Freesurfer April 2009

freesurfer@nmr.mgh.harvard.edu

80 participants
131 discussions

Fwd: mri_convert afni to mgz error reading .HEAD
by Andrea Spadoni 05 Apr '09

05 Apr '09

Hi, I'm brand new to this so bear with me, but, why is it that I can't convert my .BRIK to a .mgz file? [usrname@server DIR]$ mri_convert 100032-0104-anat+org.BRIK 100032-0104_surf/100032-0104-anat+orig.mgz [given command] mri_convert 100032-0104-anat+org.BRIK 100032-0104_surf/100032-0104-anat+orig.mgz [error given by program) reading from 100032-0104-anat+org.BRIK... afniRead(): error opening file /dirname1/dirname2/dirname3/dirname4/subnum/DIR/subnum-anat+org.HEAD [usrname@server DIR]$ Thanks, Andrea

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microparcellation
by Jose Luis Cantero Lorente 05 Apr '09

05 Apr '09

Dear Freesurfers, We are trying to subdivide the cortical surface of our average subject into a set of small and compact regions of similar area. Please have a look to the attached file (taken from Hagmann et al. (2008) in PLoS Biol) to have a better idea what I would like to get. We tried it hard by using different strategies, but results were not as expected. Could anybody give me some insights about how to approach this problem by using Freesurfer or Matlab code? Thank you very much in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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FDR
by jitesh kar 05 Apr '09

05 Apr '09

Dear Free surfer Mailing List, This is my first mail as recently I have started using free surfer. I am a research assistant in Neurology, at University of Alabama at Birmingham. I do not have much knowledge about free surfer(I will really appreciate if your reply is simple and has less technical terms) but I try to go through tutorials or free surfer wiki if I have some query. We have some data on picture response time(as a part of sentence comprehension) and we want to correlate the effect of aging on this response time. We are comparing gray matter thickness with picture response time. I tried to run qdec but I am still confused with how to use FDR function? Suppose I select a variable (e.g Picture response time) and run correlation with gray matter thickness, it gives me 4 options: 1. Does thickness differ from zero? 2. Does picture response time correlates with thickness? 3. standard deviation 4. correlation coefficient Now, if I click on no.2 I do get some points on brain which correlates with my variable, does that mean it is significant findings? or do I have to click on "set using FDR"? The problem with using FDR is all my points disappears. I am sorry but I do not have much technical knowledge about free surfer or statistics but I am curious to learn about this. Is it mandatory to click on FDR? - JK

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corpo callosum segmentation
by laura_dg80＠libero.it 04 Apr '09

04 Apr '09

on which basis the Corpo callosum is parcellated in 5 regions? on the basis of some cortical information? there are some reference I can reed ? thank you Laura

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determining sizes of clusters on surface data
by Zhong Jidan 03 Apr '09

03 Apr '09

Hi, I was trying to figure out if there is any way to determine the exact size at which clusters becomes significant given a specified significance on the surface data. Then i found there is a subject talking about this: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.h… In that talk,Don Hagler mentioned Keith Worsley's "Random Field Theory" method (http://www.math.mcgill.ca/keith/fmristat/toolbox/stat_threshold.m) can be used to directly (in seconds) estimate the cluster size thresholds given: ..total surface area ..number of vertices ..fwhm smoothness. function [cluster_threshold,peak_threshold] = fs_calc_cluster_thresh(nverts,area,fwhm,df,alpha,pval); *> % alpha: corrected p-value *>* % {default = 0.05} *>* % pval: uncorrected p-value *>* % {default = 0.001} *I tried this function, and it does give me a cluster size with mm^2, say 100 mm^2. But I don't know whether this is the right thing to do. As I'm doing some statistical analysis using GLM, so I also try the method from Keith Worsley's statistical toolbox, then I can get the cluster's No. of vertices and the corrected p-value(alpha=0.05) for the cluster. Here is one example: clusid nverts resels P --------------------------------------- 1 2205 18.2781 2.1299e-06 2 208 1.42105 0.013359 3 127 1.15533 0.026747 4 58 1.0443 0.036658 5 5 0.519762 0.20884 6 105 0.464429 0.2571 The thing I don't understand is , if we are looking for a cluster size threshold, then we can say that, the clusters above that threshold size is what we want to keep. And also, the p-value of the clusters above that threshold size should be below alpha we set, say 0.05. But when checking the tale above, the first four clusters' p- value is smaller than 0.05, then we should keep it. But according to the no. of vertices, we can caculate the cluster size in mm^2. Then the 4th cluster size is obviously below 100mm^2, the threshold we found using the function fs_calc_cluster_thresh. Oppositely, the 6th cluster has a large no. of vertices and its cluster size is above 100mm^2, while it's not kept because its p value is above 0.05. I know what happened here is because of the 'resels', but it really confuse me which one is the right one. Since you said we can use the function, then why is the result conflicted with each other? Could you tell me what's wrong here or what did I miss ? <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.h…>Thanks a lot, Jidan

