img files. At some point, the lack of >>>> valid >>>> geometry might mess things up >>>> >>>> >>>> On 05/03/2013 03:47 PM, Corinna Bauer wrote: >>>> >>>> Oh I see. I have the raw par rec files, should I try >>>> converting it again? I used dcm2nii to convert it to >>>> hdr/img >>>> files and then fslchfiletype to get it into nifti. for >>>> some >>>> reason just converting it to nifti right away doesn't >>>> look right. >>>> >>>> Will epidewarp take img files? >>>> >>>> >>>> On Fri, May 3, 2013 at 3:43 PM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >> >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>>> >>>> wrote: >>>> >>>> nope, the qform errors mean thatthere is something >>>> going >>>> on with >>>> your data. It means that the geometry is not in >>>> the nifti >>>> file. >>>> >>>> >>>> On 05/03/2013 03:41 PM, Corinna Bauer wrote: >>>> >>>> do they need to be nii.gz? >>>> >>>> >>>> On Fri, May 3, 2013 at 3:38 PM, Corinna Bauer >>>> <corinnab83(a)gmail.com >>>> <mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com >>>> <mailto:corinnab83@gmail.com>> >>>> <mailto:corinnab83@gmail.com >>>> <mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com >>>> <mailto:corinnab83@gmail.com>>**> >>>> <mailto:corinnab83@gmail.com >>>> <mailto:corinnab83@gmail.com> >>>> <mailto:corinnab83@gmail.com >>>> <mailto:corinnab83@gmail.com>> <mailto:corinnab83@gmail.com >>>> <mailto:corinnab83@gmail.com> >>>> <mailto:corinnab83@gmail.com >>>> <mailto:corinnab83@gmail.com>>**>>> >>>> >>>> wrote: >>>> >>>> I still get funny warnings about the >>>> nifti-1 qform >>>> or sform >>>> >>>> /usr/local/freesurfer/** >>>> subjects/symmetry/functional/**antonio> >>>> epidewarp.fsl --complex >>>> fieldmap/real_fmap2300.nii >>>> fieldmap/imag_fmap2300.nii >>>> fieldmap/real_fmap4600.nii >>>> fieldmap/imag_fmap4600.nii --tediff 2.3 >>>> --esp >>>> 0.59278 --epi >>>> bold/005/f.nii --vsm bold/b0dcmap.nii.gz >>>> >>>> FSLVersion 5.0.2 >>>> FSLVerMaj 5 >>>> Logfile is bold/b0dcmap.nii.gz.log >>>> FSLOUTPUTTYPE NIFTI_GZ >>>> Extension is nii.gz >>>> nframes = 245, nmidframe = 122 >>>> fslroi >>>> /usr/local/freesurfer/**subjects/symmetry/functional/** >>>> antonio/bold/005/f.nii >>>> bold/tmp-epidewarp.19137.fsl/**exf.nii.gz >>>> 122 1 >>>> mri_convert fieldmap/real_fmap2300.nii >>>> bold/tmp-epidewarp.19137.fsl/**real1.nii >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 >>>> 21:55:16 >>>> mreuter >>>> Exp $ >>>> reading from fieldmap/real_fmap2300.nii... >>>> WARNING: neither NIfTI-1 qform or sform >>>> are valid >>>> WARNING: your volume will probably be >>>> incorrectly >>>> oriented >>>> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> WARNING: it does not appear that there was >>>> sufficient >>>> information >>>> in the input to assign orientation to the >>>> volume... >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, 1, 0) >>>> k_ras = (0, 0, 1) >>>> writing to >>>> bold/tmp-epidewarp.19137.fsl/**real1.nii... >>>> mri_convert fieldmap/imag_fmap2300.nii >>>> bold/tmp-epidewarp.19137.fsl/**imag1.nii >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 >>>> 21:55:16 >>>> mreuter >>>> Exp $ >>>> reading from fieldmap/imag_fmap2300.nii... >>>> WARNING: neither NIfTI-1 qform or sform >>>> are valid >>>> WARNING: your volume will probably be >>>> incorrectly >>>> oriented >>>> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> WARNING: it does not appear that there was >>>> sufficient >>>> information >>>> in the input to assign orientation to the >>>> volume... >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, 1, 0) >>>> k_ras = (0, 0, 1) >>>> writing to >>>> bold/tmp-epidewarp.19137.fsl/**imag1.nii... >>>> mri_convert fieldmap/real_fmap4600.nii >>>> bold/tmp-epidewarp.19137.fsl/**real2.nii >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 >>>> 21:55:16 >>>> mreuter >>>> Exp $ >>>> reading from fieldmap/real_fmap4600.nii... >>>> WARNING: neither NIfTI-1 qform or sform >>>> are valid >>>> WARNING: your volume will probably be >>>> incorrectly >>>> oriented >>>> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> WARNING: it does not appear that there was >>>> sufficient >>>> information >>>> in the input to assign orientation to the >>>> volume... >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, 1, 0) >>>> k_ras = (0, 0, 1) >>>> writing to >>>> bold/tmp-epidewarp.19137.fsl/**real2.nii... >>>> mri_convert fieldmap/imag_fmap4600.nii >>>> bold/tmp-epidewarp.19137.fsl/**imag2.nii >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 >>>> 21:55:16 >>>> mreuter >>>> Exp $ >>>> reading from fieldmap/imag_fmap4600.nii... >>>> WARNING: neither NIfTI-1 qform or sform >>>> are valid >>>> WARNING: your volume will probably be >>>> incorrectly >>>> oriented >>>> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> WARNING: it does not appear that there was >>>> sufficient >>>> information >>>> in the input to assign orientation to the >>>> volume... >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, 1, 0) >>>> k_ras = (0, 0, 1) >>>> writing to >>>> bold/tmp-epidewarp.19137.fsl/**imag2.nii... >>>> WARNING: neither NIfTI-1 qform or sform >>>> are valid >>>> WARNING: your volume