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Re: [Freesurfer] Manual segmentation issues
by maryam_koochaki 31 May '16

31 May '16

Hi Antoine,Have you tried control points seeding, I usually place the control points right behind the surface in trouble areas so seeded points would push the surfaces forward.Maryam Sent from my Samsung Galaxy smartphone. -------- Original message --------From: Saturne Fox <saturne.fox(a)gmail.com> Date: 2016-05-31 1:20 AM (GMT-08:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Manual segmentation issues Dear freesurfer community, These days I am manually editing some data and this subject is giving me such a hard time. In fact I would like the near-to-cortexartefacts at the top right hand corner to be excluded from the surface but even after changing the intensity of the wanted part to 255 and the one of the excluded parts to 1 (which is nevertheless not visible on these images) the surface is still not what I would like it to become. In adition to editing the wm.mgz file, I also modified the aseg.presurf file to exclude these parts and I re-runned the -normalization2 and -maskbfs flags to generate new brain.mgz and brain.finalsurfs.mgz files. Any idea why these modifications are not affecting the surface ? Best regards, Antoine

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Retinotopy - Error in fast_selxavg3 (line 279)
by Steinmann, Iris 31 May '16

31 May '16

Dear freesurfers, I try to run a retinotopy analysis following the instruction on https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis (using Ubuntu 14.4 and freesurfer 5.3) My subject folder contains 4 runs (all 'positive polar'). After preprocessing I performed the following steps: mkanalysis-sess -a retinotopy_polar_pos_rh -TR 2 -paradigm polar_pos.par -retinotopy 30 -surface self rh -per-run -fsd bold -fwhm 5 -nskip 4 selxavg3-sess -s EP_polar -a retinotopy_polar_pos_rh The polar_pos.par file contains only the two following lines: stimtype polar direction pos selxavg3-sess stops with the following error: ... Saving X matrix to ~/PROJECTS/Retinotopy/subjects/EP_polar/bold/retinotopy_polar_pos_rh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I found a lot of similar error reports in the mailing list, but unfortunately no explanation that fix my problem. Is it maybe a problem when I only process 'polar positve' measurements? I also attached the Xtmp.mat file that contains a lot of NaN. Does someone has an idea what's going wrong here? Thanks in advance! Iris

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Group_analysis_FSGD_contrast_matrix
by Hao wen 31 May '16

31 May '16

Hello, FS experts: I am now doing the group analysis with covariates(age, gender), I am using command line, not QDEC, so my Null hypothesis is: there is no significant difference for the thickness between my two groups( 'AD' and 'CN'), my covariates are age and gender, so if I define the classes like in the tutorial, is there an interaction between the group laber and gender, no? My question is that: If I define the FSGD file like the example here(we have two factors, 1 variable):https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V [https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V> Fsgdf4G1V - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V> surfer.nmr.mgh.harvard.edu FSGD File (g4v1.fsgd) GroupDescriptorFile 1 Title OSGM Class MaleRight Class MaleLeft Class FemaleRight Class FemaleLeft Variables Age Input subject1 MaleRight 30 ... Follow the tutorial, I think my contrast matrix should be like this: 0.5 -0.5 0.5 -0.5 0 0 0 0 So I know that if you have just one factor, for example, the gender, we should have four columns, like: 1. Intercept for Females 2. Intercept for Males 3. Slope for Females 4. Slope for Males But for my data, I also have the group lable(AD, CN), so anyone can explain this to me a little? Thanks in advance!

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Question about selxavg3-sess -no-con-ok
by Leila Reddy 31 May '16

31 May '16

Hi,I was just wondering what exactly the -no-con-ok option does in selxavg3-sess. Is it the same as setting the weights for all conditions to 1 and give the baseline/fixation (i.e., 0s in the para files) a weight of 0? Thanks, Leila

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Segmentation fault: Core dumped
by Sahil Bajaj 31 May '16

31 May '16

Hello FS experts, I am running a command "fcseed-sess -s S01 -cfg abc.config" to get *.dat file for further analysis. I used the same steps to calculate FC for 40 subjects, all steps run fine with 38 subjects but for 2 subjects I am getting an error: Segmentation fault: Core dumped. I checked the segmentation of anatomical data (generated using recon-all), and it looks fine to me. Here I am also attaching the log file created when I run this command. Any help would be really appreciated. Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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Freesurfer V6 beta
by Francis Tyson Thomas 31 May '16