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Re: [Analysis-bugs] asegstats2table
by Krish Subramaniam 03 Apr '09

03 Apr '09

Hi Anita Apologies. fsutils is one of the 4 helper scripts that I forgot to put in the distribution. Please get the 4 scripts from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/datastruct_utils… ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/fsutils.py ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/misc.py ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/subject_info.py And put it in your $FREESURFER_HOME/bin directory . ( Anita, in your case put it in /home/anita/freesurfer/bin/ ) and re-run the asegstats2table.. Sorry Krish On Apr 3, 2009, at 11:30 AM, anita di iasio wrote: > Hi all, > I try to run asegstats2table following the tutorial. > I'm using the latest version 1.6.2.2 > The following version appers: > File "/home/anita/freesurfer/bin/asegstats2table", line 6, in > <module> > import fsutils > I don't have idea of what the fsutils module is!!! in the previous > versions (1.6) there isn't mention about it!! > Do you have any hint??? > thank you > anita > _______________________________________________ > Analysis-bugs mailing list > Analysis-bugs(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/analysis-bugs

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WM for ROIs
by Gabriel Go.Es. 03 Apr '09

03 Apr '09

Dear freesurfers im trying to obtain the wm volume for some ROIs created by myself, ando that not fit with the parcellation of FS, i'm using mri_segstats but i can't make it work, can any of you help me? i always recibe a message that says: "in Get MAC Adress (internal) : There was a configuration problem (or no cable !) on your platform: Success ERROR: Option X unknown the X is the name of the --sum, --i, --in or --seg that i write each time i've tried Regards Gabriel _________________________________________________________________ El nuevo Windows Live te une a los que más quieres http://www.windowslive.es

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Writing annotations
by Alex Fornito 03 Apr '09

03 Apr '09

Hi, I've been trying to customize annotation in matlab. Is there anyway to write an annotation our from matlab in a tksurfer-readable format (e.g., the writing equivalent of read_annotation.m)? Alternatively, can you provide some guidance on what the format should be? Thanks for your help, Alex -- Alex Fornito CJ Martin Post-Doctoral Fellow Brain Mapping Unit Department of Psychiatry University of Cambridge Downing Site Downing St, Cambridge UK CB2 3EB Email: af397(a)cam.ac.uk Phone: +44 (0) 1223 764670 Fax: +44 (0) 1223 336581 Australian Details: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 1 & 2, Alan Gilbert Building 161 Barry St Carlton South 3053 Victoria, Australia Email: fornitoa(a)unimelb.edu.au Phone: +61 3 8344 1861 Fax: +61 3 9348 0469

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grey/white matter volumes of cortical ROIs
by Jose Luis Cantero Lorente 02 Apr '09

02 Apr '09

Hi, I would like to obtain gray matter volume (not thickness) values for several new cortical ROIs that I have created with tkmedit, but to my knowledge this is not straight-forward with Freesurfer. We have tried this option: mris_anatomical_stats -l ?h.name.label <subject > Is that correct for my purpose? Could anybody tell me if there is another more correct way to aim this goal by using Freesurfer? How can I get the white matter volume values for the same ROIs? Any help would be very welcome. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Talairach
by Kelly Silva 02 Apr '09

02 Apr '09

Hello, If we have the brains well registered en relation to the Talairach (already checked with TKregister), is there any possibilty that the hemispheres of some subjects could be changed (left hemisphere as right and right as left) in the posterior statistical analysis? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Freesurfer April 2009