Freesurfer

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30132 discussions

error running FS on mac
by Dian "Oscar" Jiao 27 Jun '12

27 Jun '12

Hi, I just installed Freesurfer on my Mac Lion. When I ran recon-all, I got the following error. Can't locate MNI/Startup.pm in @INC (@INC contains:…………) at Applications/freesurfer/mni/bin/nu_coorect line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. Has this occurred to anyone before? How to fix it? Thanks DJ

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Correction of registration in preproc-sess stream
by Jörg Pfannmöller 27 Jun '12

27 Jun '12

Dear freesurfers, I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. In the preprocessing the functional images are registered to the anatomical ones using bbregister. This is the 3rd in a series of 8 preprocessing steps. If the preproc-sess registration fails it is possible to achieve a proper registration using various options of bbregister. Does it suffice to replace the register files created during the preprocessing with the ones received during the registration correction in order to attain proper preprocessed data or are there routines in steps 4 to 8 in the preprocessing which rely on the registration? Thanks in advance pfannmoe

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Hippocampal segmentation
by Gabriel Gonzalez Escamilla 27 Jun '12

27 Jun '12

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DTI question
by Drottar, Marie 27 Jun '12

27 Jun '12

I have a DTI dataset with 10 b0 and gradient 30 directions. I would like to remove one or two volumes from the dataset and then repackage the data. How do I do this? thank you Marie Drottar, MA Research Assistant Division of Newborn Medicine Fetal-Neonatal Neuroimaging & Developmental Science Center Boston Childrens Hospital 1 Autumn St Boston, MA 02115 http://childrenshospital.org/FNNDSC

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How to tackle large segmentation errors
by Richard Binney 26 Jun '12

26 Jun '12

Hi Freesurfers, I need some advice regarding the best approach to fixing some very large RECON errors in a highly lesioned brain. There are many problems in this RECON output, but I want to focus on one particularly bad one which is highlighted in the attached figure by yellow arrows but also have knock on effects in the ventricles. There are no examples in the tutorials or other docs that are quite like this. Can you tell me what the best approach to correcting this would be? Are WM.MGZ edits, as highlighted by purple arrows, the right approach? I can't help but feel there is a lot of room for error with this approach and it could be extremely time-consuming due to the need to accurately trace the basal surface or the subcortical mass. It is stated NOT to use control points in instances of white matter lesions. What about instances such as this? Clearly there is white and subcortical grey matter in this region - would placing control points in subcortical grey matter cause any problems? My take on control points is that it only informs the generation of the WM.MGZ image, which is not just white matter but generally all subcortical mass, and intensity changes instigated by them do not directly effect subcrotical parcellation - is this correct? If so, perhaps then control points would be OK to resolve this error. Please advise. Richard

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is it a bug of freeview? or wrong segmentation?
by Chao Suo 26 Jun '12

26 Jun '12

Hi all, I am new with freesurfer, and I found a problem when processing some data following the instruction online. When I checked the surfaces of these two timepoint together using freeview (follow the instruction online), it showed this abnormal spike on the white mater surface of my time point two scan. (fig 1, left, clear version: https://dl.dropbox.com/u/4825915/fig1.png) freeview -v SMART001aT1.long.SMART001T1/mri/norm.mgz \ SMART001bT1.long.SMART001T1/mri/norm.mgz \ -f SMART001aT1.long.SMART001T1/surf/lh.pial:edgecolor=red \ SMART001aT1.long.SMART001T1/surf/lh.white:edgecolor=blue \ SMART001bT1.long.SMART001T1/surf/lh.pial:edgecolor=255,128,128 \ SMART001bT1.long.SMART001T1/surf/lh.white:edgecolor=lightblue \ However, it was wired that I couldn't see this spike when I opened them in tkmedit. (fig1, right, https://dl.dropbox.com/u/4825915/fig1.png) tkmedit SMART001bT1.long.SMART001T1 brainmask.mgz -aux wm.mgz -surfs Further, if I inspected only the two surfaces of my time two data, there is no such spike at the same point. (fig2, clear version: https://dl.dropbox.com/u/4825915/fig2.png) freeview -v SMART001bT1.long.SMART001T1/mri/norm.mgz \ -f SMART001bT1.long.SMART001T1/surf/lh.pial:edgecolor=255,128,128 \ SMART001bT1.long.SMART001T1/surf/lh.white:edgecolor=lightblue \ So I am not sure whether these spikes are bugs when using freeview, or actually some registration error that need me to edit. Can some help me to confirm it? Or, did anyone come across this problem before? Thanks Chao Suo -------------------------------------------- PhD Candidate, School of Psychiatry, UNSW, Australia Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY Room 401, Level 4, M02K | 100 Mallett St Camperdown | NSW | 2050 T +61 2 9351 0728 | F +61 2 9351 0551 |

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Problem with mri_glmfit ill-conditioned matrix
by Carl Anderson 26 Jun '12

