date:20191013

Re: [Freesurfer] Learning dti processing tutorial

2019-10-13 Thread Greve, Douglas N.,Ph.D.

What is the input file that you are supplying? Often this happens when 
the input it a multi-echo MPRAGE. If so, you can run
mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz
then use mprage.mgz as the input to recon-all

On 10/12/2019 4:48 PM, Renew Andrade wrote:
>  External Email - Use Caution
>
> Dear freesurfer experts:
> I am trying to learn dti processing. For using Tracula it appears there is a 
> need for running "recon-all -all -i -s” on every subject before starting to 
> run Tracula. But there seems to be a problem. I have a Parkinson dwi images 
> database and every subject gives me an error of the type “input(s) cannot 
> have multiple frames!”. I am a little bit stuck on this step. Is it a problem 
> of the file as input? Am I putting the wrong file? Can it be done a recon-all 
> analysis to a dwi image? With trackvis I can obtain the results without any 
> problem. My doubt comes from FreeSurfer only and may be my little knowledge 
> about it.
> Thanks for your help!
> Sincerely,
> Andrade.
>
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Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 21

2019-10-13 Thread Juan Rivas

t;- computing centroids
>
>- computing initial transform
>
>  -- using translation info
>
>- Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
>
>- Build Gaussian Pyramid ( Limits min steps: 0 max steps: 0 )
>
>- Build Gaussian Pyramid ( Limits min steps: 0 max steps: 0 )
>
>- initial transform:
>
> Ti = [ ...
>
>  1.000 -0.9335121201217
>
>0  1.00 -0.6030049400697
>
>00  1.0 -1.9033196349668
>
>000  1.0  ]
>
>
>
>- initial iscale:  Ii =1
>
>
>
> Resolution: 0  S( 37 33 61 )  T( 37 33 61 )
>
>  Iteration(f): 1
>
>  -- diff. to prev. transform: 29.7552
>
>  Iteration(f): 2
>
>  -- diff. to prev. transform: 13.9258
>
>  Iteration(f): 3
>
>  -- diff. to prev. transform: 12.8176
>
>  Iteration(f): 4
>
>  -- diff. to prev. transform: 4.31284
>
>  Iteration(f): 5
>
>  -- diff. to prev. transform: 1.08934 max it: 5 reached!
>
>
>
>- final transform:
>
> Tf = [ ...
>
>  1.1485282870250  0.1923732018210  0.0456719546813 -8.8430815689836
>
>  0.0248585691740  1.1974718877709  0.2901612074595 -15.4946754855698
>
>  0.0132871026014  0.0262311630292  0.9721734242629 -1.7628900186542
>
>000  1.0  ]
>
>
>
>- final iscale:  If = 1
>
>
>
> **
>
> *
>
> * WARNING: Registration did not converge in 5 steps!
>
> *  Problem might be ill posed.
>
> *  Please inspect output manually!
>
> *
>
> **
>
>
>
> Final Transform:
>
> Adjusting final transform due to initial resampling (voxel or size
> changes) ...
>
> M = [ ...
>
> -0.2871321056267  0.0114179894966 -0.0480933061884 36.4485194686672
>
> -0.0062146408039  0.0725403105008 -0.2993680076302 19.7524929053736
>
> -0.0033217759975  0.2430433850326 -0.0065577915391 -0.1873902167255
>
>000  1.0  ]
>
>
>
>  Determinant : -0.020683
>
>
>
>  Decompose into Rot * Shear * Scale :
>
>
>
> Rot = [ ...
>
> -0.9973893744923  0.0079822957206 -0.0717685070543
>
>  0.0722067536928  0.1210866300984 -0.9900122285773
>
> -0.0007876362909  0.9926098483122  0.1213468939142  ]
>
>
>
> Shear = [ ...
>
>  1.0 -0.0253544642652  0.0881389503515
>
> -0.0221787471386  1.0 -0.1442736100723
>
>  0.0921761860222 -0.1724865310828  1.0  ]
>
>
>
> Scale = diag([  0.2859363885412  0.2501220610640  0.2990338055489  ])
>
>
>
>
>
> writing output transformation to trash.lta ...
>
> converting VOX to RAS and saving RAS2RAS...
>
>
>
> mapmovhdr: Changing vox2ras MOV header (to map to DST) ...
>
>
>
> To check aligned result, run:
>
>   freeview -v
