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30090 discussions

export the ROIs in 'Desikan-Killiany' cortical atlas
by Yang, Daniel 20 Jun '13

20 Jun '13

Hi FreeSurfer expert, I am interested in a particular region of the Desikan-Killiany atlas and I'd like to use it as an ROI image mask in my fMRI analysis. Could you please suggest how I can do that? From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) I see that the DK atlas files are located here: $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs Question 1: how can I read this GCS file? Question 2: After I read this GCS file, how can I create an ROI image mask? I am thinking to use the WFU PickAtlas to create an ROI (http://fmri.wfubmc.edu/software/PickAtlas) Would it be a good fit? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Longitudinal processing
by Linn Mittlestein 19 Jun '13

19 Jun '13

Dear Freesurfer group. I am having some concerns about Freesurfer and the different steps. I have used version 5.0 for the cross-sectional timepoints, and I am now using version 5.3 for the longitudinal processing. I am doing therefore the several different steps involved in longitudinal processing, for example -base, -long runs and now for the lme analysis with matlab also the smoothing steps etc. I am very concerned however because looking at the brain masks after these steps have been done (ie the cross-sectional runs), they look much worse than they did before the longitudinal editing began; large chunks of surfaces are missing. Has anybody else reported this problem? Could it be because the longitudinal steps are now being done with version 5.3 as opposed to 5? Surely this should not have such a large effect on the brainmasks, as to completely "deform" them? Kind Regards, Linn

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mri_convert segmentation fault in bash
by Caspar M. Schwiedrzik 19 Jun '13

19 Jun '13

Hi Freesurfers, I am getting a segmentation fault with the 4.5 version of mri_convert when trying to convert an AFNI BRIK file into nii. This is my command line: mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii Strangely, I only get the segmentation fault when I run mri_convert in a bash script, in which case it is called like this: `mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii` When I run mri_convert from the command line, no segmentation fault occurs. Any advice? Thanks, Caspar

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mri_convert and flips
by Ray, Siddharth 19 Jun '13

19 Jun '13

Hi all, I have some of my subjects with their A/P and L/R labels flipped and using mri_convert convert command to make them right. I was little concerned that I am just providing command with -in_ourientation and -out_orientation info to get the right labeled images, is this anyway going to change my actual image data/pixel values? Please let me know. Thanks, -Siddharth

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Re: [Freesurfer] check orientation
by Bruce Fischl 19 Jun '13

19 Jun '13

Hi Brigitte, could you cc the list so that others can answer? I'm not sure what qualifies as "turned around" in FSL. They may have some preferred oreintation. In general we don't, and as long as the direction cosines are preserved (i.e. avoid analyze format!) you should be fine Bruce On Wed, 19 Jun 2013, Brigitte Dahmen wrote: > Dear Bruce, > thank you very much! > Please excuse a (potentially naive) follow-up question (as we didn't use > external markers): So if in FSL some raw T1 data are found to be "turned > around", is it something that Freesurfer "takes care of" at a certain point > in the analysis or would you suggest to swap/correct the data after checking > w/ FSL and then analyze them with Freesurfer? > > Thanks again and kind regards! > Brigitte > > > 2013/6/19 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Brigette, > > not sure how you could do this except visually. Bring the images > up and verify that the directions that we specify are correct > (although of course this isn't possible for L/R unless you have > some type of external fiducial marker like a vitamin E tablet) > > cheers > Bruce > On Wed, 19 Jun 2013, Brigitte Dahmen wrote: > > Dear Freesurfer experts, > > is there a command in Freesurfer to check for > correct orientation (LAS vs. > PSR) of T1 images (similar to "fslhd" in FSL)? > > Thank you very much! > Brigitte > > > > > 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. > > > >

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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.

2 1

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

2 1

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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