Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

Surface Down-Sampling
by Sourena Soheilinezhad 03 Feb '12

03 Feb '12

Dear Experts, What is the best strategy to downsample a surface into diffusion (e.g. FA) resolution of the same subject? Thanks, Sourena Soheili

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What does trac-all do on the file 'bvecs'?
by Xiangzhen Kong 03 Feb '12

03 Feb '12

Hi, all~ I use trac-all with .nii data, not dicom. So I have to specify the bvecs and bvals in the config file. Trac-all requires a bvecs file in 3 columes, but FSL need that in 3 raws. I wonder what does trac-all do on the bvecs file that I specify. And I have check the code 'trac-preproc' and the log, but found nothing, except copy and Eddy-current "correction". ps: The orientation of my dicom and .nii fils are both LPS, and the bvecs is read from the DICOM header via nibabel. But FSL requires LAS. I thinks trac-all have done the transposition on the bvecs somewhere. What orientation of bvecs does trac-all need when run with .nii files? Thanks! Xiangzhen 2012-02-03

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Re: [Freesurfer] FA question
by Ed Gronenschild 03 Feb '12

03 Feb '12

Dear Antonella, In theory, FA can be sqrt(3/2) = 1.2247449. This occurs if eigenvalues 2 and 3 are zero. You will find these high FA values (>1) mainly outside the brain. Ed On 3 Feb 2012, at 11:31, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Dear all, > > I use dt_recon to process my DTI data and get my fa.nii for the > individual subjects. I wonder if the FA values can be greater that > one since for all my subjects I got the FA max? value graeter than > one. Is something wrong with my data or this is acceptable? I saw > in? most of the papers FA<1 so 0<FA<1. > > Thank you. > Antonella

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Two questions when using the new trac-all
by Xiangzhen Kong 02 Feb '12

02 Feb '12

Hi, all I am using trac-all these days. But I came across two quetions: 1. If I don't Specify Subjects To Be Analyzed, which means running the analysis on all subjects, there is an error saying "jot: Command not found.". The OS I am using is CentOS and I think jot is not installed by default. And some one says jot is part of freeBSD. Do we need to replace 'jot' in trac-all with other commands, such as seq? 2. If I run trac-all for just one subject each time,(that is to say, one config-file each subject), I wonder whether the time loss will be increase too much, compared with that one config-file for all subjects. Thanks! conxz 2012-02-01 Xiangzhen Kong

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QDEC question
by Dalwani, Manish 02 Feb '12

02 Feb '12

Hi Freesurfer users, I ran a QDEC analysis and loaded annotation. Is there a way to click on the activated cluster and print the region with co-ordinates? Thanks, Manish Dalwani

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FA question
by Antonella Kis 02 Feb '12

02 Feb '12

Dear all, I use dt_recon to process my DTI data and get my fa.nii for the individual subjects. I wonder if the FA values can be greater that one since for all my subjects I got the FA max value graeter than one. Is something wrong with my data or this is acceptable? I saw in most of the papers FA<1 so 0<FA<1. Thank you. Antonella

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Can I do multiple comparison correction in one area (not whole brain)
by zhang mingxia 02 Feb '12

02 Feb '12

Dear Freesurfer experts, Can freesurfer do multiple comparison correction in part of the brain (not the whole brain)? How can it do? Thank you very much in advance. Mingxia

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FA values
by Antonella Kis 02 Feb '12

02 Feb '12

Dear All, How I can get the FA values in a table after running the GLM group analysis for my FA data. I have GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.mgz and the gmldir. Thank you. Antonella

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Again Error with mri_glmfit-sim -- sim perm
by Antonella Kis 01 Feb '12

01 Feb '12

Hi Doug, I was trying to run what you suggested but seems that is still given me the error (without --seg): ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file. so I took out the --reg and it worked but I use the --seg from the cvs_avg35. Is correct to use this instead of the fsaverage (even if the register.dat from dt_recon is based on the fsaverage) or I should use fsaverage? In the wmparc2diff.mgz which I further use to create my fa-masks I used the register.dat files and I suppose they are coming from fsaverage but then I registered the FA data to CVS and I will need to visualize the results on my CVS/mri/norm.mgz. Also is OK to eliminate the --reg option while running the mri_volcluster? THANKS so much for helping, for making all this clear! Antonella ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wednesday, February 1, 2012 1:17 PM Subject: Re: [Freesurfer] Error with mri_glmfit-sim -- sim perm It is looking for the aparc+aseg.mgz so it can report the segmentation that each cluster is in. If you don't need this information, then run this command: mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh I got this command out of your log file and removed the "--seg" part. doug Antonella Kis wrote: > Dear all, > > I was running the simulation: > > mri_glmfit-sim \ > --glmdir GroupAnalysis_abs.glmdir \ > --sim perm 1000 3 permcsd \ > --sim-sign abs \ > --cwpvalthresh .05 > > > and unfortunately I got the following error: mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask GroupAnalysis_pos.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --csdpdf GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh > > ERROR: cannot find /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/fsaverage/mri/aparc+aseg.mgz > > > Seems that the simulation was completed saying that mri_glmfit simulation done but I did not get any clusters or any file permcsd.sig.cluster.summary. > > Also I am not sure if I need to use the while running the mri_volcluster the fsaverage or I should use the cvs_avg35 since my FA data was registered over the CVS space. > > Can I just do something further to catch my corrected clusters? I attached my log file. > > Thank you very much. > Antonella > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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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error message in tkmedit
by Rashmi Singh 01 Feb '12

01 Feb '12

While opening tkmedit using terminal I gave following command % crick:~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer> tkmedit AA471.T0 brainmask.mgz -aux T1.mgz -segmentation aseg.mgz -surfs $FREESURFER_HOME/FreeSurferColorLUT.txt The output was Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. LoadSegmentationVolume main aseg.mgz /opt/freesurfer/FreeSurferColorLUT.txt Reading /opt/freesurfer/tktools/tkm_common.tcl Reading /opt/freesurfer/tktools/tkm_wrappers.tcl Reading /opt/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /opt/freesurfer/tktools/tkUtils.tcl % 3 new windows popped up 1. The view window with the brain image ( it was similar to the one shown in you tutorial document-showed the surfaces and the segmentation in color) 2. The tool box window 3. Error message window stating the following Error: Parsing arguments Unrecognized option: /opt/freesurfer/FreeSurferColorLUT.txt This option is not recognized by tkmedit. Please explain what does this error message mean. Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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Freesurfer February 2012