Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

error in lme_mass_fit using matlab tools
by Catherine Bois 19 Jun '13

19 Jun '13

Dear Freesurfer experts, I have a question about fitting linear mixed models to mass-univariate data using the lme tools in matlab. I am currently trying to compute the initial vertex-wise temporal covariance estimates by [lhTh0lhRe] = lme_mass_fit_EMinit(X,[2],ni,lhcortex,3] However, I keep getting this error message: Undefined function 'matlabpool' for input arguments of type 'char'. Error in lme_mass_fit_init (line 74) if (prs==1) || (matlabpool('size') ~= prs) Error in lme_mass_fit_EMinit (line 69) [Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs); I have defined X, Y etc according to the previous steps available on the wiki. Would be very grateful for any clarification on why this error message keeps coming up. Thank you very much, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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MRIread.m and hippocampal subfields
by Marcos Martins da Silva 19 Jun '13

19 Jun '13

Hi, Freesurfer experts If you try to read one of the posterior*.mgz files generated by reco-all -hippo-subfield into MatLab/Octave using MRIread.m it fails like this: Ps=MRIread('posterior_left_subiculum.mgz') WARNING: error reading MR params Attempted to access mr_parms(1); index out of bounds because numel(mr_parms)=0. Error in MRIread (line 100) tr = mr_parms(1); That is because the posterior*.mgz files does not have this data. I made a creating a little customized nMRIread.m with the following changes: if numel(mr_parms) > 0 tr = mr_parms(1); flip_angle = mr_parms(2); te = mr_parms(3); ti = mr_parms(4); else mr_parms(1) = 0; mr_parms(2) = 0; mr_parms(3) = 0; mr_parms(4) = 0; tr = mr_parms(1); flip_angle = mr_parms(2); te = mr_parms(3); ti = mr_parms(4); end That works but it is only a quick workaround since MRIread,m calls load_mgh.m and it shows a warning message about the mr_parms. This message does not block my work but it is not good to see the warning all the time on my screen. Perhaps the best fix would be just creating the posterior*.mgz files with these data defined as 0. But I would be happy if I could just "edit" these files defining these values. Is there a freesurfer tool to make this simple edition? I noticed, for example, that when you use mri_concat to sum these files the resulting concatenated file is fixed and these parameters are defined. Thanks in advance, Marcos.

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recon-all error MRIthickenThinWMStrands
by Sudhin A. Shah 19 Jun '13

19 Jun '13

Hi ERROR: MRIthickenThinWMStrands: invalid x,y,z! Numerical result out of range Any tips? S

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Segmentation of MR-PET structurals
by obregon＠nmr.mgh.harvard.edu 19 Jun '13

19 Jun '13

Hi, I've started segmenting several structural scans from an MR-PET study conducted in Bay 7, and was wondering if someone has previous experience working with MPRAGE images acquired using the MR-PET coils? The scans have a very low SNR and I am trying to figure out if this could potentially affect the performance of the automated surface reconstructions. I've scrolled through the volumes and even though the surfaces seem normal, I am somewhat skeptical about their true quality given that intermediate stages, such as the intensity normalization, seem to be failing (please find an example from one of the brain masks attached). Is it essential to filter the raw structurals before segmenting them, and if so, are there any readily available denoising tools? Furthermore, are there any additional issues I should take into consideration? Thanks for your help! Gabriel

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IOError: [Errno 13] Permission denied: 'aseg_stats.txt'
by Varghese Chikku 19 Jun '13

19 Jun '13

Dear FS team, I tried to run this command asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt But got this error,permission denied, SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Building the table.. Writing the table to aseg_stats.txt Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 517, in <module> write_table(options, rows, columns, table) File "/usr/local/freesurfer/bin/asegstats2table", line 462, in write_table tw.write() File "/usr/local/freesurfer/bin/datastruct_utils.py", line 58, in write fp = open(self.filename, 'w') IOError: [Errno 13] Permission denied: 'aseg_stats.txt' freesurfer@freesurfer-VirtualBox:/usr/lib$ Many thanks Chikku

