Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

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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occipital lobe WM errors
by Walton, Matt 13 Aug '14

13 Aug '14

Hello Freesurfer team, I've used freesurfer to segment (recon-all) approximately 30 different subjects from a study. I've noticed that a large number of these subjects have a misclassification of the white and pial boundaries in the occipital lobe (such that grey matter is being classified as white matter). I believe this problem is originating from my scanner and original data. I'm acquiring a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 channel phased array head coil. For many subjects, this acquistion gives intensity inhomogeneity in the occipital lobe. I've begun using a GE based correction technique (PURE) on the images, and it appears to improve the intensity in the occipital lobe, but Freesurfer is still frequently misclassifying. I'm wondering what would be the best way to edit the data. I've often tried to edit the wm.vol, but this doesn't seem to fix anything. For the most part, the wm.vol is correct to begin with, but the wm cutting line isn't segmenting with the wm.vol. I've also tried to add control points but this doesn't seem to improve anything either. I've attached an image which I hope will further explain my problems. Thanks for any help

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V1 and V2 labels valid with clinical populations?
by krista kelly 13 Aug '14

13 Aug '14

Does anyone know of any support (i.e. articles/data) suggesting that the V1 and V2 labels automatically created in the Freesurfer pipeline, especially when looking at surface area/gyrification, are valid to use with clinical populations? In particular, visually deprived populations? Thanks! Krista

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lobes gyrification
by melinda dora 11 Aug '14

11 Aug '14

Dear freesurfer group, is there a command to extract lobar gyrification values for each subject? If so please what are the steps? if Ive already created the lobar annotation labels, can I extract gyrifaction with these if I have already passed the gyrification command? Best, Melly

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Cortical Thickness Correction Factor
by David Tate 08 Aug '14

08 Aug '14

We are working on a study that includes data from multiple scanners and initial indication suggest that there may be small differences in cortical thickness measures that are scanner related (human and other phantom data were acquired at both sites). Is it possible to include a correction factor adjusting for the scanner differences when using glmfit or qdec? Thanks, David David F. Tate, Ph.D. Research Neuropsychologist Defense and Veterans Brain Injury Center Contractor, General Dynamics Information Technology Brooke Army Medical Center MCHE MDU (DVBIC) 3551 Roger Brooke Drive JSBA Ft. Sam Houston, TX 78234-4504 Office (210) 916-8090

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Jacobian mri_cvs_register
by André Ribeiro 05 Aug '14

05 Aug '14

Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro

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uploading a surface in freeview
by carina＠van-vlodrop.de 05 Aug '14

05 Aug '14

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Freesurfer Start Up
by Isaiah C. Smith 03 Aug '14

03 Aug '14

Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith

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Repost | Re: mni152reg error
by JacobML＠nmr.mgh.harvard.edu 02 Aug '14

02 Aug '14

Hello Doug, Ideally, I am trying to take subject tstat maps from FsFast (stable3 environment) and register these native structural space maps to the MNI152_2mm standard brain. The t_000.bfloat file is what was generated relative to my contrast that was set up in FsFast stable3. There are a series of these files ranging from t_000.bfloat to t_029.bfloat and there are also these same named files with a .hdr extension. t_000.bfloat is the file I designate when I select an overlay within tkmedit. Your help sorting out this registration is very appreciated. Thank you, Jacob >> I'm not sure what you are trying to do, but that command line looks like >> things are not set up properly. What is t_000.bfloat? (And why are you using bfloats?) >> doug >> On 7/17/14 1:14 PM, JacobML(a)nmr.mgh.harvard.edu wrote: >>> Hello again Doug, >>> Thank you for sending the updated version of mri152reg. It ran without error and generated the reg.mni152.2mm.dat registration matrix. Unfortunately though, when I tried to apply the transformation to the same >>> subject's t_000.bfloat, the registration is not correct (command below). mri_vol2vol --inv --targ /.../t_000.bfloat --mov >>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o >>> CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat On a positive note, I was able to load the output image and >>> MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be shifted too far anterior. >>> With my next attempt, I used mri_convert to make the t_000.bfloat into a .mgz and than ran mri_vol2vol, but the same misalignment occurred (see attached photo). >>> Using tkmedit, I have confirmed that this file aligns properly on this subject's native structural image, so I am not quite sure why the registration matrix may be off. Given that the reg.mni152.2mm.dat file reflects the transformation of the native struc to MNI, I wonder if I need >>> to account for the reg file between the func data and the native struc? >>> Can you please let me know what I may be doing incorrectly? >>> As always, your help is very appreciated. >>> Jacob >>>> Yea, i fixed this problem. I've attached a new version with the fix. doug >>>> On 07/17/2014 10:35 AM, JacobML(a)nmr.mgh.harvard.edu wrote: >>>>> Hello Freesurfer Experts, >>>>> I am trying to view stats generated with FsFast in fslview/MNIspace, >>> and >>>>> in doing so I have run mni152reg to generate the registration matrix. >>> That said, mni152reg did not complete correctly and below I have pasted >>> the terminal output: >>>>> Thu Jul 17 09:58:10 EDT 2014 >>>>> setenv SUBJECTS_DIR >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons >>>>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons >>> /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s >>>>> CD_cerv_pat4_sess1_recon >>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 >>> UTC >>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux >>>>> fslregister --mov >>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz >>> --s CD_cerv_pat4_sess1_recon --reg >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat >>> --dof 12 >>>>> mkdir: cannot create directory >>>>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': >>> Permission denied >>>>> Log file is >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log >>> Thu Jul 17 09:58:11 EDT 2014 >>>>> --mov >>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz >>> --s CD_cerv_pat4_sess1_recon --reg >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat >>> --dof 12 >>>>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ >>>>> purkinje >>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 >>> UTC >>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux >>>>> nIters 1 >>>>> -------------------------------------- >>>>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons mri_convert >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz >>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii mri_convert >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz >>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii niiWrite(): error opening file >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii >>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... >>> TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 >>>>> i_ras = (-1, 0, 0) >>>>> j_ras = (-0, -0, -1) >>>>> k_ras = (0, 1, 0) >>>>> writing to >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... >>> ERROR: failure writing >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii >>> I tried to run the fslregister command from within the subject's directory >>>>> (in hopes to possible correct what may be a permissions issue), but >>> this >>>>> produces the same final error, "ERROR: failure writing >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." >>> Lastly, probably to no surprise, the >>>>> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any >>> ideas how I may be able to correct these errors? >>>>> Thank you for the help! >>>>> Jacob >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)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 >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Freesurfer July 2014