Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

freesurfer multithread
by Li,Tengfei 04 Jan '17

04 Jan '17

Hello, Is there some way to use multithread in recon-all to speed up? I searched the freesurfer website and try using recon-all -autorecon-all -itkthreads 8 -subjid SUBID It simply gives an error message " ERROR: Flag -itkthreads unrecognized. " Thanks! Best Tengfei The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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drawing circle around vertex on surface
by Song, Daniel 04 Jan '17

04 Jan '17

Hi all, I'm trying to create a label by making a circle with a fixed radius around a defined vertex. I'm trying to use the method described here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44098.html I made the initial surface overlay with my vertex of interest having a value of 1 and 0 everywhere else with: mri_volsynth --pdf delta --delta-crsf 108555 0 0 0 --o pBECTS007_spike.mgh --template rh.thickness Then I smoothed with fwhm: mri_surf2surf --s pBECTS007 --hemi rh --sval pBECTS007_spike.mgh --fwhm 10 --tval ./pBECTS007_spike_fwhm.mgh My question is, is there an easy way to divide all vertices by the value of my vertex of interest after smoothing in tksurfer? If not, is there a command that will allow me to extract the vertex values and indices to do so? Thank you! Dan Song Clinical Research Coordinator Massachusetts General Hospital Neurology Department

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R: Re: Use CA and other subfields as seed for FS-FAST
by stdp82＠virgilio.it 04 Jan '17

04 Jan '17

Dear Eugenio,thank you very much.How can I obtain the beta version 6.0?Moreover, given that we are planning to analyze a big sample, I wonder when will be approximately released the stable's 6.0?Thanks Kind regards Stefano ----Messaggio originale---- Da: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Data: 3-gen-2017 19.41 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Use CA and other subfields as seed for FS-FAST Ciao, Stefano, Several things: 1. In 5.3, each subfield has a probability map in an independent file, so you don’t need the codes. 2. Having said that: you should probably use the new subfields in 6.0beta. Then, you can use the codes in the range 200-226. Kind regards, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 2 Jan 2017, at 10:47, stdp82(a)virgilio.it wrote: Hi list, I would like to obtain the functional connectivity maps of CA1, CA2/3... by using FS-FAST (VERSION 5.3). Which are the codes in FreeSurferColorLUT.txt, that I should use, please? The ranges from 500 - 508 and from 550 - 558 are useful by using 5.3? Thanks Kind regards, Stefano Delli Pizzi _______________________________________________ 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.

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aseg error - ventricle mislabeled, negative values in aparc.a2009s+aseg
by Antonin Skoch 04 Jan '17

04 Jan '17

Dear experts, while testing V6beta version I encountered problem with aseg. In one subject (with quite large ventricles) posterior part of right lateral ventricle is not labeled as brain at all and part is labeled as WM-hypointensities and nonWM-hypointensities. Moreover, in aparc.a2009s+aseg there are periventricular regions with value -1 (not present in aseg.presurf). These negative values I observed in one more subject. I am uploading the problematic subject named aseg_error.tar.gz to your server. Linear Talairach registration seems OK in this subject. Could you please comment on, how to correct this error? My second question, is it possible to check non-linear Talairach registration, i.e. talairach.m3z? Regards, Antonin Skoch

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Error from trac-all prep: data and bvals/bvecs do not contain the same number of entries
by Hao wen 04 Jan '17

