Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

Cortical Normalization Questions
by Jeff Sadino 23 Apr '12

23 Apr '12

Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html) Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff

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About the GroupAnalysis
by bowang21＠mail.ustc.edu.cn 23 Apr '12

23 Apr '12

Hi All, When we do the GroupAnalysis,there is a vector(such as: 0 0 0.5 0.5).And I just want to know how this vector involve in calculating?

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Freeview Edit Capability
by Richard Binney 23 Apr '12

23 Apr '12

Hi Freesurfers, I just want to check my observation that Freeview can not currently be used for editing the WM.mgz or the brainmask.mgz (for minor skull strip errors) as is done in TKmedit (cf., Edit Tutorial). Is that correct? I can’t find any documentation on this, and whilst I would assume it to be a straightforward thing if possible, I can’t work out how I could configure Freeview voxel edit tools to do this. I assume that the only edits currently possible in freeview are label/ROI edits and control point definition. If this is correct, will the other edits become possible in later versions of Freeview? – this would be great given the ability to load multiple volumes…for example it is nice to view the brainmask.mgz over the T1.mgz with the latter’s opacity turned down in order to quickly detect minor skull strip errors. It would be then nice to delete (or clone-in) voxels on this set of images (like TKmedit). Thanks for your help R

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Error: matrix is rank-deficient by 2
by Mohana Ramaratnam 23 Apr '12

23 Apr '12

Hello, We are getting the following error while processing T1 data acquired on Philips. The image data looks ok. We have three scans with similar error. Does anyone have suggestions as to what could be wrong? Loading pixel data /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2 MRIresample(): error inverting matrix; determinant is nan, matrix is: TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -0, 0) j_ras = (-0, -0, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; Linux node159 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x 86_64 GNU/Linux recon-all -s 0180634_v00_mr exited with ERRORS at Mon Apr 2 12:25:57 CDT 2012

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your insight: parameter definition and --tnullmin necessary?
by Betina Ip 23 Apr '12

23 Apr '12

Dear Freesurfer list, I am using optseq2 for the first time and wanted to check with you whether my protocol makes sense, many thanks in advance for your insight. 1) I start by choosing the maximum scan duration equalling ~30 min: 2) set the psd window so it can capture the entire waveform of a 4 second event 3) select equal amounts of trials for each of the 4 event types, I played around with it and 80 trials give me the greatest efficiency (2.72) and variance reduction factor average (54.37). Are these values acceptable? They are the best I could get tweaking the number of trials. The command is here: ./optseq2 --ntp 440 --tr 4 --psdwin 0 20 \ --ev evt1 4 80 \ --ev evt2 4 80 \ --ev evt3 4 80 \ --ev evt4 4 80 \ --nkeep 3 \ --o gfatrial \ --focb 10 \ --nsearch 10000 A sample trial list is here: 0.0000 2 4.000 1.0000 evt2 4.0000 4 4.000 1.0000 evt4 8.0000 0 4.000 1.0000 NULL 12.0000 3 4.000 1.0000 evt3 16.0000 3 4.000 1.0000 evt3 20.0000 2 4.000 1.0000 evt2 … The other question I had concerns the position of null trials. Many trials are not separated by a NULL event, however studies of rapid event-related designs to report a minimum ITI, in this case the minimum seems to be 0? To assess the effect of forcing a minimum ITI on the sequence, I have run the search defining the --tnullmin to 4 sec (equal to 1 TR) however efficiency and VRFAvg drop to .79 and 16.07, obviously due to trade of between ntp and ntrials (ntp=440, ntrials=62). Are NULL trials between each event required at all if a standard FIR is used for the analysis? My aim is to first apply a univariate BOLD-analysis and subsequently a multivariate analysis to the dataset. Thanks for clarifying. Betina

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mri_cvs_register error in step 2
by Jackie Leung 23 Apr '12

23 Apr '12

hi, I'm trying to run mri_cvs_register and I'm getting a strange error message. MRISread(CVS_test_26to47_1/lh.resample.white): could not open file No such file or directory Error reading surface CVS_test_26to47_1/lh.resample.white I've checked the directory and the file definitely exists. It seems to be popping up in step 2 of the script, where it calls the surf2vol function. I've tried running this function on its own and didn't get this error, so I'm really confused as to what the problem may be. Any help will be greatly appreciated! thanks, jackie

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mris_expand not working since upgrading to v.5.1.0
by Andrew C Yourich 23 Apr '12

23 Apr '12

Hello, I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is: mris_expand -thickness ./lh.white $1 lh.white.expanded where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume. Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead? Thanks, - Andrew

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Re: [Freesurfer] WM modification
by Gabriel Gonzalez Escamilla 23 Apr '12

23 Apr '12

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labelling of cluster regions
by Govindarajan, Koushik Athreya 23 Apr '12

23 Apr '12

Hi, I have a question regarding how the clusters are labeled after the results of a Monte-Carlo Simulation. Similar regions from 2 different patient populations seem to be labeled differently. On one of my results, the cluster has been labeled as in the precentral region and a similar region on another population seems to be labeled as superior frontal region. Is the labeling based on which region the majority of significant vertices fall under? In that case, would a cluster that kind of falls over 2 regions of the brain be labeled as the one with more vertices? Thanks for all the help Koushik

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Re: [Freesurfer] bbregister for fmri FEAT data
by Erlend Hodneland 23 Apr '12

23 Apr '12

Hi again, the registration looks fine in tkregister2, but is apparently wrong in fslview (and also mricron). See the attached files (as link from http://vedlegg.uib.no/?id=399ad2cce1a3138f8eb4f6a06f4acfc4) showing screenshots of fslview and tkregister2. How can this be explained, and how can we visualize the correct orientation in fslview? What does this misalignment influence any further processing with fnirt and concatenation of the affine transformation fields? This is our command we run for bbregister: bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat --init-fsl --t2 --o test.nii.gz where vol0001 is the first volume in the fmri sequence and is flipped to align with LAS (as the highres). Thank you for your kind help, Erlend Hodneland ean that it is in the wrong orientation? It should be in the same orientation as the anatomical. How does the reg look in tkregister2? Note that fslview can display volumes in odd orientations even when the orientation is correct. doug On 04/13/2012 03:31 AM, Erlend Hodneland wrote: > Hi, > > we are trying to register fmri FEAT data (example_func.nii) to the > anatomical scan (processed in Freesurfer) using bbregister to opt. > the affine registration before running FNIRT. > > However, the orientation of the registered image is flipped around and > is incorrect after applying bbregister. > > We have tried: > > 1) bbregister --s subj_501 --mov example_func.nii.gz --reg > register.dat --init-header --bold --o example_func2highres-fs.nii > 2) bbregister --s subj_501 --mov example_func.nii.gz --reg > register.dat --init-fsl --bold --o example_func2highres-fs.nii > 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat > "myfeatdirectory" > 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat > (this one looks correct) > followed by > bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat > --init-reg tkreg.dat --bold --o example_func2highres-fs.nii > > 5) reorienting to match the highres: > > fslorient -swaporient example_func > fslswapdim example_func x -y z example_func_swap (correct > orientation) > > followed by > bbregister --s subj_501 --mov example_func_swap.nii.gz --reg > register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii > > with the output being flipped in wrong orientation for all options. > > We would greatly appreciate if you have any suggestions for how to > overcome this problem! > > Cheers/Sincerly/All best > > Erlend Hodneland

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Freesurfer April 2012