Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

Talairach Registration Error : recon-all -s
by Dev vasu 16 Feb '17

16 Feb '17

Dear FreeSurfer Developers, I am incurring Talairach registration error when i was running recon-all -s Error : recon-all -s KON2 exited with ERRORS at Do 16. Feb 16:23:10 CET 2017 Freesurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP Platform: Ubuntu 16.04 recon-all log : see the attachment Kindly let me know the problem with registration. Thanks, Vasudev

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DTI images, mri_glmfit-sim
by Magnús Ingvi 16 Feb '17

16 Feb '17

Hello! I'm toying with some images acquired by following the dt_recon tutorial (fa-tal). I have prepared them for group analysis and run mri_glmfit, and the results look decent. However, I wanted to correct for multiple comparisons using for example mri_glmfit-sim --sim mc-full 100 2 cdbasename --sim-sign abs -glmdir testdir --overwrite And variations of this command. None of them find any cluster, and the output file (cdbasename.sig.cluster.summary) always reports zero cluster, no matter how I change the thresh value. Am I doing something wrong?

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mris_preproc version 6
by Fotiadis, Panagiotis 16 Feb '17

16 Feb '17

Hi Doug and Bruce, I was wondering whether you know where I can download the version 6 mris_preproc! Thanks in advance, Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA, 02114 T: (617) 643-3869

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Intensity Re-scaling Relative to Full Brain Atlas <Repost>
by Anderson Napolitano 16 Feb '17

16 Feb '17

Thank you Dr. Greve. Just to clarify, the 'inputfile.nii.gz' file in the command: fscalc inputfile.nii.gz div value -o outputfile.nii.gz ,is the gtm.nii.gz file generated after the command: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output located at gtmpvc.output directory? If that's the case, fscalc will not modify gtm.stats.dat file corresponding to the image. Wouldn't that be counter intuitive, as gtm.stats.dat remains unchanged but we just normalized the image using the fscalc command? Again, thank you Dr. Greve. I really appreciate all the help. -Anderson

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Volume maps unit in FreeView
by Martin Juneja 15 Feb '17

15 Feb '17

Hi, I have a very simple question. I have cortical volume maps (averaged over 30 subjects). I can view those in FreeView using lh.pial overlaid with lh.mean.volume.mgh file. In overlay > configure option, I had to set the min as 0 and max as 4 to display the average volume. Now the color bar is showing scale between 0 (min as blue color) and 4 (red) as maximum. I am not sure what does this 0 and 4 represent here, what are its units and how the actual volume values 20,000-40,000 mm^3 converted to this range between 0 and 4? Similarly, for surface area, color bar range is between 0 and 0.9 when actual values range around 11000-14000 and for cortical thickness, color bar range is between 1 and 3 when actual values range around 2.1-3 mm. Any help please. Thanks.

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mirroring right-hemisphere cluster dimensions on left hemisphere
by Uquillas, Federico D'Oleire 15 Feb '17

15 Feb '17

Dear FreeSurfer community, We have a cluster that we drew on the surface on the right hemisphere, and we’re interested in extracting cortical thickness values from the contralateral hemisphere. Wondering if there’s a way to transform the dimensions of our cluster from the right hemisphere to the left-hemisphere? Thank you so much for any help you may be able to provide. Best regards, Fred

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display SPM results on inflated surface?
by Schoot, Lotte 15 Feb '17

15 Feb '17

Hi all, I was wondering if you knew of a way to display SPM results onto the inflated surface in Freesurfer. I have tried using SurfRend but there seem to be problems which might be due to the fact the results are obtained with SPM12 and SurfRend was designed to work with SPM5. Thanks, Lotte

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recon-all exited with ERRORS
by Dayanne Ferreira Ayres 15 Feb '17

15 Feb '17

Good morning, I tried to process a patient with the command below after editing it: Recon-all-all -sd / Applications / freesurfer / subjects -no-isrunning -subjid ArlindoRibeirodaSilvaFilhoADRIANO_2009 The file with the error log follows in the attachment. Freesurfer version: 5.3 Platform: MAC OS X yosemite, version 10.10 Att, Dayanne Ayres

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LGI error/Matlab/ a qestion for Douglas Greve
by aral ahmadi 15 Feb '17

15 Feb '17

From: Douglas N Greve So ismac.m is not defined in your matlab implementation? What version of matlab are you using? What kind of computer are you running on? Aral's answer: I am working through VPN and connect to a Linux server using my laptop (Thinkpad2011). Not sure which version of Matlab, this freesurfer5.3 home directory uses, but I have matlab2010 opened on linux when I ran LGI command. although in job output file, it shows a warning that Matlab starting without a display, then it says <MATLAB> copyright 1984-2005 the Mathwork. Inc, version7.1.0.183 (R14) service pack3, Aug2,2005 Thanks, Aral aral ahmadi wrote: > > Dear experts > > I have a question regarding Freesurfer- LGI error I got during running > LGI after all recon steps been ran with no problem. you could see the > error below. > > *reading filled volume... > * > > *??? undefined function or variable 'ismac'.* > *error in -->load_mgh at 68* > * > * > *if(strcmp(computer,'MAC') || strcmp(computer,'MAC') || ismac)* > * > * > *error in -->MRIread at 87* > * > * > *[mri, voi, M, mr_parms, volsz] = load_mgh (fspec, [], [], headeronly);* > * > * > *error in --> make outer-surface at 24* > * > * > *vol = MRIread(filled_volume);* > ** > *>> ERROR:make _outer_surface did not creat output file > 'net/storage1/usr2/onrc/home/p2/Aahmadi/onrc/data/Aral-july/test/subject* > *Linux compute31 2.6.32-504.12.2.e16.*86_64 #1 SMP Wed Mar11 UTC 2015 > 86_64 86_64 GNU/Linux* > * > * > *recon-all -s S1091RPY existed with Errors at thu jan19 2017* > * > * > The error is ...Undefined function or variable 'ismac' - matlab is > expecting that variable to be defined (it's trying to detect the OS, > whether Linux, windows/ Mac), but it isn't. * > * > > I appreciate if you give me your advice on this issue. > > Thanks, > > Aral > >

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Converting Surface Masks to Labels
by Rita Loiotile 15 Feb '17

15 Feb '17

Hi, I'm sorry for what seems like a trivial question. I couldn't find this answer in the tutorials or old archive. I have statistical data in the surface that I have thresholded and binarized to form a mask. I can load the mask as an overlay in tksurfer. My understanding is that you need to turn files into labels in order to change the color display in tksurfer. Is there a command that takes in a shape/surface binary file and converts to labels? I came across this (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-March/017668.ht…) email from Doug, but it looks like I don't have mri_seg2annot in this freesurfer release. More broadly, I would like to tksurfer to display several masks at once, in different colors, using the command line. My understanding is that I would then use mris_label2annot to put all the labels together. When using this function, does the input order of the labels determine the number reference for the color in the Lookup table? What happens in the case where some labels overlap? Thank you in advance, Rita

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