will probably be >>>> incorrectly >>>> oriented >>>> WARNING: neither NIfTI-1 qform or sform >>>> are valid >>>> WARNING: your volume will probably be >>>> incorrectly >>>> oriented >>>> Saving result to >>>> 'bold/tmp-epidewarp.19137.fsl/**mag.nii.gz' >>>> (type = >>>> nii ) [ ok ] >>>> bet bold/tmp-epidewarp.19137.fsl/** >>>> mag.nii.gz >>>> bold/tmp-epidewarp.19137.fsl/**brain.nii.gz >>>> ^C >>>> >>>> >>>> >>>> On Fri, May 3, 2013 at 3:36 PM, Douglas N >>>> Greve >>>> <greve(a)nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >> >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >>> >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >> >>>> >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>>>> >>>> wrote: >>>> >>>> Actually, it might just be that you >>>> need to >>>> give it >>>> a--exf or >>>> --epi >>>> Can you try that? >>>> >>>> On 05/03/2013 02:59 PM, Corinna Bauer >>>> wrote: >>>> >>>> epidewarp.fsl --complex >>>> fieldmap/real_fmap2300.nii >>>> fieldmap/imag_fmap2300.nii >>>> fieldmap/real_fmap4600.nii >>>> fieldmap/imag_fmap4600.nii >>>> --tediff 2.3 >>>> --esp 0.59278 >>>> --vsm bold/b0dcmap.nii.gz >>>> >>>> >>>> -- Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >> >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >>> >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >> >>>> >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >>>> >>>> >>>> Phone Number: 617-724-2358 >>>> <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >>>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 >>>> <tel:617-724-2358>>> >>>> <tel:617-724-2358 <tel:617-724-2358> >>>> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 >>>> <tel:617-724-2358> >>>> <tel:617-724-2358 <tel:617-724-2358>>>> >>>> >>>> Fax: 617-726-7422 <tel:617-726-7422> >>>> <tel:617-726-7422 <tel:617-726-7422>> >>>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >>>> <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> >>>> >>>> <tel:617-726-7422 <tel:617-726-7422>> >>>> >>>> <tel:617-726-7422 <tel:617-726-7422> >>>> <tel:617-726-7422 <tel:617-726-7422>>>> >>>> >>>> >>>> Bugs: >>>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>>> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >>>> <http://surfer.nmr.mgh.** >>>> harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> <http://surfer.nmr.mgh.** >>>> harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> >>>> FileDrop: >>>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >>>> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>>> <http://www.nmr.mgh.harvard.** >>>> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> > >>>> <http://www.nmr.mgh.harvard.** >>>> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> > >>>> < >>>> http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> > >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >>>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>>> >>>> >>>> >>>> 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<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. >>>> >>>> >>>> >>>> >>>> -- Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >> >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >>> >>>> Phone Number: 617-724-2358 <tel:617-724-2358> >>>> <tel:617-724-2358 <tel:617-724-2358>> >>>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 >>>> <tel:617-724-2358>>> >>>> Fax: 617-726-7422 <tel:617-726-7422> >>>> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 >>>> <tel:617-726-7422> >>>> <tel:617-726-7422 <tel:617-726-7422>>> >>>> >>>> Bugs: >>>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>>> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >>>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/ >>>> **BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >>>> FileDrop: https://gate.nmr.mgh.harvard.** >>>> edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> >>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >>>> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>>> <http://www.nmr.mgh.harvard.** >>>> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> > >>>> <http://www.nmr.mgh.harvard.** >>>> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> > >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >>>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>>> >>>> >>>> >>>> -- Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> > >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >>>> >> >>>> Phone Number: 617-724-2358 <tel:617-724-2358> >>>> <tel:617-724-2358 <tel:617-724-2358>> >>>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >>>> <tel:617-726-7422>> >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >>>> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.* >>>> *html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >>>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>>> >>>> >>>> >>>> -- Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>>> > >>>> Phone Number: 617-724-2358 <tel:617-724-2358> >>>> Fax: 617-726-7422 <tel:617-726-7422> >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>> > >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>>> >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> >> >

