Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

new version of mri_label2label
by APRIL CLAUSEN 05 Aug '14

05 Aug '14

I believe there was a bug in the mri_label2label script in the 5.3 install of FreeSurfer for Mac OS Lion (10.7 and up), and that this has been fixed. Can someone provide instructions on how to download and where to (directory) install this script. April Clausen

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uploading a surface in freeview
by carina＠van-vlodrop.de 05 Aug '14

05 Aug '14

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Flaws in my segmentation
by Isaiah C. Smith 04 Aug '14

04 Aug '14

Hello, There is some flaw in my segmentation that is not allowing me to change produce a mesh in MNE. How do I fix the segmentation in freesurfer so that skull surfaces do not overlap? Isaiah (Error Shown Below) Checking that inner skull surface is inside outer skull surface...[failed] Surface inner skull is not completely inside surface outer skull(sum of solid angles = 8.85217e-16 * 4*PI). Could't create the geometry

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merging segmented volumes
by Barnes Anna (UNIVERSITY COLLEGE LONDON HOSPITALS NHS FOUNDATION TRUST - RRV) 04 Aug '14

04 Aug '14

Dear All What is the simplest way to reduce the number of regions that the segmentation code produces. Very best regards Anna Anna Barnes, PhD, CSci, MIPEM Clinical Scientist (PETMRI) UCL Institute of Nuclear Medicine UCL Hospitals NHS Foundation Trust 235 Euston Road | London NW1 2BU | UK anna.p.barnes(a)ucl.ac.uk<mailto:anna.p.barnes@ucl.ac.uk> or anna.barnes1(a)nhs.net<mailto:anna.barnes1@nhs.net> 0203 447 0524 ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ********************************************************************************************************************

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Please need help with mris_convert.
by Tara Miskovich 04 Aug '14

04 Aug '14

Hi all, I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required here. I understand I put in the label after label and the output at the end, but in this example I am not sure what the V1 and lh.white are for. Thanks, Tara -- Thank you, Tara

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Freesurfer and MNE
by Isaiah C. Smith 03 Aug '14

03 Aug '14

I have the MRI data, but I am confused as to how to proceed with the mne_setup_mri for the brain, skull and scalp volume conduction models because the brain and T1 are the defaults. Do I need to add some other slices? And does the subject data need to be placed in /freesurfer/subjects for it to be read by MNE? Isaiah

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Freesurfer Start Up
by Isaiah C. Smith 03 Aug '14

03 Aug '14

Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith

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Repost | Re: mni152reg error
by JacobML＠nmr.mgh.harvard.edu 02 Aug '14

