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Tracula: trac-all prep badly formed if error
by Katherine Damme 17 Dec '15

17 Dec '15

Hello Everyone! I am getting a badly formed number error in my trac-all any ideas?

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Display NV-GLX error
by Chuck Theobald 16 Dec '15

16 Dec '15

When trying to run the Display command, I get the following messages and no imaging of the .mnc file. machine7 ~ $ Display /home/research/bamlab/ATLAS/001/antsreg/data/coronalspace/rois/drawn/l_hip.mnc Xlib: extension "NV-GLX" missing on display "localhost:11.0". Could not get requested colour_map_mode(0), got(1,256) Xlib: extension "NV-GLX" missing on display "localhost:11.0". Could not get requested colour_map_mode(0), got(1,256) Inputting /home/research/bamlab/ATLAS/001/antsreg/data/coronalspace/rois/drawn/l_hip.mnc. Objects input. Xlib: extension "NV-GLX" missing on display "localhost:11.0". Could not get requested colour_map_mode(0), got(1,256) G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. When using version 5.3.0, I get: chuck@ong7 ~ $ Display /home/research/bamlab/ATLAS/001/antsreg/data/coronalspace/rois/drawn/l_hip.mnc Xlib: extension "NV-GLX" missing on display "localhost:11.0". Xlib: extension "NV-GLX" missing on display "localhost:11.0". Inputting /home/research/bamlab/ATLAS/001/antsreg/data/coronalspace/rois/drawn/l_hip.mnc. Objects input. Xlib: extension "NV-GLX" missing on display "localhost:11.0". and the output windows appear as in the attached image. Is this normal behavior? If not, how can I get rid of the nv-glx errors? Thanks, T-- Chuck Theobald System Administrator The Robert and Beverly Lewis Center for Neuroimaging University of Oregon P: 541-346-0343 F: 541-346-0345

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Recon Error
by Hamel, Maura K. 16 Dec '15

16 Dec '15

Hi Freesurfer experts, I’m looking for some help with some recons I tried running yesterday for about 60 subjects. The command I submitted was: recon-all -i /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/${subject}/MPRAGE/0*/001.mgz -s ${subject} -all I have attached the log files, and I’m hoping you can explain the error I received and what I need to do fix it. Thanks in advance for your help! FREESURFER_HOME: /usr/local/freesurfer/stable6 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151208 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 4.1.8-1.el6.elrepo.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: tyra SUBJECTS_DIR: /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60 PWD: /autofs/cluster/maury/users/gcoombs/College_Risk ssh tyra setenv SUBJECTS_DIR /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60 cd /autofs/cluster/maury/users/gcoombs/College_Risk Best, Maura Hamel Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th St, Room 2602A Charlestown, MA 02129 Phone: 617-643-4441 Fax: 617-726-4078

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wm-hypointensities label on MS subjects
by Guido Orlando Pascariello 16 Dec '15

16 Dec '15

Hi FS Experts: I've been using T1 data from MS subjects in order to try to identify lesion volume using wm-hypointensities label from aseg. I wonder if there is any tool which uses T2-flair sequence to the same goal? I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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R: Re: R: Re: FDR in FS-FAST
by stdp82＠virgilio.it 16 Dec '15

16 Dec '15

I have run mri_fdr --help but I obtained this warning: /Applications/freesurfer/bin/mri_fdr: Permission denied. I would also ask you if is possible to threshold the FDR map (p<0.05), eliminating clusters < 5 voxels. Thanks Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 11-dic-2015 20.23 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST > >$FREESURFER_HOME/bin > >On 12/11/15 2:08 PM, stdp82(a)virgilio.it wrote: >> Thanks, in which folder I should put this file? >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: greve(a)nmr.mgh.harvard.edu >>> Data: 7-dic-2015 19.23 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] FDR in FS-FAST >>> >>> >>> >>> On 12/07/2015 08:35 AM, stdp82(a)virgilio.it wrote: >>>> Hi list, >>>> I have two concerns, please: >>>> 1) It is possible to apply FDR correction on rs-fMRI seed based >>>> analysis by FS-FAST? If yes, I can I do it? >>> try this binary >>> ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/mri_fdr >>>> 2) I have apply the FS guidelines and I have used Montecarlo >>>> correction with threshold at 1.3 but in the within group analysis >> the >>>> clusters are very large. In the guide I read examples with a >> threshold >>>> at 3. Is there a specific reason? >>> There is not a hard-and-fast criteria for the voxel-wise threshold. 3 >> is >>> fine as is 1.3 >>>> Thanks >>>> >>>> Stefano >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard. >> edu/transfer/outgoing/flat/greve/ >>> _______________________________________________ >>> 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 >