1 0

Re: [Freesurfer] epi correction of fmri data
by Douglas N Greve 03 May '13

03 May '13

It should actually run all the way through. If your field maps have the same geometry as your fmri volumes, and your fmri runs have correct geometry, then you can run mri_convert imag_fmap2300.nii imag_fmap2300.geo.nii --in_like fmri.nii Also note that you are just creating a voxel shift map with the epidewarp command, not applying it to the fmri. The application is done in a more complicated way during preproc-sess doug On 05/03/2013 04:10 PM, Corinna Bauer wrote: > hmm. can anything be done to fix it? > > Work the preproc-sess and mkanalysis-sess steps work if I used B0 > corrected images right from the get-go instead of raw fmri runs? > > > On Fri, May 3, 2013 at 4:04 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > yep, it is basically the same error > > > On 05/03/2013 03:57 PM, Corinna Bauer wrote: > > I would imagine so. I tried it with the img files. > > /usr/local/freesurfer/subjects/symmetry/functional/antonio> > epidewarp.fsl --complex > fieldmap/20130409_153340FieldMappings011a001x1.img > fieldmap/20130409_153340FieldMappings011a001x3.img > fieldmap/20130409_153340FieldMappings011a001x2.img > fieldmap/20130409_153340FieldMappings011a001x4.img --tediff > 2.3 --esp 0.59278 --epi bold/005/f.nii --vsm bold/b0dcmap.nii.gz > FSLVersion 5.0.2 > FSLVerMaj 5 > Logfile is bold/b0dcmap.nii.gz.log > FSLOUTPUTTYPE NIFTI_GZ > Extension is nii.gz > nframes = 245, nmidframe = 122 > fslroi > /usr/local/freesurfer/subjects/symmetry/functional/antonio/bold/005/f.nii > bold/tmp-epidewarp.19423.fsl/exf.nii.gz 122 1 > mri_convert fieldmap/20130409_153340FieldMappings011a001x1.img > bold/tmp-epidewarp.19423.fsl/real1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from fieldmap/20130409_153340FieldMappings011a001x1.img... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x1.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x1.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/real1.nii... > mri_convert fieldmap/20130409_153340FieldMappings011a001x3.img > bold/tmp-epidewarp.19423.fsl/imag1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from fieldmap/20130409_153340FieldMappings011a001x3.img... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x3.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x3.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/imag1.nii... > mri_convert fieldmap/20130409_153340FieldMappings011a001x2.img > bold/tmp-epidewarp.19423.fsl/real2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from fieldmap/20130409_153340FieldMappings011a001x2.img... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x2.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x2.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/real2.nii... > mri_convert fieldmap/20130409_153340FieldMappings011a001x4.img > bold/tmp-epidewarp.19423.fsl/imag2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from fieldmap/20130409_153340FieldMappings011a001x4.img... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x4.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x4.mat file > ----------------------------------------------------------------- > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to bold/tmp-epidewarp.19423.fsl/imag2.nii... > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x1.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x1.mat file > ----------------------------------------------------------------- > ----------------------------------------------------------------- > INFO: could not find > fieldmap/20130409_153340FieldMappings011a001x3.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse > unflipped (default). > INFO: if not valid, please provide the information in > fieldmap/20130409_153340FieldMappings011a001x3.mat file > ----------------------------------------------------------------- > Saving result to 'bold/tmp-epidewarp.19423.fsl/mag.nii.gz' > (type = nii ) [ ok ] > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > analyzeRead() roi_scale 2.639800072 > analyzeRead() changing type to float > analyzeRead() scaling by 2.639800072 > bet bold/tmp-epidewarp.19423.fsl/mag.nii.gz > bold/tmp-epidewarp.19423.fsl/brain.nii.gz > fslmaths bold/tmp-epidewarp.19423.fsl/brain.nii.gz -bin > bold/tmp-epidewarp.19423.fsl/brain.nii.gz > fslmaths