02 Aug '14

Hello Doug, Ideally, I am trying to take subject tstat maps from FsFast (stable3 environment) and register these native structural space maps to the MNI152_2mm standard brain. The t_000.bfloat file is what was generated relative to my contrast that was set up in FsFast stable3. There are a series of these files ranging from t_000.bfloat to t_029.bfloat and there are also these same named files with a .hdr extension. t_000.bfloat is the file I designate when I select an overlay within tkmedit. Your help sorting out this registration is very appreciated. Thank you, Jacob >> I'm not sure what you are trying to do, but that command line looks like >> things are not set up properly. What is t_000.bfloat? (And why are you using bfloats?) >> doug >> On 7/17/14 1:14 PM, JacobML(a)nmr.mgh.harvard.edu wrote: >>> Hello again Doug, >>> Thank you for sending the updated version of mri152reg. It ran without error and generated the reg.mni152.2mm.dat registration matrix. Unfortunately though, when I tried to apply the transformation to the same >>> subject's t_000.bfloat, the registration is not correct (command below). mri_vol2vol --inv --targ /.../t_000.bfloat --mov >>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o >>> CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat On a positive note, I was able to load the output image and >>> MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be shifted too far anterior. >>> With my next attempt, I used mri_convert to make the t_000.bfloat into a .mgz and than ran mri_vol2vol, but the same misalignment occurred (see attached photo). >>> Using tkmedit, I have confirmed that this file aligns properly on this subject's native structural image, so I am not quite sure why the registration matrix may be off. Given that the reg.mni152.2mm.dat file reflects the transformation of the native struc to MNI, I wonder if I need >>> to account for the reg file between the func data and the native struc? >>> Can you please let me know what I may be doing incorrectly? >>> As always, your help is very appreciated. >>> Jacob >>>> Yea, i fixed this problem. I've attached a new version with the fix. doug >>>> On 07/17/2014 10:35 AM, JacobML(a)nmr.mgh.harvard.edu wrote: >>>>> Hello Freesurfer Experts, >>>>> I am trying to view stats generated with FsFast in fslview/MNIspace, >>> and >>>>> in doing so I have run mni152reg to generate the registration matrix. >>> That said, mni152reg did not complete correctly and below I have pasted >>> the terminal output: >>>>> Thu Jul 17 09:58:10 EDT 2014 >>>>> setenv SUBJECTS_DIR >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons >>>>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons >>> /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s >>>>> CD_cerv_pat4_sess1_recon >>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 >>> UTC >>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux >>>>> fslregister --mov >>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz >>> --s CD_cerv_pat4_sess1_recon --reg >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat >>> --dof 12 >>>>> mkdir: cannot create directory >>>>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': >>> Permission denied >>>>> Log file is >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log >>> Thu Jul 17 09:58:11 EDT 2014 >>>>> --mov >>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz >>> --s CD_cerv_pat4_sess1_recon --reg >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat >>> --dof 12 >>>>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ >>>>> purkinje >>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 >>> UTC >>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux >>>>> nIters 1 >>>>> -------------------------------------- >>>>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons mri_convert >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz >>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii mri_convert >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz >>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii niiWrite(): error opening file >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii >>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from >>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... >>> TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 >>>>> i_ras = (-1, 0, 0) >>>>> j_ras = (-0, -0, -1) >>>>> k_ras = (0, 1, 0) >>>>> writing to >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... >>> ERROR: failure writing >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii >>> I tried to run the fslregister command from within the subject's directory >>>>> (in hopes to possible correct what may be a permissions issue), but >>> this >>>>> produces the same final error, "ERROR: failure writing >>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." >>> Lastly, probably to no surprise, the >>>>> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any >>> ideas how I may be able to correct these errors? >>>>> Thank you for the help! >>>>> Jacob >>>>> _______________________________________________ >>>>> 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 >>> _______________________________________________ >>> 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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High intensity blood vessels in children with meMPRAGE
by McLaughlin, Katie 01 Aug '14

01 Aug '14

Hi Doug, Bruce, et al. We've used the MGH meMPRAGE protocol successfully with children and adolescents previously on a Siemens 3T. I've recently moved to a new institution and am using the protocol on a Philips 3T Achieva scanner and we've been having a lot of issues with high-intensity blood vessels (appearing bright white and interfering with segmentation in FreeSurfer). Screenshot of an example attached. We have added some rest slabs/sat bands to the protocol to address this, but it hasn't fully solved the problem. I'm wondering if you have any recommendations about adjusting things in FreeSurfer to help us get better segmentation? Thanks for your thoughts on this, Kate

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QDEC Cluster Analysis
by Mohammed Goryawala 01 Aug '14

01 Aug '14

Hello All, I have some questions related to the qdec analysis I have run. 1. On running the qdec I see that FWHM is an input which changes cluster definition significantly. How would I choose the right FWHM for the analysis and can it be related to any imaging parameters? 2. Secondly, on completion of the qdec analysis I want to export the clusters created by the qdec analysis into a volumetric file (which I can later convert to .nii). Please also suggest a way that would let me only export clusters above a particular size threshold. Thank you very much in advance. Mohammed Goryawala Department of Radiology University of Miami, Miller School of Medicine

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Freesurfer August 2014