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30085 discussions

Mri_glmfit, paired analysis protocol
by Stidd, Reva (NIH/NIMH) [F] 20 Jan '10

20 Jan '10

Hi there, I'm trying to compare a sample with a T1 and T2 for each subject using the paired analysis protocol. I've completed everything *except* for the mri_glmfit step without error. I think it might have to do with the way my second FSGD file was created/saved. The command I'm entering and the subsequent error message is below: CHP-MP6:subjects revastidd$ mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C intercept.mtx --glmdir lh.longitudinal_age.glmdir gdfReadHeader: reading paired-diff.fsgd ERROR: FSGDF version 0 unsupported (paired-diff.fsgd) CHP-MP6:subjects revastidd$ My paired-diff.fsgd file was made in TextEdit: GroupDescriptorFile Class Main Variable Gender Input sub1pair Main 1 Input sub2pair Main 1 Input sub3pair Main 0 Input sub4pair Main 0 Input sub5pair Main 1 Input sub6pair Main 1....... FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Kernel info: Darwin 9.8.0 i386 Current Working Directory: /Applications/freesurfer/subjects Which freesurfer: /Applications/freesurfer/bin/freesurfer Please let me know if you need anything else! Thank you so much, -Reva

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WM.mgz corrections in the ventricles & Individual Normalization
by Sherri Novis 19 Jan '10

19 Jan '10

Hello - I have two questions: 1) I noticed on wm.mgz volumes that were segmented properly, that even when the ventricles were automatically filled in, on some slices they are somewhat patchy (partially filled in with white, with some black/blank voxels). Do these patchy wm fill-ins require manual fill-ins to make them entirely opaque? I went through the tutorial, and it was not clear whether a patchy fill-in required a correction or not. 2) What is the best automated measurement that can be used to normalize an individual's cortical segmentation volumes for between subject comparison? We have been using gray+white volumes (why we need the ventrical volume processing to be consistent) - but not sure if ICV would be better individual normalizer. Thank you for your time - Sherri

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FreeSurfer two atalses
by Guang Zeng 19 Jan '10

19 Jan '10

Hi, there, Are there any place in FreeSurfer Wiki or journal paper explain why FreeSurfer need to atlases; Subcortical and Surface? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/

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Vol index to Talairach
by Oya, Hiroyuki 19 Jan '10

19 Jan '10

Dear experts, I like to find Tarairach and MNI coordinate from volume index (data has been already processed with recon-all) off line using Matlab. Which transform should I use to find it ? Thank you. Hiroyuki

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brainmask
by Satrajit Ghosh 19 Jan '10

19 Jan '10

if one wants to get at the brain only (similar to bet), is brainmask.mgz the best file to use? on some of our data, we are noticing a lot of eyeball. i presume one can use aseg as an alternative. is this more recommended than brainmask.mgz? also, is the total brain volume computation based on aseg or some other file? cheers, satra

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Paired Analysis, Smoothing Step
by Stidd, Reva (NIH/NIMH) [F] 19 Jan '10

19 Jan '10

Hi there, I've got a sample of subjects with T1 and T2 scans that I'm trying to compare. I did the entire longitudinal stream protocol, and am now doing the paired analysis protocol. I'm stuck on the Spatial Smoothing step: I've only gotten either a ">" or a message reading, "ERROR: Option -sval unknown." Is there any reason why? Thanks, -Reva ---------------------------- CHP-MP6:subjects revastidd$ ls (all *.long.* files, base files and timepoint scans are listed plus the following files/folders:) 12SIB FSGD README Random Output V1_average bert fsaverage lh.paired-diff.thickness.mgh mris_preproc.surface.lh.log mris_preproc.surface.rh.log random rh.paired-diff.thickness.mgh sample-001.mgz sample-002.mgz wmparc.vol.table CHP-MP6:subjects revastidd$ mri_surf2surf --s fsaverage --hemi lh --fwhm 5 \ --sval lh.paired-diff.thickness.mgh \ --tval lh.paired-diff.thickness.sm05mgh ERROR: Option --sval unknown CHP-MP6:subjects revastidd$ mri_surf2surf --s faverage --hemi lh --fwhm 5 \ --sval lh.paired-diff.thickness.mgh \ --tval lh.paired-diff.thickness.sm05.mgh \ FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Kernel info: Darwin 9.8.0 i386 Current Working Directory: /Applications/freesurfer/subjects Which freesurfer: /Applications/freesurfer/bin/freesurfer I've also attached a screenshot of the current files in my subject directory. Please let me know if you need anything else. Thank you for your help! -Reva

