Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

editsFail
by Timothy Quang-Tin Le 15 Oct '15

15 Oct '15

Hello, I am using free surfer version 5.0.0; how do I continue to edit the brain with the previous edits made if the brain was processed under applyEdits, but is now in editsFail? Does this mean that I have to redo the entire brain, or can I have it restored somehow? Thank you Timothy Le

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Make average subject from additional data
by Jones, Richard 15 Oct '15

15 Oct '15

I have a group of subjects that I have run through the standard freesurfer (version 5.3) pipeline, for the same subjects I also have T2 volumetric data and I have created T1/T2 ratio images for each subject. I have registered the ratio images into Freesurfer space and used mri_vol2surf to create surface overlays at different depths into the cortex for each subject, and these look reasonable when displayed with freeview. I now want to create average subjects for the ratio images at each depth, but I'm not sure what's the best way of doing this? Any suggestions would be appreciated. Thanks, Richard

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error using mri_glmfit
by Gold, Andrea (NIH/NIMH) [F] 15 Oct '15

15 Oct '15

Hi, I got the following error during my first time running the mri_glmfit command: mri_glmfit --y Model1_Maltx_ParentEd_Sex_Age_n58-lh-thickness.mgh --fsgd Model1_Maltx_ParentEd_Sex_Age_n58.fsgd --C Model1_Maltx.mtx --C Model1_ParentEd.mtx --surf fsaverage lh --glmdir Model1_Maltx_ParentEd_Sex_Age_n58-lh-thickness.glmdir -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. We are trying to look at the main effects of two discrete variables in the same model (I.e., effect of var1 while controlling for var2), while also regressing out sex (class) and age (variable). We don’t care about the interaction term(s). There are 16 regressors = 8 classes * (1 variable +1) = 16. The FSGD file is attached, and I copied the design matrix below. >From reading the archives, I tried Doug’s suggestion of "cat old.fsgd | sed 's/\\r/\\n/g' > new.fsgd” but that did not fix it. Then I tried removing the overall mean (across all 58 subjects) and got the same error – see attached “*_demeaned.fsgd” file. Thank you for your help with troubleshooting this error. Best, Andrea Design matrix ------------------ 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 18.053 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.052 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.267 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 19.120 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.195 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 18.558 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.895 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.862 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.974 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.733 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.260 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.941 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.712 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.257 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.446 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.741 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.718 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.750 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.111 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.335 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.329 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.786 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.990 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.886 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 18.497 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.569 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.604 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.802 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.851 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.858 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.640 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.597 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.410 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 19.160 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.636 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.749 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.056 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 18.302 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.333 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.668 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 20.236 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.671 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 19.058 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.376 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 19.209; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.246; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.640; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.483; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.214; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 18.820; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.955; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.645; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.514; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.331; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.189; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.387; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.231; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 18.335; -- Andrea Gold, Ph.D. Section on Development and Affective Neuroscience National Institute of Mental Health Room 201, Bldg. 15K, MSC 2670 Bethesda, MD 20892-2670 Phone: 301-827-9804 Fax: 301-402-2010 Email: andrea.gold(a)nih.gov<applewebdata://D38F487B-BA2B-4BF6-A9C4-96248AB2BE51/andrea.gold@nih.gov>

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Tracula stats COR-.info does not exist
by Simon Jones 15 Oct '15

15 Oct '15

Dear Tracula developers I thought I had nearly reached the end of tracula processing. However, when I perform the step, trac-all -stat -c dmrirc_ind_mni_cvs_all_stats.all I receive this error message . Base name of output files: /work/imagingC/Rowe/p00363/freesurfer/all/subs_tracts/stats/lh.cst_AS.avg33_ cvs_flt Text file with list of individual inputs: /work/imagingC/Rowe/p00363/freesurfer/all/subs_tracts/stats/lh.cst_AS.avg33_ cvs_flt.inputs.txt Loading output reference volume from /home/spj24/app/freesurfer/subjects/cvs_avg35 corRead(): can't open file /home/spj24/app/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /home/spj24/app/freesurfer/subjects/cvs_avg35 There is no file called COR-.info in the directory /home/spj24/app/freesurfer/subjects/cvs_avg35/ I have commented nearly all lines from the file dmrirc_ind_mni_cvs_all_stats.all to leave a minimum configuration file and then the script runs without error. However, in that case the stats directory created only contains files related to avg33_mni_bbr ( and mni_flt if I add the switch set doregflt = 1). There are no cvs files. I am using tracula.update.centos4_x86_64.5.3.2014_05_26 in freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0. I performed all tracula processing steps before stats without the tracula.update.centos4_x86_64.5.3.2014_05_26, and then added the update to perform the stat step. Thanks for your help, Simon

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Error during long_mris_slopes
by Benedikt Wenk 15 Oct '15