04 Jan '17

Hello: I followed the tutorial for tracula, because of the tutorial data that you give dont have the T1 image, so I use on of my own diffision data and the reconall-ed T1 image, and I always get the same errors: data and bvals/bvecs do not contain the same number of entries , So I guessed that it is the problem from the data(dwi.nii, T1.nii, .bvec, bval), but I tried to figure out the data dimension differences between my data and the tutorial data(tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm), Here is the output: 1) FS tutorial data(dicom format): This is the bval info and i guess the bvec dimension is the same bValue = 700 nB0 = 10 nDir = 60 this is the dwi.dicom information: dimensions: 128 x 128 x 60 x 70 So the nFrames is equal to the bvel and bval columns(70), which makes sense. 2) My data information(which is .nii.gz format): The bvec and bval info: number of columns for bval and bvec is 136 The dwi.nii.gz dimensions: dimensions: 96 x 96 x 59 x 137 So for my data, the number of columns(or transpose the files, the same spirit) is nFrames-1, I guess that is the problem, but my data can be run for Mrtrix and Dipy, even in the dipy tutorial, the data that they offer, the number of columns is the number of frames(volumes) minus 1, So for TRACULA, is it a mandatory that the number of columns in bvec and bval is equal to the number of volumes in dwi image??? I know sometime people dont write the first 0 in bvec and bval, so if I just add it, and run it for TRACULA, it will work??? I will try it tomorrow!!! Really need your help, I stuck for this in a while:) the log file is attached. Thanks in advance

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View sig map on anatomical volume from volume-based group anaysis
by Hao wen 04 Jan '17

04 Jan '17

Hello: I have a question, after recon-all, I did some group analysis with the aseg.stats( not surface-based), so my question is : Does freesurfer has some volume-based group analysis(not for fMRI) for plotting the significance map, I searched google, and wanna some results like this: [cid:e4f431a9-4e18-4dec-8275-ce4080b061f2] I know here is for fMRI-sMRI based analysis: So i want to map some values for the subcortical structures in the anatomical image, but for the command here, how can I get the sig.nii(right now, we just have the result p-value for every subcortical structures), I know in FS, we can use mri_glmfit to have the significance map Any advice will be appreciated Hao

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Tracula Set: No Match
by Katherine Damme 03 Jan '17

03 Jan '17

Hello! I have been getting a "set: No match." error. I haven't been able to sort out what is causing it. Attached you will find the configuration file, command, and log files associated with this error. "mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs set: No match."

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Assign p value for every voxel and plot it in freeview
by Hao wen 03 Jan '17

03 Jan '17

Hello: I have a very simple question, after recon-all, I did some statistical analysis with some other softwares, so for example I got the p value for every voxel(volume_based),or p value for every vertex(surface-based), so I know how to map theses p values for surface-based pipeline, but for volume-based, how can we do that??? I know that in FMRI pipeline, we can use the significance map(sig.nii) as the overlay, but this is created by the group analysis(mri_glmfit), but can we created this sig.nii mannually and upload it to the oig.mgz and apar+aseg.mgz??? Really need your help. Thanks in advance

2 1

preproc-sess brain masks in masks subdirectory
by Ladan Shahshahani 03 Jan '17

03 Jan '17

Dear experts, Hi, I ran the preproc-sess command. I was following the tutorial page. looking at the files in the the masks directory, I see one mask: brain.nii.gz. However, the tutorial mentions more masks. Should I be worried?? What may be the cause? Bests, Ladan

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Problem with trac-all correction step for DTI image processing
by Farahbakhsh, Mahtab 03 Jan '17

03 Jan '17

Dear FreeSurfer, I am trying to pre-process my DTI data using TRACULA. But I receive an error when I run the pre-processing stage of DTI image processing. On the Correction step (1st step) I receive this error: ------------------------------------------------------------- MRIresample(): error inverting matrix; determinant is nan, matrix is: -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; Darwin Mahtabs-MBP 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Jan 2 03:23:23 IRST 2017 ------------------------------------------------------------ My DTI images are in enhanced DICOM format. In addition, I receive a warning earlier in the processing stage. The warning is: WARNING: it appears that the image position for all slices is the same. This is a problem with the DICOM file. Using direction cosines from col and row to compute slice direction, but the output may be misoriented. Please also find my log file attached to the mail. Any kind guidance from you is much appreciated. Kind Regards, Mahtab. -- Mahtab Farahbakhsh PhD Candidate Dept. Visual Neuroscience, UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL

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Freesurfer January 2017