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example #PBS Torque script for FreeSurfer on a HPC cluster & multithreading question
by Riphagen Joost (NP) 16 Dec '15

16 Dec '15

Dear all, I'm learning how to work with Freesurfer on a #PBS/Torque HPC cluster. There is enough documentation about using #PBS, but I have not been able to find anything on the net about how to process multiple subjects in FS in this environment. If somebody is willing to share an example script that would be most helpful. Am I right in thinking that by using the "-itkthreads" flag FS can make use of multiple threads but not use multiple cores ? The nodes use two Xeon processors with 8 cores and 16 threads per CPU and have 64 GB per node. I have to book per node so the more I can use it the better. Regards Joost Riphagen

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Meaning of resample type in mri_convert
by Gronenschild Ed (NP) 16 Dec '15

16 Dec '15

Hi FreeSurfer developers, Can you please provide information on the resample types "interpolate" and "weighted" which can be specified with option -rt in mri_convert? Cheers, Ed

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Get summary stats for ROI
by Bronwyn Overs 15 Dec '15

15 Dec '15

Hi Freesurfer Mailing List, I have just completed a GLM analysis with monte carlo correction and now have my "cache.th13.abs.sig.cluster.mgh" files showing the significant clusters for a specific contrast. I would now like to get mean cortical thickness values for these ROIs in another unrelated MRI sample. What is the simplest means of mapping these clusters to my other sample so that I can extract the stats? 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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PALS B12
by Woo, Jonghye 15 Dec '15

15 Dec '15

I am trying to a brodmann mask using PALS B12 atlas in fsaverage. I used the following command to create the volume from annotation file. I have two questions associated with it. mri_aparc2aseg --s my_subject --annot PALS_B12_Brodmann --o PALS_B12_Brodmann_Mask.nii --annot-table lh_PALS_B12_table.txt 1. When I visualized the mask, it seems that the labels are not corresponding to the regions (the annot-table is not working). Does anyone know this issue? 2. In this case, I only used lh table. Then do I need to use rh table again? What should I to incorporate both lh and rh? Thank you in advance.

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Problem with mri_surf2surf inside mris_preproc
by Ed Vessel 15 Dec '15

15 Dec '15

Hello - I am having a similar error to this post from 2011: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019290.html ...but as far as I can tell, no answer was given to this post. Perhaps I am just not seeing it? I am taking some contrasts that I computed in volume space for a subject and am converting them to surface space for a group analysis. I am running mris_preproc, using the following command: mris_preproc --target fsaverage --hemi lh --out lh.my_Contr.mgh --iv my_Contr.nii reg/freesurfer/anat2exf.register.dat ..but I get the following error in the call to mri_surf2surf: mri_surf2surf --srcsubject ZM --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgs urfreg sphere.reg --tval ./tmp.mris_preproc.3995/ZM.1.mgh --sval ./tmp.mris_preproc.3995/subjsurfvals.mgh --noreshape --no-cortex ERROR: dimension inconsistency in source data Number of surface vertices = 133192 Number of value vertices = 138083 Any advice on what might be causing this issue? Is it possible that I originally created the subject's segmentation using a slightly older version of freesurfer, or that I did manual edits, and this is leading to this inconsistency? Any suggestions on how to get this working? Thanks for your help, Ed -- Ed Vessel Center for Brain Imaging New York University ed.vessel(a)nyu.edu 4 Washington Place, Rm. 156 New York, NY 10003 http://www.cns.nyu.edu/~vessel (212) 998-8217

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