Freesurfer

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30088 discussions

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

3 2

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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Re: [Freesurfer] Load Brodmann surface area into inflated surface
by _andreia_＠sapo.pt 23 Apr '12

23 Apr '12

(forgot to do answer all, here it goes for the list too) Citando _andreia_(a)sapo.pt: > Hi Bruce, > > The ideia is to show one control subject vs. one patient inflated > surface with BA surface (not volume, sorry) to show the difference > (reduced surface area in one patient). Loading the relevant labels > worked (I have the statistics shown in bar graphs, the images are > only for visualizing the difference between controls and patients). > When I threshold the labels in the subject's inflated surface they > shrink a lot, is this supposed to happen? > > The BA are V1, V2 and MT. What is the thresghold for V2? > > And is it correct to load ?h.sulc in a gray scale to have the usual > cortex representation, or I should do it other way? > > > And getting back to my previous email: > > Another question is, how is the volume of the BA calculated? Is it >>> from the surface-based stream? >>> >>> And, which surface area is the on in the output of the BA stats? Is it >>> the pial or wm? > > Thanks, > Andreia > > > Citando Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > >> Hi Andreia >> >> sorry, I don't understand. What do you mean when you say you want >> to " show the resulting Brodmann area (only 3 BA) volume in the >> inflated surface of my subjects". Do you mean just to show what >> portion of the surface is in each of 3 Brodmann areas? That you >> would do by loading the relevant labels, although you will probably >> want to threshold them differently (e.g. V1 you could threshold at >> .9 which is 90% and it would have about the surface area of an >> individual, while MT would need to be closer to .4 or .5). Or do >> you actually mean the volume of gray matter within each BA? If the >> latter, it's just 3 numbers/subject, so I would think you would >> want a scatter plot or something, not a map on the surface. >> >> cheers >> Bruce >> >> >> On Mon, 23 Apr 2012, _andreia_(a)sapo.pt wrote: >> >>> Hi all, >>> >>> I'm sorry if these questions have already been covered here, but I've >>> looked into the archives and still can't do what I need (and since I'm >>> running out of time for this task I decided to post here): >>> >>> I'm using version 5.0.0. >>> >>> I want to show the resulting Brodmann area (only 3 BA) volume in the >>> inflated surface of my subjects to show the differences between >>> patients and controls (for visualization purpose only). I've managed >>> to overlay the volume in the curvature menu but this is for the entire >>> cortex and I can't show the values bar. How can I show the volume of >>> only 3 BAs and have the scale bar? >>> >>> Another question is, how is the volume of the BA calculated? Is it >>> from the surface-based stream? >>> >>> And, which surface area is the on in the output of the BA stats? Is it >>> the pial or wm? >>> >>> Thanks in advance, >>> Andreia >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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.

2 1

Neuroscience project, hippocampus segmentation
by Paweł Dembiński 23 Apr '12

23 Apr '12

Hi, I'm currently doing a project for my neuroscience course. I've decided to compare automatic segmentation methods (comparing hippocampus volumes) (using Freesurfer and FIRST). My question is, whether there is a set of commands in Freesurfer which will enable me to segment only hippocampus. I'm only intrested in volumes, nothing else. I've noticed that recon-all takes a lot of time and been wandering if there is a faster way. Pawel

2 1

prefrontal cortex values
by Ahmed, F, Me <fahmed＠sun.ac.za> 23 Apr '12

23 Apr '12

Hello FS experts, A quick question for you all. Does the FS stream produce any values for the Prefrontal Cortex specifically? Thanks, Fatima ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

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