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number of vertices per hemisphere using mri_glmfit
by Stefan Brauns 19 Jan '10

19 Jan '10

Hi there, I am running surface based analysis of cortical thickness using FreeSurfer. Sometimes I constrain the analysis to certain regions of the brain, e.g. only frontal lobes. I would like to find out how many vertices per hemisphere are analysed with the mri_glmfit I am running. Is there a possibility to get these values from any of the log-files? What is the usual number of vertices per hemisphere? Many thanks, Stefan

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a question about rebuild_gca_atlas.csh
by Guang Zeng 19 Jan '10

19 Jan '10

Hi, there, In rebuild_gca_atlas.csh, I read something like: # A talairach registration should be generated for this first subject as well, # in order to align the final atlas to the Talairach space. Is this talairach registration file the same as the talairach.xfm under each subject's /mri/transforms/ direcotry? Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/196390709/direct/01/

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fs-fast sfa-sess retinotopy error
by Jason Connolly 19 Jan '10

19 Jan '10

Dear freesurfer experts: I am new to fs-fast and I am currently running sfa-sess on some retinotopy data and I think the main error is "cannot determine format of 005/f" I read in a previous post related to retinotopy that you need to add the full path to the .nii files and then it will work. My question is: where do you add the full path? Many thanks, Jason. Error message: sfa-sess -analysis rtopy -s jason-functional -------------------------------------------------------------- sfa-sess logfile is /usr/local/freesurfer/subjects/jason/brainmapper/log/sfa-sess-bold-rtopy-1001181608.log -------------------------------------------------------------- ------------------------------------------- /usr/local/freesurfer/subjects/jason/brainmapper/jason-functional Mon Jan 18 16:08:48 GMT 2010 INFO (jason-functional): RunList = 005 007 012 013 -------------------------------------------------- /usr/local/freesurfer/subjects/jason/brainmapper/jason-functional/bold selfreqavg -TR 1.5 -o rtopy/polar/h -i 005/f -i 007/f -i 012/f -cfg /usr/local/freesurfer/subjects/jason/brainmapper/rtopy/analysis.cfg -parname rtopy.par -------------------------------------------------- --- Parsing Config File: /usr/local/freesurfer/subjects/jason/brainmapper/rtopy/analysis.cfg ---- -ncycles 15 -delay 0 -nskip 0 -fwhm 0 DirectionList: +1 -1 +1 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 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Extension format = >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> nii >> >> >> >> >> >> >> hanrad = 0 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ERROR: cannot determine >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> format of 005/f >> ??? Attempt to reference field of non-structure array. >> ??? Attempt to reference field of non-structure array. >> ??? Attempt to reference field of non-structure array. >> >> ??? Attempt to reference field of non-structure array. >> >> ??? Undefined function or variable 'lastslice'. >> ??? Attempt to reference field of non-structure array. >> >> >> ??? Attempt to reference field of non-structure array. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Index exceeds matrix dimensions. >> >> >> >> >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >> >> >> >> >> >> >> >> >> >> >> >> >> Slice >> ??? Undefined function or variable 'lastslice'. >> >> >> >> ??? Attempt to reference field of non-structure array. Error in ==> MRIwrite at 94 hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> ??? Attempt to reference field of non-structure array. Error in ==> MRIwrite at 94 hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> ??? Attempt to reference field of non-structure array. Error in ==> MRIwrite at 94 hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> >> Saving header to rtopy/polar/h >> >> >> selfreqavg COMPLETED mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 niiRead(): error opening file rtopy/polar/h.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from rtopy/polar/h.nii...

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mri_glmfit-sim and longitudinal analysis
by Thomas, Adam (NIH/NIMH) [E] 18 Jan '10

18 Jan '10

I have a small group of subjects where each subject has been scanned once a week for five weeks while learning a task. I'd like to look for changes in cortical thickness across the scans. I've already looked at grey matter density in FSL using randomise (http://www.fmrib.ox.ac.uk/fsl/randomise/index.html) for clusterwise multiple comparison correction and would like to do something similar for cortical thickness. It doesn't look like mri_glmfit-sim allows you to specify exchangeability blocks so that scans are only swapped with scans of the same subject in the simulation. Or can it do this and I'm just not seeing it? Any other recommendation on how to approach this analysis in FS? Thanks, -Adam --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room 1D80 Bethesda MD. 20892-1148 Phone: 301-402-6351

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