bold/tmp-epidewarp.19423.fsl/brain.nii.gz -dilM > bold/tmp-epidewarp.19423.fsl/head.nii.gz > ^C > > > > On Fri, May 3, 2013 at 3:52 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > yes, it should take img files. At some point, the lack of > valid > geometry might mess things up > > > On 05/03/2013 03:47 PM, Corinna Bauer wrote: > > Oh I see. I have the raw par rec files, should I try > converting it again? I used dcm2nii to convert it to > hdr/img > files and then fslchfiletype to get it into nifti. for > some > reason just converting it to nifti right away doesn't > look right. > > Will epidewarp take img files? > > > On Fri, May 3, 2013 at 3:43 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > nope, the qform errors mean thatthere is something > going > on with > your data. It means that the geometry is not in > the nifti > file. > > > On 05/03/2013 03:41 PM, Corinna Bauer wrote: > > do they need to be nii.gz? > > > On Fri, May 3, 2013 at 3:38 PM, Corinna Bauer > <corinnab83(a)gmail.com > <mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>> <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>>>>> > > wrote: > > I still get funny warnings about the > nifti-1 qform > or sform > > > /usr/local/freesurfer/subjects/symmetry/functional/antonio> > epidewarp.fsl --complex > fieldmap/real_fmap2300.nii > fieldmap/imag_fmap2300.nii > fieldmap/real_fmap4600.nii > fieldmap/imag_fmap4600.nii --tediff 2.3 --esp > 0.59278 --epi > bold/005/f.nii --vsm bold/b0dcmap.nii.gz > > FSLVersion 5.0.2 > FSLVerMaj 5 > Logfile is bold/b0dcmap.nii.gz.log > FSLOUTPUTTYPE NIFTI_GZ > Extension is nii.gz > nframes = 245, nmidframe = 122 > fslroi > /usr/local/freesurfer/subjects/symmetry/functional/antonio/bold/005/f.nii > bold/tmp-epidewarp.19137.fsl/exf.nii.gz 122 1 > mri_convert fieldmap/real_fmap2300.nii > bold/tmp-epidewarp.19137.fsl/real1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from fieldmap/real_fmap2300.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > WARNING: it does not appear that there was > sufficient > information > in the input to assign orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/real1.nii... > mri_convert fieldmap/imag_fmap2300.nii > bold/tmp-epidewarp.19137.fsl/imag1.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from fieldmap/imag_fmap2300.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > WARNING: it does not appear that there was > sufficient > information > in the input to assign orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/imag1.nii... > mri_convert fieldmap/real_fmap4600.nii > bold/tmp-epidewarp.19137.fsl/real2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from fieldmap/real_fmap4600.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > WARNING: it does not appear that there was > sufficient > information > in the input to assign orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/real2.nii... > mri_convert fieldmap/imag_fmap4600.nii > bold/tmp-epidewarp.19137.fsl/imag2.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 > mreuter > Exp $ > reading from fieldmap/imag_fmap4600.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > TR=20.00, TE=0.00, TI=0.00, flip angle=0.00 > WARNING: it does not appear that there was > sufficient > information > in the input to assign orientation to the > volume... > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to > bold/tmp-epidewarp.19137.fsl/imag2.nii... > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > WARNING: neither NIfTI-1 qform or sform > are valid > WARNING: your volume will probably be > incorrectly > oriented > Saving result to > 'bold/tmp-epidewarp.19137.fsl/mag.nii.gz' > (type = > nii ) [ ok ] > bet bold/tmp-epidewarp.19137.fsl/mag.nii.gz > bold/tmp-epidewarp.19137.fsl/brain.nii.gz > ^C > > > > On Fri, May 3, 2013 at 3:36 PM, Douglas N > Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > Actually, it might just be that you > need to > give it > a--exf or > --epi > Can you try that? > > On 05/03/2013 02:59 PM, Corinna Bauer > wrote: > > epidewarp.fsl --complex > fieldmap/real_fmap2300.nii > fieldmap/imag_fmap2300.nii > fieldmap/real_fmap4600.nii > fieldmap/imag_fmap4600.nii > --tediff 2.3 > --esp 0.59278 > --vsm bold/b0dcmap.nii.gz > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 > <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

