Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

eTIV in qdec
by dolphinede＠aol.com 18 Oct '11

18 Oct '11

Dear FreeSurfer experts, my idea was to put the eTIV as a variable in qdec. I have put this in my qdec.table.dat and when I run qdec and choose eTIV as variable I get the following error and qdec closes some seconds later automatically: Creating output directory /Users/dolphinede/Desktop/Probanden/qdec/Untitled Loading y from /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/Xg.dat Normalized matrix condition is 389.695 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148142 voxels in mask Saving mask to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73700.662359 DOF = 77 Starting fit and test Fit completed in 0.0607667 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995148, ar1std=0.005328, gstd=5.802773, fwhm=13.664487 Writing results lh-Avg-Intercept-thickness maxvox sig=35.9893 F=546.618 at index 1515 0 0 seed=1319335878 lh-Avg-thickness-eTIV-Cor maxvox sig=6.48644 F=31.2833 at index 51144 0 0 seed=1319335878 mri_glmfit done ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Users/dolphinede/Desktop/Probanden/qdec/Untitled/contrasts.sig.mgh reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /Users/dolphinede/Desktop/Probanden/qdec/Untitled/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 eTIV 1.45233e+06 147517 Class Means of each Continuous Variable 1 Main 1452332.4051 MatrixMultiply: m1 is null! No such file or directory I have no idea what is wrong. Best regards Daniel Klein

2 1

Surface area measure
by krista kelly 18 Oct '11

18 Oct '11

When I extract surface area data using the following commands, which measure of surface area am I getting, the pial surface, the WM surface, or the total of both combined? aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh --meas area --tablefile aparc_stats_rh.txt Thanks! Krista

2 1

QDec questions
by krista kelly 18 Oct '11

18 Oct '11

Hi, just wondering if anyone has any advice on the following questions: I'm using QDEC to analyze cortical thickness differences between groups and I have a few questions: 1) There are a few variables that I need to control for. First variable is scanner - I used two different scanners of different field strengths (1.5T GE and 3T Siemens) so I wanted to control for scanner. I also wanted to control for age and gender. Here's my ideal design setup: discrete variables - groups, scanner, gender nuisance variable - age contrast would be 1 -1 0 0 0 0 I realize that scanner, gender, and group are all discrete variables, and that age would be a continuous one. However, in the design tab, I am not able to select all 3 discrete variables (groups, scanner, and gender). Should I designate scanner or gender as a nuisance variable instead? Would it matter which one I use as the nuisance variable? Possible setup: discrete vars - groups, scanner nuisance vars - age, gender contrast - 1 -1 0 0 (Correct?) 2) If I use DODS, should I demean the ages if age is a nuisance variable? 3) If I use a smoothing kernel during the analysis, then create an ROI and map that ROI to each individual subject, will the resulting .stats file in each subjects stats folder reflect the smoothed data or does mapping onto each ROI just extract the raw unsmoothed data from each vertex? Thanks! Krista

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reg-feat2anat failure
by Michelle Umali 18 Oct '11

18 Oct '11

Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed. When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off. I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit? How can I fix this so that the masks are accurate? Thanks. Michelle

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mri_ca_register error
by Oya, Hiroyuki (UI Health Care) 18 Oct '11

18 Oct '11

Hello , I am running recon-all with -cm switch and getting following error. Is there any workaround? Without -cm switch , recon-all completes all the processing just fine. Thank you. Hiroyuki mri_ca_register -invert-and-save transforms/talairach.m3z mri passed volume size is different from the one used to create M3D data Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM ERROR: mri_ca_register with non-zero status 0 ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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Re: [Freesurfer] coregistration - FA to Freesurfer
by Ed Gronenschild 18 Oct '11

18 Oct '11

Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where "subject" is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Dear Bruce and Anastasia, > > Thanks for the quick reply! > > I tried the bbregister as you suggested but when i visualize the > target and > dti image they don't look registered at all. > > This is the comand i used: > > bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg > /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out > /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/ > flirt.tmx > > I tried to use the bbregister tools to align them but I didn't get > very > far... > > Did i miss something? > > I read in another mail something about using the register.dat > created in > bbregister and do mri_label2vol but i'm not sure how to do it. > > Thanks, > > Joana