31 May '16

Hello Fresurfer admin! I was looking for the v6 beta and it looks like it still hasn't been released after it was pulled down the last time. I would like to know what is the expected ETA for the beta. Last I remember it was mentioned it was on the verge of release about two weeks ago.I'm looking forward to get my hands on the beta! Thanks, Tyson

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Postdoctoral position available
by Olivier Coulon 31 May '16

31 May '16

Dear list members, please find below a link to a postdoc position annoucement that might be of interest, in the field of cortical morphometry for developmental studies and autism. http://www.meca-brain.org/2016/05/31/we-are-looking-for-a-post-doc/ O. Coulon -- Olivier Coulon, Aix-Marseille University, LSIS Laboratory CNRS Director of Research, olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univ-amu.fr> http://olivier.meca-brain.org MeCA Research Group http://www.meca-brain.org Institut des Neurosciences de La Timone Faculté de Médecine, 27 Bd Jean Moulin, 13005 - Marseille, France Tél: +33 (0)4 91 32 40 59

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ERROR: mpr2mni305 failed
by Barbara Kreilkamp 31 May '16

31 May '16

Dear FSL experts, I am running freesurfer-Darwin-lion-stable-pub-v5.3.0 on MAC 10.10.5. Could you please help me with this error message? I think it relates to the library, this is what it states in talairach_avi.log. But I am unsure how to solve this issue. Any help is greatly appreciated, Thank you very much, Barbara #@# Talairach Sat May 28 14:18:53 CEST 2016 /Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 recon-all -s REF088c exited with ERRORS at Sat May 28 14:19:12 CEST 2016 For more details, see the log file /Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting talaraich_avi.log output /Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri /Applications/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 Sat May 28 13:27:28 CEST 2016 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from orig_nu.mgz... crypt_gkey = FSaWN44YqKOYA TR=8.21, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... crypt_gkey = FSaWN44YqKOYA Analyze Output Matrix -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -146.00000; 0.00000 -1.00000 0.00000 148.00000; 0.00000 0.00000 0.00000 1.00000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Sat May 28 13:27:29 CEST 2016 /Applications/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Sat May 28 13:27:30 2016 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted

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Manual segmentation issues
by Saturne Fox 31 May '16

31 May '16

[image: Inline image 3][image: Inline image 1][image: Inline image 2][image: Inline image 4] Dear freesurfer community, These days I am manually editing some data and this subject is giving me such a hard time. In fact I would like the near-to-cortexartefacts at the top right hand corner to be excluded from the surface but even after changing the intensity of the wanted part to 255 and the one of the excluded parts to 1 (which is nevertheless not visible on these images) the surface is still not what I would like it to become. In adition to editing the wm.mgz file, I also modified the aseg.presurf file to exclude these parts and I re-runned the -normalization2 and -maskbfs flags to generate new brain.mgz and brain.finalsurfs.mgz files. Any idea why these modifications are not affecting the surface ? Best regards, Antoine

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ERROR with pial-lgi for one subject
by Vikas Bandalli 30 May '16

30 May '16

Hello FS experts, I am currently running an analysis for pial_lgi between control and patient group. But when I try to run the analysis using qdec for Right Hemisphere (rh),I get the following error with one particular subject Error in Analyze: Couldn't open /Applications/freesurfer/subjects/HC122/surf/rh.pial_lgi.fwhm0.fsaverage.mgz or .mgh file. However,the analysis works fine for Left Hemisphere (lh) without errors. I tried running the command recon-all -s HC122 -qcache -measure pial_lgi -hemi rh But output was #@# Qdec Cache rh pial_lgi fsaverage Mon May 30 20:19:32 IST 2016 INFO: File rh.pial_lgi does not exist! Skipping creation of smoothed data for rh.pial_lgi But trying to run '-localGI' did not create 'surf/rh.pial_lgi' btu it creates 'surf/lh.pial_lgi' I checked the euler number for the surface it is 2. Any suggestions to correct the error is highly appreciated . Regards, Vikas Bandalli -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825

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