Freesurfer

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30086 discussions

trac-all -prep problem
by Shantanu Ghosh 18 Aug '14

18 Aug '14

Hi Freesurfer experts, I ran the command <trac-all -prep -c dmrirc.txt> on a bunch of subjects and all of them finished in ~90 minutes except one. This subject keeps on going into a seemingly endless loop. It has been running for almost 12 hours now. A section of the console output is reproduced below. What is the issue here, and how can this be solved? I am using the dev version on a Linux box. Thanks in advance for all help. Shantanu ------ SAMPLE CONSOLE OUTPUT ------ INFO: Distances between consecutive points in test subject's space are 11 11 10 10 10 WARN: Could not find satisfactory control point fit - try 1831 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 91 voxels Selecting 6 points on center streamline INFO: Minimum allowable distance between dominant points is 9 INFO: Minimum allowable curvature at a dominant point is 0.0283381 INFO: Points where local peeks in curvature occur are 106 105 67 (curv = 0.0284049) 112 108 77 (curv = 0.0450985) 115 108 98 (curv = 0.0526145) 113 104 116 (curv = 0.0460477) 107 103 128 (curv = 0.0759711) INFO: Intermediate dominant points are 103 98 50 112 108 77 114 108 89 115 108 98 107 103 128 105 106 145 INFO: Final dominant points are 103 98 50 112 108 77 114 108 89 115 108 98 107 103 128 105 106 145 WARN: Defaulting to equidistant dominant points WARN: Defaulting to equidistant control points INFO: Selected control points are 103 98 50 108 106 69 114 108 89 114 105 108 108 103 126 105 106 145 INFO: Distances between consecutive points are 21 21 19 19 19 INFO: Selected control points in test subject's space are 80 62 23 81 66 31 84 68 40 84 66 48 82 64 56 81 65 64 INFO: Distances between consecutive points in test subject's space are 9 10 8 8 8 WARN: Could not find satisfactory control point fit - try 1832 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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Diffusion analysis qs
by Rotem Saar 18 Aug '14

18 Aug '14

Dear Anastasia, I followed your suggestion: I calculated the FA maps in freesurfer using the script below (see last message): I did it with both the rotated and the not rotated gradient table. The FA maps were identical as u said. BUT ! - when I used the rotated gradient table in FSL and tried to create the FA & MD maps (as in the first step of tracula), I got the attached results: http://tinypic.com/r/skzwqa/8 Does this map seems ok to u ? I think that something is wrong but can't specify what. I will appreciate your help here again:) ____________________________________________________________________ Hi Rotem - The FA values are actually invariant to a rotation of the gradient vectors. You can test that yourself. If, however, you get different FA maps with the different gradient tables, then something else is going on and not a simple rotation. a.y On Wed, 23 Jul 2014, Rotem Saar wrote: > Dear Anastasia & Michael, > > Thank u for your answers (I attached my last email and your answers at the > end of this email. > > I still want to specify my question. If I only want to extract FA values > using the following script (see script below), and I know that an angle was > applied during the dMRI scans, should I use the rotated gradient matrix ? > > When I first analyzed 20 subjects with the gradient matrix that is published > for a T3 Philips magnet (I also read the gradients from the dicom header - > they were the same) I got reasonable results - but now I don't know what to > think of them... > > source ~/Desktop/fs_script > > dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s > Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec > > To check results, run: > > tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii > --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii > /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/mri/ brain.mgz/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii:reg= register.dat:colo > rmap=heat:heatscale=.2,.2,1 > > tkmedit Anatomy0207?orig.mgz -aux brain.mgz -seg wmparc.mgz -reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??????????? --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/ wmparc.mgz > \ > ??????????? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > ??????????? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??????????? --targ > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ > ??????????? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ > ??????????? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ > ???????????/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+ aseg2diff.mgz:colormap > =lut > > > mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ > ???????? /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > ???????? /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz > > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa- masked.mgz/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+ aseg2diff.mgz:colormap > =lut > > mri_segstats --seg > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum > /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked > > It'd be nice if things were that simple, but! > > Although the pre-processing is done with FSL tools, tractography is done > with locally written code. Some gradient sets may appear to work with FSL, > but they won't work for us. For example, some dicom converters may perform > a L-R flip as preparation for feeding the gradient vectors into FSL. We > need the unflipped vectors because, instead of flipping vectors, we > convert both vectors and images to LAS orientation. This ensures that they > work both for FSL and for us, and that you can view things correctly in > both freeview and fslview, without the subject looking like it's hanging > upside down from its bat cave or some such awkward arrangement. > > In the end, the best way of knowing that the gradient table is correct is > to run one example subject through and view the eigenvectors of the > tensors as lines to see if they're pointing in the right direction. (Even > though the tensors themselves aren't used for tractography, they're good > for troubleshooting.) > > On Mon, 21 Jul 2014, Harms, Michael wrote: > > > > > FS uses FSL tools under the hood, so you want to use the bvecs that are > > rotated into the axes of the scan. > > > > cheers, > > -MH > > > > --? > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO ?63110 Email:?mharms@wustl.edu > > > > From: Rotem Saar <saar.rotem(a)gmail.com> > > Reply-To:?Freesurfer?support list <freesurfer(a)nmr.mgh.harvard.edu> > > Date: Monday, July 21, 2014 1:54 PM > > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > Subject: [Freesurfer] Diffusion analysis qs - gradient matrix > > > > Dear?freesurfer?experts, > > > > For diffusion analysis in?freesurfer?- I want to know which gradient > matrix > >?freesurfer?expects. > > > > The thing is - when I look at the gradient matrix created using a MATLAB > > script that reads the directions from the dicom header - I get one table, > > but the bvecs file created in MRIconvert (for converting dicoms to nifti) > > looks different. > > > > This is the situation when an angle is applied during the acquisition of > the > > dMRI scans, which means that each subject has its own gradient matrix. > > > > So my question is which table should I use for diffusion analysis in > >?freesurfer? The one that was created from the dicom header or the one > > created for NIFTI format using MRIconvert ?? Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel

