Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Re: [Freesurfer] hippocampal subfields - multispectral segmentation with FLAIR
by Luigi Antelmi 14 Mar '16

14 Mar '16

Ciao Eugenio, thanks a lot for the support. We made some tests and clearly the high res T2 gives the best subfields contrast. We will proceed with the ADNI like parameters. Have a nice day, Luigi.

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General diffusion workflow questions: QC and extracting FA from subcortical structures
by Elijah Mak 13 Mar '16

13 Mar '16

Dear Freesurfer Community, 1) I am just starting out on some diffusion analyses and I'd like to use the dt_recon for this. Is there any information about a general workflow for quality control for the outputs from dt_recon? From the tutorials, I only see information about checking the registration. In particular, I would like to know how dt_recon cope with the occasional flipping/swapping of some components of the diffusion gradient directions? 2) Another aim of mine is to quantify DTI indices in subcortical regions segmented from the ASEG pipeline. How does Freesurfer handle partial volumning via seg-erode in "mri_vol2vol"? I have pasted my workflow below and I'd like to check if this is correct, thanks! 1) After processing the scans on recon-all and dt_recon , i resample the structural data to diffusion space mri_vol2vol --mov subjectname/dtrecon/lowb.nii.gz --targ subjectname/mri/aparc+aseg.mgz --inv --interp nearest --o subjectname/mri/aparc+aseg2diff.mgz --reg subjectname/dtrecon/register.dat --no-save-reg Should I use ASEG instead of APARC+ASEG or WMPARC (which also has labels for the subcortical regions?) 2) Then, I mask the FA/MD maps with mri_mask subjectname/dtrecon/fa.nii.gz subjectname/mri/aparc+aseg2diff.mgz subjectname/dtrecon/fa-masked_aparcaseg.mgz; done 3) Finally, I collect the FA in the regions with mri_segstats --seg subjectname/mri/aparc+aseg2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subjectname/dtrecon/fa-masked_aparcaseg.mgz --seg-erode 1 --sum subjectname/stats/fa_aparc+aseg2diff_segerode_1;done Thanks a lot for your time and help! Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Alpha channel in color lookup tables (CLUT)
by Michael Bannert 12 Mar '16

12 Mar '16

Dear Freesurfer community, I have a problem using the alpha channel in the color lookup tables. No matter what values I choose, none of them seem to affect the transparency in any way. Here is what I would like to do: I have a number of labels that I want to visualize on an inflated brain surface of fsaverage (with a binarized curvature map). So I use mris_label2annot to create an annotations file which I later load in freeview. mris_label2annot \ --s fsaverage \ --h rh \ --annot-path path/to/rh.output.annot \ --ctab /Applications/freesurfer/SegmentNoLUT.txt \ --l path/to/first.label \ --l path/to/second.label When I load this file into freeview, I can see the two labels without a problem. However, everything outside the labels is just black. I assume that's because all vertices that don't fall into any of the labels, are assigned the first RGBA value, which is [0 0 0 0] by default. Now, I would of course like to see the rest of the brain surface. I figured I could do that by changing the alpha channel of the Seg0 entry in the color lookup table. But no luck: everything outside the labels appears black. I also don't understand the function of the --no-unknown argument. I was under the impression that this would make sure that vertices that are not part of any label would not be assigned any color and therefore... well, appear transparent? (which whould be good) ... appear black? (which would be bad) Any ideas? Thanks & best, Michael

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Freesurfer v6 beta
by Francis Tyson Thomas 11 Mar '16

11 Mar '16

Hi folks, I was just wondering if there was any major bug in the freesurfer v6 beta that necessitated the removal of the beta from your servers because I cannot find them anymore. Does that mean I will have to go with the dev version at this point which are like the nightlies of the freesurfer v6 updated every few days. Thanks, Tyson

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Using qdec to view cluster results
by Sahil Bajaj 11 Mar '16

