Freesurfer April 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
102 discussions

A question about Local Gyrification index in freesurfer
by yczhang 17 Apr '08

17 Apr '08

Dear Mr or Miss: I want to use the local gyrification index in freesurfer. However, my computer was installed with the former edition 4.0.1 without lGI, In order to use the lGI,I have to update the freesurfer software, I want to know whether other codes, for example ,the codes that calculated the thickness of cerebral cortex, were also changed or modified for integrating the lGI into the freesurfer software? I mean whether the other parts of the updated edition with lGI differs from the former edition without lGI. Thank you very much!! Best Regards. yczhang 2008-04-17

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LGI : cannot allocate memory
by Leila BH 17 Apr '08

17 Apr '08

Hello, Do you know why I have a memory problem with LGI ? This is my output: thanks [cammoun@lts1pc72 ~]$ recon-all -lgi -sid chuv60 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /home/cammoun/freesurfer -rwxrwxrwx 1 root root 620884 Apr 16 08:58 /usr/local/freesurfer/subjects/chuv60/scripts/recon-all.log Linux lts1pc72.epfl.ch 2.6.20-1.2944.fc6 #1 SMP Tue Apr 10 17:46:00 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /home/cammoun/freesurfer/ Previous: /usr/local/freesurfer /usr/local/freesurfer/subjects/chuv60/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Apr 16 08:58:15 CEST 2008 mris_compute_lgi --i lh.pial ================= rm -Rf tmp-mris_compute_lgi ================= ================= mkdir -p tmp-mris_compute_lgi ================= ================= mris_fill -c -r 1 lh.pial tmp-mris_compute_lgi/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to tmp-mris_compute_lgi/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('tmp-mris_compute_lgi/lh.pial.filled.mgz',15,'tmp-mris_co mpute_lgi/lh.pial-outer') ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.5.0.338 (R2007b) August 9, 2007 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit <http://www.mathworks.com> www.mathworks.com. >> reading filled volume... closing volume... morphological closing done. writing outer surface... >> ================= mris_extract_main_component tmp-mris_compute_lgi/lh.pial-outer tmp-mris_compute_lgi/lh.pial-outer-main ================= counting number of connected components... 65824 voxel in cpt #1: X=2 [v=65824,e=197466,f=131644] located at (-21.428276, -4.355502, 11.833313) For the whole surface: X=2 [v=65824,e=197466,f=131644] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 tmp-mris_compute_lgi/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= TAGskip: failed to calloc 1814053888 bytes! Cannot allocate memory Linux lts1pc72.epfl.ch 2.6.20-1.2944.fc6 #1 SMP Tue Apr 10 17:46:00 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Apr 16 09:01:17 CEST 2008

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Too many files open(selxavg3-sess).
by Zhen Zonglei 17 Apr '08

17 Apr '08

Hi all When I run selxavg3-sess with a sessid which contain more than six subjects, the procedure report some error as following: Error in ==> fast_selxavg3 at 270 >> >> >> ??? /matlab2006b/toolbox/matlab/iofun/tempname.m: Too many files open. >> >> >> >> /nfs/h1/r1/jliu/new_soft_test/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> ??? /nfs/h1/r1/jliu/new_soft_test/freesurfer/fsfast/toolbox/fast_fileexists.m: Too many files open. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? /freesurfer/fsfast/toolbox/fast_selxavg3.m: Too many files open. >> ??? /freesurfer/fsfast/toolbox/fast_fileexists.m: Too many files open. >> >> ??? /matlab2006b/toolbox/matlab/iofun/tempname.m: Too many files open. >> >> >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Is this a bug or my misused? My freesurfer version is stable 4.0.1. I guess some fclose(files) is missed in fast_selxavg3.m.Please help us. Thanks very much. Zonglei Zhen

2 4

Pimples on my inflated surface
by Avram Holmes 16 Apr '08

16 Apr '08

All, I'm attempting to process data from subject who has an excessive number of pimples/dots on the inflated surface of both hemispheres (see attached images). I've tried to complete autorecon2 both with and without control points but my attempts to correct the problem seem to be having little to no effect. I have two questions: 1) Could this be due to the white matter intensity normalization step? I've check the tal transform and that is fine and the other recon1 steps seem to check out. 2) If not is there another step which could cause this issue? Thanks, Avram -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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cortical surface in MNI space?
by Stark, David Ernest 15 Apr '08