26 Jun '12

Dear Freesurfer, We have a recurrent problem with an ill-conditioned matrix. Could someone shed some light on our problem. Here is the command line: mri_glmfit --y lh.ELS-CON.thickness.10.mgh --fsgd CAT-SP_June26.FSGF dods --C ELSvsCON_COV-Gen-Age-ICV.mtx --surf fsaverage lh --cortex --glmdir ELS_CON_June26_contrast_one Below is the Design matrix and attached is the fsgd Thanks very much, Creating output directory ELS_CON_June26_contrast_one Loading y from /Applications/freesurfer/subjects/SP-CAT_data/lh.ELS-CON.thickness.10.mgh INFO: gd2mtx_method is dods Saving design matrix to ELS_CON_June26_contrast_one/Xg.dat Normalized matrix condition is 44113.9 Design matrix ------------------ 0.000 0.000 0.000 1.000 0.000 0.000 0.000 29.600 0.000 0.000 0.000 1302835.625; 0.000 1.000 0.000 0.000 0.000 30.000 0.000 0.000 0.000 1785397.750 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 29.930 0.000 0.000 0.000 1350884.250; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 29.610 0.000 0.000 0.000 1492907.500; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 29.380 0.000 0.000 0.000 1479810.250; 0.000 1.000 0.000 0.000 0.000 30.220 0.000 0.000 0.000 1408085.125 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 30.470 0.000 0.000 0.000 1257495.875; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 30.810 0.000 0.000 0.000 1221350.500; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 29.740 0.000 0.000 0.000 1325784.500; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 29.770 0.000 0.000 0.000 1428926.125; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 30.310 0.000 0.000 0.000 1099130.750; 0.000 1.000 0.000 0.000 0.000 29.000 0.000 0.000 0.000 1766575.750 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 29.050 0.000 0.000 0.000 1311269.250; 0.000 1.000 0.000 0.000 0.000 29.550 0.000 0.000 0.000 1749889.250 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 22.440 0.000 0.000 0.000 1617660.625 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 25.560 0.000 0.000 0.000 1749327.375 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 22.190 0.000 0.000 0.000 1532579.000 0.000; 1.000 0.000 0.000 0.000 25.530 0.000 0.000 0.000 2144050.750 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 25.950 0.000 0.000 0.000 1664001.125 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 22.790 0.000 0.000 0.000 1544209.625 0.000; 1.000 0.000 0.000 0.000 25.800 0.000 0.000 0.000 1718912.750 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.810 0.000 0.000 0.000 1624601.625 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 22.800 0.000 0.000 0.000 1706050.125 0.000; 1.000 0.000 0.000 0.000 21.250 0.000 0.000 0.000 1508681.750 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 25.720 0.000 0.000 0.000 1526436.125 0.000; 1.000 0.000 0.000 0.000 25.600 0.000 0.000 0.000 1558595.125 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.950 0.000 0.000 0.000 1523555.500 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 22.280 0.000 0.000 0.000 1436572.375 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.840 0.000 0.000 0.000 1391633.500 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.790 0.000 0.000 0.000 1484742.375 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.770 0.000 0.000 0.000 1523672.500 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 24.130 0.000 0.000 0.000 1616389.875 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 25.790 0.000 0.000 0.000 1620330.625 0.000; 1.000 0.000 0.000 0.000 23.830 0.000 0.000 0.000 1785148.125 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 23.790 0.000 0.000 0.000 1685555.500 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 24.960 0.000 0.000 0.000 1791343.625 0.000 0.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 44113.9 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.ELS-CON.thickness.10.mgh --fsgd CAT-SP_June26.FSGF dods --C ELSvsCON_COV-Gen-Age-ICV.mtx --surf fsaverage lh --cortex --glmdir ELS_CON_June26_contrast_one 2. The FSGD file (if using one) 3. And the design matrix above -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Re: [Freesurfer] pars triangular and BA44 segmentation bug?
by Gabor Perlaki 26 Jun '12

26 Jun '12

Dear Bruce, In the paper "Left-right asymmetry in volume and number of neurons in adult Broca's area." by Katrin Amunts, 10 subjects (5 men and 5 women) were studied, and the volume of BA44 was greater in the left hemisphere than in the right in all ten cases. So, it is very strange that the volume of BA44 was greater in the right hemisphere in all of the 80 subjects analyzed by Eniko. Thanks, Gabor

3 6

trac-all: error during trac-paths due to tract missing
by Torben Prokscha 26 Jun '12

26 Jun '12

Dear all, while running trac-all, I got the following error: ERROR: Could not open /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt Obviously, a similar problem was discussed before (here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019570.h…) However, no general solution was publicly mailed. Since it was requested then, I attach the trac-all.log file. Thanks in advance for any help! Best Torben Prokscha

3 3

skull strip (ss) and pial/wm/orig surf
by Kushal Kapse 26 Jun '12

26 Jun '12

hi FS users; have two questions which i am having issue across ss and pial/wm/orig surf boundaries 1- it has happened that sometimes the sagittal view of individual was flipped from left to right. but the pial/wm boundaries look good. was wondering why this happened only for countable ppl? i tried to look up in forum for anyone with similar issue but no clue yet...has anyone come across this issue and if yes, how to flip back the orientation in sagittal view 2- how much ss issue should be considered. ss issue= skull pieces left behind, or large GM cut. the reason i m asking is because sometimes there would be a huge piece of skull remaining but that individual would have perfect visual alignment of boundaries and nice inflated surface. sometimes they have mediocre skull remaining or GM cut, and that would make pial/wm boundaries go wrong and inflation is with holes and droplets. my question is how much of skull stripping errors( pieces of skull remaining, gm/wm removed beyond limit or orientation flipped) matters to segmentation, inflation and further analysis. any help would be appreciated thanks kk

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