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dmri_trk2trk issue
by raij＠nmr.mgh.harvard.edu 18 Aug '14

18 Aug '14

Hi, I am attempting to morph deterministic tractography results (.trk file) from the individual diffusion space into the average brain cvs_avg35_inMNI152. However, something goes wrong, as the output trk file is greatly misplaced / strongly distorted / wrongly sized. The input file (dsi60.trk, a TrackVis trk file with an angle threshold of 60 degrees) loads fine in Trackvis, as do the inref and outref volumes (in .nii format). The rigid body (.mat) and nonlinear (.m3z) registrations also appear ok. The mat file (or more precisely, the corresponding register.dat file) looked fine with tkregister2 and the latter was successfully used to morph the corresponding probabilistic tractography results from the individual diffusion space to cvs_avg35_inMNI152 (= the same transformation I am trying to do here). Any suggestions what I am doing wrong? For example, could this be related to inref/outref voxel sizes or coordinate systems? Just in case, I already tried using the inverse rigid registration (anat2diff.mat) and the FDT-generated files inside DSI.bedpostX/xfms (diff2str.mat and its inverse) but the results were in all cases very much wrong, just in different ways. FS 5.3 (nmr-std-env) on machine avml cd $SUBJECTS_DIR dmri_trk2trk \ --in $SUBJECT/DSI/dsi60.trk \ --out TMSDSIGA_19Jul14/${SUBJECT}inCVS35MNI152_dsi60.trk \ --inref $SUBJECT/mri/norm.mgz \ --outref $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz \ --reg $SUBJECT/DSI/${SUBJECT}_diff2anat.mat \ --regnl $SUBJECT/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z \ reg (.mat) was computed as follows: bbregister --mov dsi_b0.nii --frame 0 --bold --s $SUBJECT --init-fsl --reg DSIregister.dat --fslmat ${SUBJECT}_anat2diff.mat I would be happy to copy the data to a location of your choosing if you would like to replicate the error. Thanks! Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Tracula : Path not entirely in the white matter
by ebelleau＠uwm.edu 18 Aug '14

18 Aug '14

Hello, I was looking at a trac-all log file to get my bearings on what is being done and making sure things were done successfully, I did not get any errors for this subject but when I was looking at the right uncinate fasciculus: It would say "Path from initial control points not entirely in the white matter" and then it attempted to perturb control points. I noticed that for this tract, it did not say that it did not say sucess after how ever many control points. It just said that it reverted back to the initial control points. Do I then need to be concerned about the validity of this particular tract for this subject? Thanks, Emily

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Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
by Anastasia Yendiki 18 Aug '14

18 Aug '14

Hi Yoon - The update is here: http://freesurfer.net/fswiki/Tracula#Updates There will also be a new freesurfer release in the next couple of months, but I don't anticipate making more changes to longitudinal tracula before that, so this should be the same as in the future 5.4 version. a.y On Wed, 23 Jul 2014, Yoonho Chung wrote: > Thank you for your input. Before we go ahead and reprocess our recon and DTI data with FS v 5.3 we were wondering if you plan an update on the TRACULA DTI longitudinal stream anytime soon. > I think I saw somewhere in the email chain that this is likely to happen soon with additional features and bug fixes. If so, I think it would be worth the wait. > > Thank you! > > Yoon > > > > > On May 22, 2014, at 5:37 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > >> >> Hi Yoon - If you are getting an error from longitudinal tracula, do check the tracula updates at the link that I gave you in my previous email. >> >> As for 5.2 recon-all, others can chime in here, but like I said it is not recommended to use it. Sorry about that. >> >> a.y >> >> On Thu, 22 May 2014, Yoonho Chung wrote: >> >>> Thanks for the quick response! >>> >>> If I already have all the T1 data processed using recon-all with FS v5.2, do you think it is okay to switch the stream to FS v.5.3 and run Tracula? - without having to do the recon-all again for the T1 data? It is because I am also experiencing DTI longitudinal error due to the OS issue (according to other threads). And if possible, I would like to avoid having to redo all the recons if we have to switch it to v5.3. >>> >>> Thanks again! >>> Yoon >> >> >> 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. >> > > > >

