Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

failed Talairach quality check; alternatives?
by Jeff Phillips 21 Jan '09

21 Jan '09

Hi all, I have an MPRAGE which consistently fails the Talairach quality check (see attached error) in autorecon1. (A 32-channel coil was used in this scan, and I suspect that might be a cause of the failure.) Per the wiki's suggestion, I have tried to manually fix the transform in tkregister2 and rerun reconstruction, but despite multiple attempts, I haven't been able to get a transform which satisfies the quality check. From similar list posts, I thought it might be possible for me to Talairach in an external program (BET, AFNI, etc.) and create a transform file that FreeSurfer can read. If this is possible, could you give me an overview of the process, or point me to existing documentation? Thanks, Jeff Phillips

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contrast + interpretation
by Siddharth Srivastava 21 Jan '09

21 Jan '09

Hi group, I have some questions about the interpretation of my results based on the contrasts that i have used in my analysis. It is, i am sure a very basic question, and i would like to check if my interpretation of the results is correct/valid. I have 2 groups, and 1 variable, and i am setting up a dods design, hence i have used 4 regressors. I query with a contrast vector of [0 0 1 -1], intending to discover regions where the measure x variable interaction between the groups is significant. Am i correct in the interpretation of the design and contrasts so far? In case yes, does the sign of the value in sig.mgh file indicate the direction of the interaction (i.e +ve values for positive correlation, and vice-versa) ? I realize that i am using "interaction" and "correlation" interchangeably: is this valid? How do i proceed from inferences about interactions to statements about correlation? thanks, sid.

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Registered or not?
by Jürgen Hänggi 21 Jan '09

21 Jan '09

Dear FS experts We divided the parcellations aparc.a2005s into about 1000 smaller parcellations and would like to compare the cortical thickness of these parcellations across subjects. Due to the fact that the parcellations aparc.a2005s are in the native space of each subject I am wondering whether I have to register the divided parcellations in order to be sure that the finer parcellations (1000) are in spatial correspondence across subjects. If I have to spatially register them, how to do this? Thanks in advance Reggards Jürgen ---------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------

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Subdividing the automated cortical parcellation
by Diana Wotruba 21 Jan '09

21 Jan '09

Dear experts Using cortical thickness analysis with Freesurfer I would like to compute small world network indices in a special population. The automated parcellating system is resulting in 66 cortical areas. For our purpose, I would like to subdivide these areas into smaller ones. (A similar methodology was applied by Hagmann et al., PLoS Biol 6: 14791493, 2008.) Does a finer parcellation scheme become part of future Freesurfer releases? Or have someone some experience in such a procedure? Any information would be much appreciated. Kind regards Diana Wotruba

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talairach registration
by Lucia Garrido 21 Jan '09

21 Jan '09

Dear freesurfers, I'm having some troubles deciding whether the output from the Tailarach registration is good or not. I don't have hugely distorted brains as can be seen in the tutorials. But though they seem roughly aligned, there are some cases in which it seems it could benefit from changing the moveable image. In some cases, it seems that the moveable image is slightly 'smaller' than the actual brain. In other scans, it seems it could be slightly rotated. I'd be very grateful if you could check those images and let me know if this output is 'normal' or if I should improve it. Could I send you those images? What be the best way to do that? Finally, I'd be very grateful if you could let me know for which stages of the analysis is the Talairach transformation needed. I'm doing morphometry and pretend to compare cortical thickness between 2 groups. As far as I understand, the transformations are needed to be able to report the coordinates of results. Is that right? Are they needed for any other step? Thanks very much. Best regards, Lucia

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Smoothing
by Rodd Pribik 20 Jan '09

20 Jan '09

Hello All, Is it possible to adjust the amount of smoothing? I am interested in making my surfaces a bit rougher. Thanks, Rodd

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Problem with lgi
by Christian Scheel 20 Jan '09

20 Jan '09

Dear all, I am trying to compute the local gyrification index but unfortunately encounter the problem below. Matlab Version (7.7.0.471 - R2008b) and also the Image Processing Toolbox are installed on my computer. As I understand 'make_outer_surface' does not find 'tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz'. However when checking the surf directory I can see that tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz exists. So maybe it is just a path problem? Any help is greatly appreciated! Best wishes, Christian Scheel --- Here is the output: [root@localhost christian]$ recon-all -s bert -localGI Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /home/freesurfer/christian Actual FREESURFER_HOME /usr/local/freesurfer_410 -rw-rw-r-- 1 freesurfer freesurfer 906671 Jan 20 14:30 /home/freesurfer/christian/bert/scripts/recon-all.log Linux localhost.localdomain 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer_410 Previous: /space/freesurfer/build/pub-releases/freesurfer /home/freesurfer/christian/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Jan 20 14:43:39 CET 2009 mris_compute_lgi --i lh.pial ================= rm -Rf tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= ---------------------------------------------------------------------------- Warning: glibc 2.3.4 - Your version glibc 2.3.6 - MATLAB built using this version ---------------------------------------------------------------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.7.0.471 (R2008b) September 17, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... zcat: tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz: No such file or directory ERROR: problem reading fname ??? SWITCH expression must be a scalar or string constant. Error in ==> load_mgh at 158 switch type Error in ==> MRIread at 88 [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly); Error in ==> make_outer_surface at 24 vol=MRIread(filled_volume); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Jan 20 14:43:55 CET 2009 [root@localhost christian]$ -- Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger

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topo_defect_before subject
by Sam Torrisi 20 Jan '09

20 Jan '09

Hi all- I'm doing the online tutorial and I can't find the subject topo_defect_before as instructed in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData i've downloaded all the data except for the Feat-related stuff. Am I missing something? I apologize in advance for a potentially annoying newbie question. THANKS -Sam

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bad pial surfaces
by Derin Cobia 19 Jan '09

19 Jan '09

Any suggestions on how to correct the pial surface on this subject? The wm.mgz volume appears to be segmented properly, yet there are many 'strands' of gray matter in the left temporal lobes left outside of the pial surface. We have several like this; subjects are diagnosed with primary progressive aphasia. Thanks. -Derin

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mri_convert
by Feng-Xian 19 Jan '09

19 Jan '09

Hi, I am finished to run my subjects using recon-all and I would like to know the usage of mri_convert to convert the results of FreeSurfer into the analyze format or nifti. Some of the results of FreeSurfer are volumes (e.g. brainmask.mgz) and some of them are surfaces (e.g. lh inflated). What can I do to convert these formats to analysis format or nifti? Thanks in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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