15 Apr '08

Hi all, I am new to Freesurfer and would like to generate a cortical (pial) surface of 1 subject's brain, but I need the surface in MNI 152 space (this is for display purposes, so that I can overlay clusters already in MNI space). What is the best way to accomplish this? I already have the subject's freesurfed output (if any of those files can be of use). Also, if a pial surface already exists for one of the standard brains out there, that would also be of use. Thanks! David

3 2

LGI
by Leila BH 15 Apr '08

15 Apr '08

Hi I am trying to launch the LGI option, but the program seems to wait for a response, here is the complete output,. Even if I type yes it doesn't seems to continue. Do you know how to solve this? Thanks in advance Leila [cammoun@lts1pc72 ~/freesurfer]# recon-all -lgi -sid chuv60 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /home/cammoun/freesurfer -rwxrwxrwx 1 root root 569567 Apr 15 18:20 /usr/local/freesurfer/subjects/chuv60/scripts/recon-all.log Linux lts1pc72.epfl.ch 2.6.20-1.2944.fc6 #1 SMP Tue Apr 10 17:46:00 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /home/cammoun/freesurfer Previous: /usr/local/freesurfer /usr/local/freesurfer/subjects/chuv60/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Apr 15 18:21:04 CEST 2008 mris_compute_lgi --i lh.pial ================= rm -Rf tmp-mris_compute_lgi ================= ================= mkdir -p tmp-mris_compute_lgi ================= ================= mris_fill -c -r 1 lh.pial tmp-mris_compute_lgi/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to tmp-mris_compute_lgi/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('tmp-mris_compute_lgi/lh.pial.filled.mgz',15,'tmp-mris_co mpute_lgi/lh.pial-outer') ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.5.0.338 (R2007b) August 9, 2007 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... rm: remove regular file `/tmp/tmp8147237.mgh'?

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Mean Centering
by Jerry Yeou-Wei Chen 15 Apr '08

15 Apr '08

Hello, Are regressors mean centered for mri_glmfit? Judging by one of my previous Xg.dat files, it does not appear so. If not, I plan to manually enter my design matrix, with mean centered regressors. Do I need to enter the corresponding values in the FSGD file as mean centered? or can they remain non- mean centered? Thanks, - Jerry

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Re: [Freesurfer] recon-all ERROR
by SHRIKANTH KULASHEKHAR 15 Apr '08

15 Apr '08

Hi, on thecommand line: recon-all -autorecon1 -subjid SUBJECT_NAME -i /data/10456139 shriks ----- Original Message ---- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: SHRIKANTH KULASHEKHAR <contactshriks(a)yahoo.co.in> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Tuesday, 15 April, 2008 5:06:04 PM Subject: Re: [Freesurfer] recon-all ERROR Hi Shriks, can you send us: 1. The full command line you ran. 2. The recon-all.log file for this subject cheers, Bruce On Tue, 15 Apr 2008, SHRIKANTH KULASHEKHAR wrote: > Hi, > > When I run the recon-all -autorecon1 on my DICOM data I end up with an errror. In the error.log I find the following error. > > " MRIresample(): source matrix has zero determinant; matrix is: " > > How can I proceed futher ? > > thanks in advance. > > shriks > > > > > Meet people who discuss and share your passions. Go to http://in.promos.yahoo.com/groups/bestofyahoo/ Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/

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recon-all ERROR
by SHRIKANTH KULASHEKHAR 15 Apr '08

15 Apr '08

Hi, When I run the recon-all -autorecon1 on my DICOM data I end up with an errror. In the error.log I find the following error. " MRIresample(): source matrix has zero determinant; matrix is: " How can I proceed futher ? thanks in advance. shriks Meet people who discuss and share your passions. Go to http://in.promos.yahoo.com/groups/bestofyahoo/

2 1

mri_watershed: distorted inner skull surface
by Silviu Podariu 14 Apr '08

14 Apr '08

Hi, In order to get the three BEMs for EEG/MEG 3D source reconstruction for subject X, I used mri_watershed with -atlas, -useSRAS and -surf options, which created the BEMs in X/bem/watershed/, but the inner_skull and the brain were significantly distorted. I followed the tutorial on troubleshooting the surfaces in the X/surf/ folder, but that does not address fixing these BEMs, so I was wondering if anybody knows how to get around this problem. Actually, what concerns us most is if it's possible to get at least the inner skull surface right, as we shall be using the pial surface in X/surf/ (downsampled from 150k vertices) for the brain instead of the mri_watershed output (but I did not find there an inner skull surface). Thank you, Silviu Podariu UNMC Omaha, NE

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Freesurfer April 2008