11 Mar '16

Dear all, I have a very basic question regarding the usage of qdec. I am using qdec to view cortical thickness for a set of patients vs. controls. I am able to create table.dat, design the comparison and display the results. After that, my results are saved as sig.mgh in qdec folder. Now when I try to reopen the same results by loading surface and overlaying with sig.mgh, although it shows me the results but when I click on 'Find Clusters and go to max' it gives me following error: Error generating cluster stats GeneratingClusterStats: white surface was not found and it doesn't display any cluster results in terminal window. If I do everything from very first step, starting from loading table.dat, creating design once again, everything is working fine. I would really appreciate any help. 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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selxavg3-sess question
by Ji Won Bang 11 Mar '16

11 Mar '16

Dear. Freesurfer experts. Hi. i appreciate your help in advance! I'm using freesurfer version 5.3.0. I tried selxavg3-sess and got the error dimension mismatch between mask and 2th run. Actually, the number of slices of the 1st run and the rest are different. Is it the reason why I get this error message? Please let me know what I should do to correct this error! Below are command and error lines. command: selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile error: -------------------------------------------------------------- selxavg3-sess logfile is /home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino-160309115326.log -------------------------------------------------------------- ------------------------------------------- /home/jbang/Projects/replay/epi/replay06 Wed Mar 9 11:53:33 EST 2016 anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /home/jbang/Projects/replay/log >> sxa3cmd = /usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06 -analysis retino -df sessdirfile >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# replay06 ############################### /home/jbang/Projects/replay/epi/replay06 ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m ------------------------- outtop = /home/jbang/Projects/replay/epi Extension format = nii.gz 1 HorVer.mat 2 UpperLower.mat nruns = 4 autostimdur = outanadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino Found 62211/180708 (34.4) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 0 ntptot = 480, nX = 28, DOF = 452 Saving X matrix to /home/jbang/Projects/replay/epi/replay06/bold_retino/retino/Xtmp.mat XCond = 199.451 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.499283 (t=0.024843) 2 -0.25 -0.268756 (t=0.047925) 3 0 -0.0441607 (t=0.069497) 4 0.25 0.16942 (t=0.093633) 5 0.5 0.359032 (t=0.117433) AR1 Correction M: 0.0657489 1.15858 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean 855.07 run 2 t= 3.1 ERROR: dimension mismatch between mask and 2th run >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you very much! Best, Ji Won

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Fsaverage
by Kasper Jessen 11 Mar '16

11 Mar '16

Dear FreeSurfer experts, In regard to fsaverage, we are wondering whether it is recommended to use the default fsaverage or if a new fsaverage should be created for the individual dataset. If there are no recommendations, what are the advantages and disadvantages? Best regards, Kasper Jessen MD, PhD student -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk

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FA maps surface based analysis
by John Anderson 11 Mar '16

11 Mar '16

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mri_glmfit
by John Anderson 11 Mar '16

11 Mar '16

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For Monte Carlo simulation, QDEC GUI or in-line command?
by Karl Liu 11 Mar '16

11 Mar '16

Dear Freesurfer Experts: I repost a question I have when applying Monte Carlo simulation to control for multiple comparisons. Your help is much appreciated. I did the correction via QDEC GUI. In the section of Monte Carlo Null-Z simulation, I set Threshold: 2.0 (0.01) and Sign: neg. This generates a "mc-z.neg.th20.sig.cluster.summary" file in each contrast folder. Later, I use the in-line: command mri_glmfit-sim instead. My input is: ri_glmfit-sim --glmdir Untitled --cwpvalthresh .05 --cache 2 neg --2spaces. This generates a "cache.th20.neg.sig.cluster.summary" file for each contrast. My question is : are these two summary files the same, one from QDEC GUI with name " mc-z..." and the other from in-line command with name "cache..."? My next question is: In QDEC GUI, when the simulation is finished, the GUI automatically illustrates the clusters/brain, based on a file named "mc-z.neg.th20.sig.cluster.mgh". But I doubted if this is post-correction results. What is the right way to view results after correction? Thank you very much. Karl

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Freesurfer March 2016