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Hippocampal Subfields missing nonPartialVolumeStatsRight.txt file
by Chung, Yoonho 18 Aug '14

18 Aug '14

Hi, I am running Hippocampal subfield processing stream and I think I got all the appropriate "posterior_*.mgz files" I need to get the stats, but I am not seeing "nonPartialVolumeStatsRight.txt" anywhere as described in the wiki under $subjectsdir. What I am seeing is "volumeStats_left.txt" and "volumeStats_right.txt" files under the "$subject/mri" directory and one of the text files look like this. ------------------------------------ volumeInVoxels: Left-Hippocampus: 2616.97 left_presubiculum: 4050 left_CA1: 2880.55 left_CA2_3: 8120.59 left_fimbria: 212.439 left_subiculum: 5985.02 left_CA4_DG: 4459.07 left_hippocampal_fissure: 358.59 ------------------------------------- If I look at the end of the "hippo-subfields.log" file, it is saying it is skipping the partial volume segmentation (see below). --------------------------- ... Debug: Off Observers: none Matrix: -0.5 0 0 0 0 0.5 0 -0.5 0 Offset: [41.7047, -40.8148, -4.10007] Center: [0, 0, 0] Translation: [41.7047, -40.8148, -4.10007] Inverse: -2 0 0 0 0 -2 0 2 0 Singular: 0 spacing: [0.5, 0.5, 0.5] origin: [41.7047, -40.8148, -4.10007] direction: -1 0 0 0 0 1 0 -1 0 done! Skipping the partial volume segmentation part ------------------------------------------- Can please someone tell me what I am missing? Also, what do I need to do to extract the values to a spreadsheet? Should I use asegstats2table? under '-help' it doesn't say which options it should be used to get the subfields. Thank you so much for the help in advance. Cheers, Yoon

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ERROR: QdecGlmDesign::Create: zero factors!
by Minjeong Wang 18 Aug '14

18 Aug '14

Dear freesurfer user, I'm new in this freesurfer and i want to analysis of the thickness of two groups, dementia and normal. I was trying to use qdec but when i pressed "analyze" button, there was some message at the bottom, which is "Error during design creation". At the same time, on the terminal, the following message came up. "ERROR: QdecGlmDesign::Create: zero factors! " For details, See below. Please let me know what the problem is. Thanks. *M.J. * ------------------------------------------------ Reading /Applications/freesurfer/tktools/tkUtils.tcl Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Loading data table /Applications/freesurfer/subjects/qdec.table.dat... Number of columns: 3 fsid column: 1 Number of factors: 2 Number of subjects: 10 Reading discrete factor levels from config file /Applications/freesurfer/subjects/diagnosis.levels AD Normal done. Data table /Applications/freesurfer/subjects/qdec.table.dat loaded. Verifying subject data..........Subject verification complete. Input table: /Applications/freesurfer/subjects/qdec.table.dat Subj#, SubjID, Data... 1 a1002 AD 75.000000 2 a1003 AD 63.000000 3 a1009 AD 71.000000 4 a1015 AD 80.000000 5 a1019 AD 75.000000 6 n1004 Normal 72.000000 7 n1005 Normal 71.000000 8 n1006 Normal 57.000000 9 n1007 Normal 62.000000 10 n1008 Normal 62.000000 1 diagnosis discrete 2 1 AD 2 Normal 2 age continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 68.800 7.361 Number of subjects: 10 Number of factors: 2 (1 discrete, 1 continuous) Number of classes: 2 Number of regressors: 4 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/Applications/freesurfer/subjects' ERROR: QdecGlmDesign::Create: zero factors!

1 0

Removing dura fails to correct pial errors
by Elijah Mak 17 Aug '14

17 Aug '14

Hi Freesurfer Team, I am encountering a situation where some pial errors in a few subjects persist even after removing the non-brain voxels. It appears that pial surface has not changed although the portion in the brainmask has been erased. What could be some of the reasons for this? I have attached a screenshot. Many thanks for your help! Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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No voxel in mask using mri_binarize
by wang kangcheng 17 Aug '14

17 Aug '14

Dear experts I want to create a mask for prefrontal gyrus. I used labels ( 1001, 1003, 1012,1014,1018 etc,)in FreeSurferColorLUT.txt and run the command like following mri_binarize --i con_sub01/mri/aparc.a2009s+aseg.mgz --out segment.nii.gz --match 1001, 1003, 1012,1014,1018 ----erode 1 But it found 0 voxels in final mask. How should I do ? Thank you Wang Kangcheng

2 1

missing cortical parcellation labels in aparc+aseg
by Mehul Sampat 15 Aug '14

15 Aug '14

Hi Folks, We have a strange error for one case. For one case there are missing cortical parcellation labels in aparc+aseg.mgz file in the right hemisphere (see screenshots) I looked at the recon-all.log file and no errors are reported. Also I recreated aparc+aseg.mgz file using the following command but the issue persists: mri_aparc2aseg --s subjid --volmask I looked at the rh.white and rh.pial and those look good. I cannot figure out what would cause such an issue ? I was wondering if anyone has seen something similar ? Thanks Mehul

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