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Re: [Freesurfer] problem downloading Xhemi files
by Douglas Greve 19 Jun '13

19 Jun '13

try now On 6/18/13 9:37 PM, amirhossein manzouri wrote: > I have version 5.1 so please recreate the links! > BR > > > On Tue, Jun 18, 2013 at 8:43 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Amir, if you are using 5.2 or 5.3, then you should already have > it. If not, I'll have to recreate the links. let me know > doug > > > On 6/17/13 6:52 AM, amirhossein manzouri wrote: >> Dear Doug, >> I can not download the files needed for Xhemi in mentioned link. >> Would you please advise how to download them? >> >> -- >> Best regards, >> Amir >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > -- > Best regards, > Amirhossein Manzouri > >

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qdec differences in FS 5.0 vs 5.3
by Maria Kharitonova 19 Jun '13

19 Jun '13

Hi, I'm learning how to use QDEC and was comparing results that it produces under FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS or DOSS method of producing a design matrix, while the 5.3 only has DODS. This suggests that results should be identical (or at least similar) across versions if I select DODS. However, I'm getting very different results based on the version I select: complete lack of differences across groups in 5.3 and a predicted pattern of differences in 5.0 using DODS. I'd like to understand where the differences are stemming from -- any ideas? Thanks in advance! Maria ******************************* Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital

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How to make inflated or white/pial surface of fsaverage atlas
by 堀川友慈 18 Jun '13

18 Jun '13

Hi, I have a question about how to make surfaces in shape of inflated or white/pial (fiducial) surface for the fsaverage atlas. In my understanding, to make a population average surface from multiple individual surfaces, the surfaces should be first in shape of sphere. But, I'm not clear how can we obtain population average surface in shape of inflated and original white/pial surface which do not depend on specific individual. This is my question. Freesurfer seems to have such surfaces like inflated.avg or white.avg. And from the logs for creating fsaverage (make_average_surface.log), it seems that this is done by averaging individual surfaces after being transformed into each type of configuration(inflated, white, etc...). But in that case, what was averaged for example in case of averaging inflated surface? 3D coordinate (x,y,z)? But if so, it will lose the topology of cortical surface. If you have any answers or comments to this question, please give some advice. Regards, Tomoyasu ++++ HORIKAWA Tomoyasu ATR CNS Dept. of Neuroinformatics

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Fs Tutorial data bert.recon.tgz md5sum mismatch
by ye tian 18 Jun '13

18 Jun '13

Dear freesurfer support group, I keep getting 9a5dcc7ebb7aa8564c4bba47ef0293e9 as the md5sum for the bert.recon.tgz file which I downloaded from the following link ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz The correct md5sum is supposed to be 04d6fa1703787e546aaafbfade17cab2. I downloaded the file several times with different terminals, using the command curl -O. I do get the correct md5sum for fsfast-functional.tar.gz, fbert-feat.tgz, diffusion_recons.tar.gz and diffusion_tutorial.tar.gz. I haven't completed downloading the other three files. I will write to you if I have similar problems, too. Do you, by any chance, have a different version of bert.recon.tgz on that link? Thank you very much! Sincerely, Ye Tian

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ERROR! FOV=348.000 > 256
by Ray, Siddharth 18 Jun '13

18 Jun '13

Hi all, I am coming across this error for couple of my subjects: WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (240.00 mm, 240.00 mm, 347.20 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 348 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) ==================================================++++++++++++++++++++++++=============== $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/sray2/Data/50183/50183/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (0.468746, 0.468746, 1.4) mm size and (512, 512, 248) voxels. Data is conformed to 1 mm size and 348 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/sray2/Data/50183/50183/mri/orig.mgz... **************************************** ERROR! FOV=348.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux localhost.localdomain 2.6.32-71.el6.x86_64 #1 SMP Wed Sep 1 01:33:01 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 50183 exited with ERRORS at Sat Jun 15 06:02:30 CDT 2013 Do anyone know whats wrong and how can I fix this? Thanks in advance. -Siddharth

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Freesurfer June 2013