Freesurfer April 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
102 discussions

resend: remaining questions about average subjects
by Mischka Gerken 19 Apr '08

19 Apr '08

Hello to the kind folks at FreeSurfer. I'm resending this e-mail as I'm thinking it may not have come through.. We have some remaining questions surround average subjects and group analysis: 1) In visualizing the surface of an average subject (such as when running QDEC analyses) the brain surface seems to be "incompletely inflated" compared to viewing a single subjects inflated hemisphere in tksurfer (major sulci still show depressions on the average subjects surface). What is the reason/explanation for this? 2) The main discussion I have seen on the validity of using an average subject vs a custom one (M. Harms and Mr. Fischl) have centered around registration. If I understand correctly, registration will align various surfaces (and thereby influence which voxels fall into a particular ROI/label), but will not substantively change the thickness values of the surfaces in question. Is this correct? If this is so, it would appear that the primary issue with using the buckner40 average subject would be the mapping of vertices into various regions, but that this would NOT interfere with generating accurate statistical maps of thickness measures for ones own data set. I can see that imperfect alignment of vertices across a group may introduce errors in the averages for a given point. It seems make_average_subject essentially does precisely this, so accurate registration for a particular population would maximize the accuracy of any given vertices average. Is this what making a custom subject atlas seeks to do: the make the registration between subjects in an average as "linear" as possible to maximize the accuracy of each averaged vertex? If anyone could answer this issue for me/point me towards a more complete resource I would very much appreciate it. 3) There has been an exchange between Graham Wideman, Mr. Fischl and Mr, Greve about creating one's own average subject. Mr. Greve metioned adding "hooks" into make_average_subject in order to make the generation of a custom atlas more accessible (and then using -surfreg-to-subject in the recon-all stream). Is there any documentation/further explanation of what these hooks are and how to go about completing this process (can't find anything on the wiki)? Many thanks in advance! -Mischka

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LGI: EXITS with ERRORS
by Juranek, Jenifer 19 Apr '08

19 Apr '08

I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my new 64bit linux box running RHEL 5 (Tikanga). I didn't see any special notes on the download page for RHEL 5 (only RHEL 4 is noted). While test-driving my first dataset through the fsv403 pipeline, I encountered some difficulties with my explorations of the new feature of calculated local gyrification index. I tried the following cmd lines...each yielded the same standard out message pasted below Any ideas? Jenifer [jjuranek@localhost subjects]$ recon-all -subjid SB_09_H20089 -localGI [jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 [jjuranek@localhost subjects]$ recon-all -lgi -sid SB_09_H20089 [jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 jjuranek jjuranek 768975 Apr 18 17:30 /usr/local/freesurfer/subjects/SB_09_H20089/scripts/recon-all.log Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/SB_09_H20089/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Apr 18 17:45:32 CDT 2008 mris_compute_lgi --i lh.pial Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Apr 18 17:45:32 CDT 2008

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LocalGI:exit with errors
by yczhang 18 Apr '08

18 Apr '08

Hi, I download the Freesurfer 4.0.3 and installed it on linux,I tested it on the subject bert which is included in /freesurfer/subjects, I run "recon-all -s bert -localGI" but it exited with errors as follows: lGI for vertex number 20101 of the outer mesh is 3.0478 lGI for vertex number 20201 of the outer mesh is 3.0267 lGI for vertex number 20301 of the outer mesh is 2.4033 lGI for vertex number 20401 of the outer mesh is 3.2432 lGI for vertex number 20501 of the outer mesh is 1.7832 lGI for vertex number 20601 of the outer mesh is 2.5316 lGI for vertex number 20701 of the outer mesh is 2.4154 lGI for vertex number 20801 of the outer mesh is 3.2481 lGI for vertex number 20901 of the outer mesh is 1.2247 lGI for vertex number 21001 of the outer mesh is 2.7509 lGI for vertex number 21101 of the outer mesh is 1.9534 WARNING -- Problem for vertex iV = 21201, lGI value is aberrantly high (lGI=47.7803)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. >> ERROR: compute_lgi did not create output file 'tmp-mris_compute_lgi/rh.pial_lgi.asc'! Linux bioinformatics-desktop 2.6.22-14-generic #1 SMP Sun Oct 14 23:05:12 GMT 2007 i686 GNU/Linux recon-all exited with ERRORS at Sat Apr 19 03:56:52 CST 2008 could you help me? yczhang 2008-04-19

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"Talairach failure detection" in longitudinal processing
by Sky Raptentsetsang 18 Apr '08

18 Apr '08

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subcortical segmentation
by abel cruz vadell 18 Apr '08

18 Apr '08

Hello Im doing a thalamus volumetric analysis between two populations and checking the thalamus segmentation I found some pixels classified as white matter hipointensities inside the thalamus. Do they affect the volume measure of this structure reported by FreeSurfer. In the positive case, how can I fix that problem? I attached an image. Thanks Abel ______________________________________________ Enviado desde Correo Yahoo! La bandeja de entrada más inteligente.

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Monte Carlo Simulation w/ custom design matrix
by Jerry Yeou-Wei Chen 18 Apr '08

18 Apr '08

Hello, I have a question regarding performing Monte Carlo simulations when a custom design matrix is being used. The wiki says that "For both MC simulations, you must supply the smoothness of your data as Full-Width/Half-Max (FWHM) of the residual. This can be obtained from the ResidualFWHM value in y.fsgd in the glm output directory." If I understand correctly, this means that the --fwhm flag should be specified when running mri_glmfit to generate CSD's... However, when running a custom design matrix, the y.fsgd file is not generated (since the --fsgd flag cannot be specified at the same time as --X). So, my question is: how do I get the required FWHM value? Thanks, - Jerry

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Re: [Freesurfer] qdec error
by Sky Raptentsetsang 17 Apr '08

17 Apr '08

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qdec error
by Sky Raptentsetsang 17 Apr '08

17 Apr '08

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Re: [Freesurfer] qdec error
by Sky Raptentsetsang 17 Apr '08

17 Apr '08

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Qdec on leopard
by Alex Fornito 17 Apr '08

17 Apr '08

Hi, I've just installed version 4.0.3 for leopard and can't open qdec. I get the error below. Any help is appreciated. Alex qdec & [1] 956 [pspc83:MRI_data/freesurfer/subjects_cann] alexfornito% X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 1605 Current serial number in output stream: 1605

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Freesurfer April 2008