Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

Issues with Cluster generation
by Joshua deSouza 03 May '13

03 May '13

Hello all, I am facing a problem whereby after running GLMfit and cluserwise correction for multiple comparisons using the monte-carlo method, I was unable to generate any clusters. I do have significant images produced for the glmfit. All procedures were done according to the tutorial to match the effects under FSGD. There are no clusters available even when I set the cwpvalthresh to .999 which is supposed to show all clusters. What is the cluster generation dependent upon? As my glmfit does show significant areas. Please advise

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epi correction of fmri data
by Corinna Bauer 03 May '13

03 May '13

Is there a way to correct fmri data for epi distortions in freesurfer? Or does the data need to be first fun through FSL's B0 unwarping? Corinna

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Re: [Freesurfer] Longitudinal analysis of one timepoint
by Sarah Whittle 03 May '13

03 May '13

Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah .... Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote: > Hi Freesurfer experts, > > > > This week a read the article of Bernal-Rusiel et al. titled > “Statistical analysis of longitudinal neuroimage data with Linear > Mixed Effects models”. In this article you described the submission of > single time-point scans to the longitudinal pipeline of Freesurfer. > I’m very interested in how to do this. Your help will be appreciated. > > > > Thanks in advance, > > > > Henk-Jan > > > > ______________________________________________________________________ > > De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de > afzender direct te informeren door het bericht te retourneren. Het > Universitair Medisch Centrum Utrecht is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van > Koophandel voor Midden-Nederland onder nr. 30244197. > > Denk s.v.p aan het milieu voor u deze e-mail afdrukt. > > > ______________________________________________________________________ > > This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the sender > immediately by return e-mail. University Medical Center Utrecht is a > legal person by public law and is registered at the Chamber of > Commerce for Midden-Nederland under no. 30244197. > > Please consider the environment before printing this e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Question
by Jerskey, Beth 03 May '13

03 May '13

What effect, if any, would the implantation of a Vagus Nerve Stimulator have on registration? Thank you, Beth

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tracula FS 5.2
by Antonenko, Daria 03 May '13

03 May '13

Hi FS experts, I tried to run Tracula with the new FS 5.2 release and came across memory allocation problems in the preprocessing step and would appreciate some advice on solving them: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 i686 i686 i686 GNU/Linux trac-preproc exited with ERRORS at Tue Apr 9 22:21:43 CEST 2013 I attached the log-file. Let me know if you need further information about my system. Thank you in advance, Daria

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Flattening a specific surface parcellation or a group of spatially adjacent parcellations
by Bilal Ahmed 02 May '13

02 May '13

Hi, I was wondering if there is a simple way to flatten specific surface parcellations without manually specifying cuts. For example if I want a flattened patch pertaining to the left temporal pole for fsaverage, I would have to manually specify the cut points and then extract and flatten it. As we already know the boundary for this parcellation can we use this information to automatically extract the patch and then flatten it, by providing the boundary points as the cut points? thanks,

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mri_convert Segmentation fault (core dumped) lubuntu 13.04
by Joerg Pfannmoeller 02 May '13

02 May '13

Dear freesurfer administrators, recently upgraded our system to freesurfer 5.2 on lubuntu 13.04. After the installation I accounted problems when testing freesurfer. tkmedit did not display the subject bert, instead an error message was shown: tkmedit bert orig.mgz =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : Content of .xdebug_tkmedit is: tkmedit started: Thu May 2 08:44:48 2013 /usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /home/mrt-physician/subjects Set subject home dir to /home/mrt-physician/subjects/bert Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x284adf70, isSource=/home/mrt-physician/subjects/bert/mri/orig.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=/usr/local/freesurfer/tktools/tkmedit.bin ) 02: Loading volume orig.mgz 01: main() 01: Parsing command line arguments 00: 00: As I found in the web this problem seems to be due to mri_convert on fedora 18 (https://bugzilla.redhat.com/show_bug.cgi?id=905638) This bug is know reproduced for lubuntu 13.04. The output if mri_convert ist called is the following: cd $SUBJECTS_DIR mri_convert sample-001.mgz test.mgh $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... Segmentation fault (core dumped) Is there a bugfix? Sincerely yours Joerg

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Inputting specific talairach coordinates?
by Natalie Garcia 02 May '13

02 May '13

Dear FreeSurfers, I have a very basic question (which I'm hoping also has a basic answer!): I know that the Talairach coordinates provided in tksurfer are based on a conversion using MNI space, but I'm wondering: is there a way to input specific Talairach coordinates into Freesurfer to identify a specific ROI, then use those those coordinates can be examined across different surfaces (i.e. different subjects)? Any help would be greatly appreciated! All my best, Natalie -- Natalie V. Garcia Doctoral Graduate Student Cognitive Neuroscience The Pennsylvania State University 106 Chandlee Phone: (814) 863-0159 Alt. Email: nvg109(a)psu.edu

1 0

ROI analyses
by Tudor Popescu 02 May '13

02 May '13

Dear Freesurfers, I am doing an ROI analysis (group comparison) of cortical thickness, and I have some questions that I could use some help with. Many thanks in advance! Tudor 1) I used aparcstats2table to extract CT values for structures from the Destrieux atlas, but I cannot identify some important cortical structures among the names in that list. For example, I don't see anything corresponding to the Superior Parietal Lobule, or the Intraparietal Sulcus (the latter actually does appear but is coupled with another structure, under the name "lh_S_intrapariet_and_P_trans_thickness") 2) Can the same table (of the average CT of each cortical parcellation) be extracted using parcellations based on an atlas other than the Destrieux (e.g. the Harvard-Oxford, or the Julich)? 3) (I can't see whether there's a tutorial for this, as the main FS site seems to be down at the moment) How can a group comparison of CT be done inside a given ROI, and in what ways can the ROI be specified? I guess the command line version of QDEC would produce, in this case, the same contrasts as QDEC, but within the ROI as opposed to the whole brain 4) How do the results of these two different types of ROI group analyses differ, and is one of them more "correct" than the other: A) running the command prompt version of QDEC within the confines of a certain atlas-defined ROI, and looking at the resulting statistical map (clusters), as per question 3; B) extracting the CT values for that ROI for all subjects using aparcstats2table, and doing t-tests to look for a group difference.

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(no subject)
by Ashley Hannah 02 May '13

02 May '13

Has anyone ever ran a post contrast sequence in FreeSurfer? Thanks, Ashley -- * *

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