15 Oct '15

Dear FreeSurfer Experts While performing the long_mris_slopes --qdec I receive the following error: Traceback (most recent call last): File "/Applications/freesurfer/bin/long_mris_slopes", line 1125, in <module> shutil.rmtree(dirname) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 253, in rmtree File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 251, in rmtree OSError: [Errno 66] Directory not empty: './tmp-lhab_2ur8.base_lh_thickness_f9caSb' I tried to solve the problem with tips from the internet but could not fix it. The directory is empty and every time I try for perform a new long_mris_slopes --qdec I receive the same error concerning another subject's folder like: Traceback (most recent call last): File "/Applications/freesurfer/bin/long_mris_slopes", line 1125, in <module> shutil.rmtree(dirname) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 253, in rmtree File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 251, in rmtree OSError: [Errno 66] Directory not empty: './tmp-lhab_1lwe.base_lh_thickness_E_ExHB' Can you please help me with this? Thank you in advance. Sincerely, Ben

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Extracting individual vertex values for surfaces mapped to fsaverage
by Bronwyn Overs 15 Oct '15

15 Oct '15

Dear mailing list, For each of the subjects in our study, we would like to extract the thickness values at each vertex for the surface that has been mapped to fsaverage (so that the number of vertices is identical for all of our subjects). After changing to a specific participants "surf" directory and starting matlab, could I use the following command and file to extract the data I want?: [thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh') Also, how do I then determine the annotation associated with each vertex for each subject? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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malloc error with mri_glmfit-sim
by Frances Robertson 15 Oct '15

15 Oct '15

Dear FreeSurfer experts We are getting a malloc error in mri_segstats when trying to run mri_glmfit_sim (v5.3.0 on Ubuntu) as follows: mri_glmfit-sim --glmdir lh.pial_lgi.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --overwrite The output ends with: Reporting on 2 segmentations Computing spatial average of each frame 0 1 *** Error in `mri_segstats': malloc(): memory corruption: 0x302df138 *** Writing to lh.pial_lgi.glmdir/before-after/cache.th13.abs.y.ocn.dat Abort (core dumped) Any suggestions? Many thanks, Frances

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Error in Monte Carlo simulation
by Baumann Philipp 15 Oct '15

15 Oct '15

Dear Expert, I'm using Qdec to run some correlation analysis (cortical thickness). When I try to apply Monte Carlo simulation, I get the following error message: Error in Monte Carlo simulation: Error running mri_surfcluster! I tried to use different paramers (e.g. different smoothing) which didn't change anything at the error message. What's going wrong ? Many thanks for your help, Best regards, Philipp

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Error during long_mris_slopes
by Benedikt Wenk 15 Oct '15

15 Oct '15

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Re: [Freesurfer] percent difference adjust to results {Disarmed}
by pablo najt 15 Oct '15

15 Oct '15

Hello Doug, Group.mean.mgh doesn't look negative see when opening with tksurfer, below. I re-run the computation to make sure. When I opened the pctdiff and increased the minimum threshold from 3 to 4 and above the colour maps changed from light blue to yellow. Pctdiff with threshold 3 With threshold 4 Could you advice which would be the right setup and also how do I figure it out how much percent difference in the cluster of my results below, please? Date: Mon, 5 Oct 2015 19:28:06 -0400 From: greve(a)nmr.mgh.harvard.edu To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] percent difference adjust to results {Disarmed} It looks like the pctdiff changed sign which would happen if group.mean.mgh had negatives. Does it? On 10/3/15 2:38 AM, pablo najt wrote: Hi my message was lost in the long correspondences. Would anyone advice about below, please? Thank you. Pablo From: pablonajt(a)hotmail.com To: freesurfer(a)nmr.mgh.harvard.edu Date: Thu, 1 Oct 2015 11:47:10 +0000 Subject: [Freesurfer] percent difference adjust to results {Disarmed} Dear FS experts I have a query about how can I make that the percent difference results matches the same clusters of my output from my main glm analysis. I run a glm analysis g4v1 (Male_Pt, Male_HC, Fem_Pt, Fem_HC) with Age and sex as covariates. My contrasts are as follow -0.5 0.5 -0.5 0.5 0 0 0 0 This contrast is meant to test "is there a difference between HC and PT controlling for age and sex. I separately run contrast of PT agains "0" 0.5 0 0.5 0 0 0 0 0 and HC against "0" 0 0.5 0 0.5 0 0 0 0 calculated percent difference as follows fscalc Pt_group/gamma.mgh add HCgroup/gamma.mgh div 2 -o group.mean.mgh Then computed the percent difference: fscalc HCgroup/gamma.mgh sub Pt_group/gamma.mgh div group.mean.mgh mul 100 -o pctdiff.mgh Now when I open my results from the first contrast above and the pctdiff.mgh separately, I am not quite sure they match. How could I adjust the min and saturation values to make them match and show how much percent difference is between the groups in the cluster shown in the main contrast. I have embedded the two results and parameters to give you an idea of how I am setting this up and if there is anything I can tune to improve visualisation. Thank you very much in advance. Pablo results from main contrast pctdiff _______________________________________________ Freesurfer mailing list Freesurfer(a)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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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Freesurfer October 2015