Freesurfer

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30131 discussions

RE: [Freesurfer] Measuring cortical thickness with high resolution data
by Nick Schmansky 06 Apr '09

06 Apr '09

Falk, There are no plans in the near future, but in the long term we'd like to remove the dependence on conforming the data. It just occurred to me that you could have the best of both worlds: first run your data through the normal stream (conforming) up through autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same resolution as that created using the -hires stream, and copy it over. At least that would eliminate having to edit the original hires brainmask, which would save hours of work. If i get few minutes i will try this. You can copy that recon-all over top your existing v4.x freesurfer installation (attached again for the list). Nick On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote: > Hi Nick, > > Thank you very much. I'll have to look into that and try to process some other volumes which might work a bit better, with less manual intervention. > > Are there any plans to improve Freesurfer in the (near) future so that hires data can be processed within the currently available stream? > > Regards, > Falk > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Wednesday, April 01, 2009 7:53 PM > To: Falk Lüsebrink > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] Measuring cortical thickness with high resolution data > > Falk, > > Attached is a modified recon-all script where I've added a -hires switch to force the stream to not conform the data to 1mm^3, and to not use the atlases. > > Note that you should add the -clean flag to delete any work that had been done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz). > > However, in working with the .8mm data that you sent me, working with hires data will require quite a bit of manual intervention due to the fact that the atlases normally used cannot be used. The first problem occurs in skull-stripping, where quite a bit of dura and skull remains, and seems to have intensity values close to gray matter. This would have to be manually erased on each of the slices. If it is not erased (I did not do this because of the amount of time required), then the wm.mgz file, which is what is tessellated to create the initial surface, will be very wrong (it tessellates the garbage surrounding the gray matter). > > See also Bruce's prior posting on the problems of working with hires data in freesurfer. > > Nick > > > On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote: > > Hi Freesurfers, > > > > > > > > I’m trying to evaluate the usefulness of high resolution scans > > acquired at 7T with an isometric voxel size of .6mm for the > > measurement of cortical thickness. The inhomogeneities are taken care > > of by dividing the scans with another scan of another sequence, so > > they are not an issue anymore. > > > > > > > > My problem is that Freesurfer usually conforms the voxel size to 1mm > > which is not desirable. I tried using the –cm and –noaseg flags for > > the recon-all process to avoid the conformation and to skip the > > subcortical segmentation, but another problem arises while using these > > flags. > > > > > > > > The error I receive is occurring after the WM Segmentation and states > > as follows: > > > > > > > > #-------------------------------------------- > > > > #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009 > > > > > > > > cp wm.mgz wm.seg.mgz > > > > > > > > > > > > mri_segment -keep brain.mgz wm.seg.mgz > > > > > > > > preserving editing changes in output volume... > > > > doing initial intensity segmentation... > > > > using local statistics to label ambiguous voxels... > > > > computing class statistics for intensity windows... > > > > WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0] > > > > GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0] > > > > setting bottom of white matter range to 77.9 > > > > setting top of gray matter range to 89.4 > > > > doing initial intensity segmentation... > > > > using local statistics to label ambiguous voxels... > > > > using local geometry to label remaining ambiguous voxels... > > > > > > > > reclassifying voxels using Gaussian border classifier... > > > > > > > > removing voxels with positive offset direction... > > > > smoothing T1 volume with sigma = 0.250 > > > > removing 1-dimensional structures... > > > > thickening thin strands.... > > > > 20 segments, 4813 filled > > > > 10270 bright non-wm voxels segmented. > > > > 5589 diagonally connected voxels added... > > > > white matter segmentation took 2.4 minutes > > > > writing output to wm.seg.mgz... > > > > ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 > > height=320. > > > > > > > > The dimensions of the data I’m trying to process is 320 x 320 x 224 > > and is changed to 320 x 320 x 320 while using the –cm flag. It seems > > the mri_segment process can’t handle any dimensions above 256 or I’m > > missing another flag. > > > > > > > > Does someone has any ideas about that issue? > > > > > > > > Regards, > > > > Falk > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Problem changing the colourmap properties of the overlay ...
by Lloyd Elliott 06 Apr '09

06 Apr '09

Hi, I am trying to modify the colour map of an overlay in tksurfer. Unfortunately, the changes I make to the View -> Configure -> Overlay tcl/tk control are either ignored, or end in errors. For example, if I left click on the histogram to set the lower thresh hold, and then click 'coppy settings to layer', then the thresh hold resets to the original value. If I change the X Axis Range manually, for example by entering '6' in the Max edit box, then I get something like this error whenever I try to change something: ERROR updating histo: impossible limits (min 6.73089 >= max 6.73089) for axis "x" I'm guessing that this is a bug --- that is, it's not that I am misusing these controls. I just want the brain to be coloured according to the whole range of values in my w file --- ie, for the heat map, the minimum should be the darkest blue and the maximum should be the brightest red (no gray where I guess freesurfer assumes p>whatever --- this overlay is not a statistical test). Any suggestions? lloyd$ tksurfer --version stable4 lloyd$ uname -a Darwin 307-the-philosophers-foothold.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 surfer: current subjects dir: /Users/lloyd/work/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/lloyd surfer: Reading header info from /Users/mathpunk/work/subjects/AAA03/ mri/T1.mgz surfer: vertices=123084, faces=246164 Thanks! L PS --- a screenshot of these errors: http://mathpunk.churchturing.org/overlay-problems.png

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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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