> /cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz
> imageDump_coregistered.mgz
>
>
>
>
>
> Registration took 0 minutes and 1 seconds.
>
>
>
>  Thank you for using RobustRegister!
>
>  If you find it useful and use it for a publication, please cite:
>
>
>
>  Highly Accurate Inverse Consistent Registration: A Robust Approach
>
>  M. Reuter, H.D. Rosas, B. Fischl.  NeuroImage 53(4):1181-1196, 2010.
>
>  http://dx.doi.org/10.1016/j.neuroimage.2010.07.020
>
>  http://reuter.mit.edu/papers/reuter-robreg10.pdf
>
>
>
> Reading contexts of file
> /usr/local/freesurfer/dev/average/HippoSF/atlas/compressionLookupTable.txt
>
> Constructing image-to-world transform from header information
> (asegModCHA.mgz)
>
> Constructing image-to-world transform from header information
> (/cluster/neuromod/rivas/imagenes/FS/test1/tmp/hippoSF_T1_v21_left/imageDump.mgz)
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Transforming points
>
> Reading contexts of file
> /usr/local/freesurfer/dev/average/HippoSF/atlas/compressionLookupTable.txt
>
> --
>
> Making Left-Cerebral-Cortex map to reduced label 1
>
> Making alveus map to reduced label 1
>
> Making subiculum-body map to reduced label 1
>
> Making subiculum-head map to reduced label 1
>
> Making Hippocampal_tail map to reduced label 1
>
> Making molecular_layer_HP-body map to reduced label 1
>
> Making molecular_layer_HP-head map to reduced label 1
>
> Making GC-ML-DG-body map to reduced label 1
>
> Making GC-ML-DG-head map to reduced label 1
>
> Making CA4-body map to reduced label 1
>
> Making CA4-head map to reduced label 1
>
> Making CA1-body map to reduced label 1
>
> Making CA1-head map to reduced label 1
>
> Making CA3-body map to reduced label 1
>
> Making CA3-head map to reduced label 1
>
> Making HATA map to reduced label 1
>
> Making fimbria map to reduced label 1
>
> Making presubiculum-body map to reduced label 1
>
> Making presubiculum-head map to reduced label 1
>
> Making parasubiculum map to reduced label 1
>
> Making Lateral-nucleus map to reduced label 1
>
> Making Paralaminar-nucleus map to reduced label 1
>
> Making Basal-nucleus map to reduced label 1
>
> Making Accessory-Basal-nucleus map to reduced label 1
>
> Making Corticoamygdaloid-transitio map to reduced label 1
>
> Making Central-nucleus map to reduced label 1
>
> Making Cortical-nucleus map to reduced label 1
>
> Making Medial-nucleus map to reduced label 1
>
> Making Anterior-amygdaloid-area-AAA map to reduced label 1
>
> --
>
> Making Left-Cerebral-White-Matter map to reduced label 2
>
> --
>
> Making Left-Lateral-Ventricle map to reduced label 3
>
> --
>
> Making Left-choroid-plexus map to reduced label 4
>
> --
>
> Making hippocampal-fissure map to reduced label 5
>
> Making Unknown map to reduced label 5
>
> --
>
> Making Left-VentralDC map to reduced label 6
>
> --
>
> Making Left-Putamen map to reduced label 7
>
> --
>
> Making Left-Pallidum map to reduced label 8
>
> --
>
> Making Left-Accumbens-area map to reduced label 9
>
> --
>
> Making Left-Caudate map to reduced label 10
>
> Error using segmentSubjectT1_autoEstimateAlveusML (line 365)
>
> The vector of prior probabilities in the mesh nodes must always sum to one
> over all classes.
>
>
>
>
>
>
>
> How may I correct it?
>
> Thanks  lot,
>
> JC.
> -- next part --
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>
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> End of Freesurfer Digest, Vol 188, Issue 21
> ***
>
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Re: [Freesurfer] Learning dti processing tutorial

Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 21

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