4 8

MCSRCH ERROR
by Kenichiro Tanaka 18 Oct '11

18 Oct '11

Hello All, While processing a brain image data(.mgz) through ver5.0.0, I got the following errors. I have no idea how to resolve them. I need outputs in stats directory, there are only lh.aparc.a2009s.stats, lh.aparc.stats, and lh.curv.stats. What caused them? How should I resolve them? IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10318.1 tol 0.000010 . . . inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.699, avgs=0 005/300: dt: 0.9000, rms radial error=175.446, avgs=0 010/300: dt: 0.9000, rms radial error=174.904, avgs=0 015/300: dt: 0.9000, rms radial error=174.193, avgs=0 020/300: dt: 0.9000, rms radial error=173.383, avgs=0 025/300: dt: 0.9000, rms radial error=172.518, avgs=0 030/300: dt: 0.9000, rms radial error=171.620, avgs=0 035/300: dt: 0.9000, rms radial error=170.706, avgs=0 040/300: dt: 0.9000, rms radial error=169.784, avgs=0 045/300: dt: 0.9000, rms radial error=168.860, avgs=0 050/300: dt: 0.9000, rms radial error=167.935, avgs=0 055/300: dt: 0.9000, rms radial error=167.012, avgs=0 060/300: dt: 0.9000, rms radial error=166.092, avgs=0 065/300: dt: 0.9000, rms radial error=165.175, avgs=0 070/300: dt: 0.9000, rms radial error=164.262, avgs=0 075/300: dt: 0.9000, rms radial error=163.352, avgs=0 080/300: dt: 0.9000, rms radial error=162.447, avgs=0 085/300: dt: 0.9000, rms radial error=161.547, avgs=0 090/300: dt: 0.9000, rms radial error=160.651, avgs=0 095/300: dt: 0.9000, rms radial error=159.759, avgs=0 100/300: dt: 0.9000, rms radial error=158.871, avgs=0 105/300: dt: 0.9000, rms radial error=157.989, avgs=0 110/300: dt: 0.9000, rms radial error=157.110, avgs=0 115/300: dt: 0.9000, rms radial error=156.236, avgs=0 120/300: dt: 0.9000, rms radial error=155.367, avgs=0 125/300: dt: 0.9000, rms radial error=154.502, avgs=0 130/300: dt: 0.9000, rms radial error=153.642, avgs=0 135/300: dt: 0.9000, rms radial error=152.786, avgs=0 140/300: dt: 0.9000, rms radial error=151.934, avgs=0 145/300: dt: 0.9000, rms radial error=151.087, avgs=0 150/300: dt: 0.9000, rms radial error=150.245, avgs=0 155/300: dt: 0.9000, rms radial error=149.407, avgs=0 160/300: dt: 0.9000, rms radial error=148.573, avgs=0 165/300: dt: 0.9000, rms radial error=147.744, avgs=0 170/300: dt: 0.9000, rms radial error=146.919, avgs=0 175/300: dt: 0.9000, rms radial error=146.098, avgs=0 180/300: dt: 0.9000, rms radial error=145.282, avgs=0 185/300: dt: 0.9000, rms radial error=144.470, avgs=0 190/300: dt: 0.9000, rms radial error=143.663, avgs=0 195/300: dt: 0.9000, rms radial error=142.860, avgs=0 200/300: dt: 0.9000, rms radial error=142.061, avgs=0 205/300: dt: 0.9000, rms radial error=141.266, avgs=0 210/300: dt: 0.9000, rms radial error=140.476, avgs=0 215/300: dt: 0.9000, rms radial error=139.693, avgs=0 220/300: dt: 0.9000, rms radial error=138.914, avgs=0 225/300: dt: 0.9000, rms radial error=138.140, avgs=0 230/300: dt: 0.9000, rms radial error=137.370, avgs=0 235/300: dt: 0.9000, rms radial error=136.604, avgs=0 240/300: dt: 0.9000, rms radial error=135.842, avgs=0 245/300: dt: 0.9000, rms radial error=135.085, avgs=0 250/300: dt: 0.9000, rms radial error=134.332, avgs=0 255/300: dt: 0.9000, rms radial error=133.583, avgs=0 260/300: dt: 0.9000, rms radial error=132.838, avgs=0 265/300: dt: 0.9000, rms radial error=132.098, avgs=0 270/300: dt: 0.9000, rms radial error=131.362, avgs=0 275/300: dt: 0.9000, rms radial error=130.629, avgs=0 280/300: dt: 0.9000, rms radial error=129.901, avgs=0 285/300: dt: 0.9000, rms radial error=129.177, avgs=0 290/300: dt: 0.9000, rms radial error=128.456, avgs=0 295/300: dt: 0.9000, rms radial error=127.740, avgs=0 300/300: dt: 0.9000, rms radial error=127.028, avgs=0 spherical inflation complete. . . . epoch 4 (K=1280.0), pass 1, starting sse = 541.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.32/19 = 0.01710 finalwriting spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 . . . pass 1: epoch 1 of 3 starting distance error %21.36 pass 1: epoch 2 of 3 starting distance error %21.04 unfolding complete - removing small folds... starting distance error %20.80 removing remaining folds... final distance error %20.81 364: 0 negative triangles . . . Thanks, Kenichiro Tanaka.

2 1

aparc+aspec to T1
by Hsiao-Ying (Monica) Wey 17 Oct '11

17 Oct '11

Dear experts, I would like to move my aparc+aseg.mgz image back to the native T1 space (rawavg.mgz). I tried: mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz ./subj001_aparc+aseg2raw.nii.gz However, it there a way that I don't change the value within the original aparc+aseg.mgz, so that I can use the LUT to define ROIs for additional processes? Thanks. Monica

3 2

Incorrect pial surface
by Jordan Pierce 17 Oct '11

17 Oct '11

We're trying to reconstruct pial and white matter surfaces for cortical thickness analysis and sections of the gray matter are being excluded, particularly in the temporal lobes. As far as we can tell, there is no way to add this back to the pial surface...is there a solution to this problem? Jordan Pierce

4 10

open-access article on TRACULA now available
by Anastasia Yendiki 17 Oct '11

17 Oct '11

Hi all - Since a few of you have inquired about a TRACULA reference in the past, here's one: http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstra… There's a link on the right where you can download the PDF. Happy reading! a.y

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Freesurfer October 2011