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Re: [Freesurfer] epi correction of fmri data
by Douglas N Greve 03 May '13

03 May '13

What is your cmd line? Can you run it with --debug as the first arg, capture the output, and send it to me? eg, dewarp.fsl --debug ... |& tee dng.log On 05/03/2013 01:43 PM, Corinna Bauer wrote: > I get this: > > FSLVersion 5.0.2 > FSLVerMaj 5 > FSL Version is 5.0.2, must be 3.X or 4.X > > > > On Fri, May 3, 2013 at 1:42 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > What is going wrong when you run FSL 5? > > > On 05/03/2013 01:38 PM, Corinna Bauer wrote: > > oh great. Is there a way to get this to work with FSL 5? > > > On Fri, May 3, 2013 at 1:11 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > It needs to be 0 to 4095, see below > > --ph phasevolid > > Phase volume from the B0 fieldmap (if the phases from > Echo1, Echo2 are > available instead of their difference). These are assumed > to be scaled > between 0 to 4095 for -pi to pi. Eg, ph.ext, where ext is > either nii, > nii.gz, or img. Not with --complex or with --dph. > > This is made to work with the default Siemens field map. > Note that > you can also use complex inputs instead of mag and phase > > doug > > > > > > On 05/03/2013 01:05 PM, Corinna Bauer wrote: > > Should the phase image be in rads? and does the magnitude > image need to be skull-stripped first? > > > On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer > <corinnab83(a)gmail.com <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com>> > <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com > <mailto:corinnab83@gmail.com>>>> > > wrote: > > thanks Doug, I will give that a try. > > > On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > Create the B0 voxel shift map. Call it > b0dcmap.nii.gz > and put > it in > the bold folder, eg: > > epidewarp.fsl \ > --mag mag.nii.gz \ > --dph dphase.nii.gz \ > --tediff YOUR_TE_DIFF --esp YOUR_ESP \ > --vsm bold/b0dcmap.nii.gz > > When you run mkanalysis-sess and preproc-sess, add > "-b0dc" to the > command lines. > > doug > > > On 05/03/2013 12:16 PM, Corinna Bauer wrote: > > Yes, I am using FSFAST. > > > On Fri, May 3, 2013 at 12:08 PM, Douglas N > Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > Hi Corinna, are you using FSFAST? If > not, are you > still going to the > surface? > doug > > On 05/03/2013 11:07 AM, Corinna Bauer > wrote: > > Is there a way to correct fmri data > for epi > distortions in > freesurfer? > > Or does the data need to be first fun > through FSL's > B0 unwarping? > > > > Corinna > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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>>> > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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>>> > <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 > <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. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

2 4

Re: [Freesurfer] epi correction of fmri data
by Douglas N Greve 03 May '13

03 May '13

Create the B0 voxel shift map. Call it b0dcmap.nii.gz and put it in the bold folder, eg: epidewarp.fsl \ --mag mag.nii.gz \ --dph dphase.nii.gz \ --tediff YOUR_TE_DIFF --esp YOUR_ESP \ --vsm bold/b0dcmap.nii.gz When you run mkanalysis-sess and preproc-sess, add "-b0dc" to the command lines. doug On 05/03/2013 12:16 PM, Corinna Bauer wrote: > Yes, I am using FSFAST. > > > On Fri, May 3, 2013 at 12:08 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Corinna, are you using FSFAST? If not, are you still going to the > surface? > doug > > On 05/03/2013 11:07 AM, Corinna Bauer wrote: > > Is there a way to correct fmri data for epi distortions in > freesurfer? > > Or does the data need to be first fun through FSL's B0 unwarping? > > > > Corinna > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

2 5

determine the peak vertex
by limengsecret 03 May '13

03 May '13

Hi freesurfer, I have a label and each vertex in this label has a probability value. My problem is that how to determine the peak vertex (or the center of gravity) of this label and get the coordinates. And I also want to know, in the tksurfer interface, whether the vertex index has a correspondence to the vertex RAS. Thanks a lot! Best wishes, Meng

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