Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

[FSL or FREESURFER] SIEMENS FIELDMAP B0 UNWARPING FOR DTI
by VA Research 22 Mar '17

22 Mar '17

Hello FSL and FS pros, I am trying to pre process DW images but am not sure how to unwarp images. We are using Siemens Skyra 3T and output fieldmaps; 2 files output from the scanner; the first file contains two magnitude files in one the second file contains the single phase difference image ------------------------------------------------------------------------------------------------------- FSL ------------------------------------------------------------------------------------------------------- through FSL we have run eddy correct, bet the magnitude file, and run fsl prepare fieldmap (example code below) I am not sure how to use the prelude and FUGUE command and am unclear on their inputs/outputs Does anyone in FSL land have a clear tutorial of how to utilize these tools? for example, given my type of fieldmaps do i need to use prelude? later through FSL stream we would like to complete bet preprocessed DW images, dtifit, bedpostx ---------------------------------------------------------------------------------------------------- FREESURFERS ---------------------------------------------------------------------------------------------------- I have read over the TRACULA requirements and how to edit the configuration files. There is mention of eddy current correction that is available through tracula but nothing mentioned for dealing with the warping issue. Does anyone in freesurfer land have any suggestions on how to tackle this as a part of the tracula data stream? Any input will be appreciated, Thanks so much Joseph Veliz Brentwood Biomedical Research VA Hospital West Los Angeles ---------------------------------------------------------------------------------------------------- example ---------------------------------------------------------------------------------------------------- #Eddy correction eddy_correct ${name}_dti.nii.gz /Users/seahorse/Studies/NN/DTI/${name}/${name}DTI_eddy.nii.gz 0 #BET fieldmap mag super tight; exclude all non brain voxels bet 10001_dtiFMmag1mag2.nii.gz /Users/seahorse/Studies/NN/DTI/10001/10001dtimags_brain.nii.gz -F -m -f 0.85 #generate fieldmap in rad/s for FEAT or FUGUE fsl_prepare_fieldmap SIEMENS 10001_dtiFMphase.nii.gz 10001dtimags_brain.nii.gz fmap_rads 2.46 #Prelude prelude -c data --unwrap=result prelude --complex=data -u result #FUGUE Utility for Geometrically Unwarping EPIs; performs unwarping of an EPI image based on fieldmap data fugue -i epi -p unwrappedphase --dwell=dwelltime --asym=asymtime -s 0.5 -u result fugue -i epi --dwell=dwelltime --loadfmap=fieldmap -u result

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Hippocampal Subfields Posterior Probability
by Bharadwaj, Pradyumna - (prad) 22 Mar '17

22 Mar '17

Hello Dr. Iglesias, I'm currently examining the distributions of the posterior probabilities of the different hippocampal subfields, and I'm interested in obtaining the probability distribution images for the subfields that correspond to the volumes output in the subjects text file. While I can use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain the subfield masks and use them to obtain the posterior probabilities distribution after soft segmentation, is there some other straighforward way to obtain these posterior probabilities for the volumes stated in the output text file ? A follow up question - It appears that the soft segmentation approach approximates thresholding the posteriors by a value around 0.5 ? In your opinion, is this value acceptable and have you found similar values in your testing ? Thanks! -Prad

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preproc-sess -per-run vs. -per-session
by Feilong Ma 22 Mar '17

22 Mar '17

Hi FreeSurfer Experts, I was reading the document of preproc-sess, and it seems -per-run is recommended instead of -per-session. Here is the part: > -per-run > Motion correct and register using the middle time point of each run. > This is the option that you should use. > -per-session > Motion correct and register using the first time point of the first > run. This is mainly for compatability with version 4. > Is there a reason to preprocess each run separately? I know some people motion correct and register all EPI volumes to the same reference EPI volume, which also works well. Thanks, Feilong

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Custom brain segmentation to equal sized regions
by david.kamson＠pet.wayne.edu 22 Mar '17

22 Mar '17

Freesurfers, Is there a way to segment each hemisphere to an identical number of equal sized regions which are as close in size and location as possible to their contralateral homotopic regions. Eg. Id like to segment the left hemisphere to regions with a 2 cm2 surface and do the same for the right in order to compare asymmetries in these small regions. Anybody had done this before? David

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Re: [Freesurfer] display SPM results on inflated surface?
by Schoot, Lotte 22 Mar '17

22 Mar '17

Hi Doug and others, A while ago, I got this reply to my question below (thanks!). I tried to look in to it, but I am a bit confused (probably because I am very new to Freesurfer). My results are on the MNI 152, but I don't understand what you mean with 'run the mni152 through freesurfer'. Is this the process to get the register.dat file that is required in mri_vol2surf? What would you recommend to get the register.dat file? Is it possible to use bbregister for that? I have tried this, but I don't know whether it is correct: bbregister --s fsaverage --mov con_0001.nii --init-spm --reg register.dat --bold Thanks! Lotte >If your results are on the MNI152, you can run the mni152 through >freesurfer, then use mri_vol2surf to map the data to the surface then >view it with freeview (or tksurfer). You should not confuse this with >doing the fMRI analysis on the surface. You will not have the benefits >of surface-based analysis On 02/15/2017 03:37 PM, Schoot, Lotte wrote: > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Phone Number: 617-724-2358 Fax: 617-726-7422

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White matter volume in each lobe
by Ahearn, T 22 Mar '17

22 Mar '17

Hello I need separate grey and white volumes for the frontal and temporal lobes. I have values for grey volume from mri_annotation2label --subject 01 --hemi lh --lobesStrict lobar_annotation mris_anatomical_stats on the lh.lobar_annotation.annot file to generate a text file. I've also run similar to the following and now have a text file wmparc.a2009.stats. mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz mri_segstats --seg mri/wmparc.a2009s.mgz --sum stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject --surf-wm-vol --ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv Is there a standard list of labels in this file that are used to create the frontal and temporal lobes? Thanks The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.

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xhemi label
by Marissa Pifer 22 Mar '17

22 Mar '17

Hi freesurfers, I am using xhemi to map the right hemisphere of each subject to the left hemisphere of the same subject. The first xhemi command works fine, but the 2nd step for mapping the label, I get this error: "Option --src-label unknown" Do you know how to fix this? Marissa

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Re: [Freesurfer] Dimensions question
by Yendiki, Anastasia 22 Mar '17

22 Mar '17

The first is the number of voxels, the second is the size of a single voxel. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of yusif Al-kheder <yusif93(a)live.com<mailto:yusif93@live.com>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, March 22, 2017 at 9:31 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Dimensions question For a skull-stripped anatomical nifti file, What’s the difference between '91 x 109 x 91’ and 2mm x 2mm x 2mm? [image1.png] Youssif

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Dimensions question
by yusif Al-kheder 22 Mar '17

22 Mar '17

For a skull-stripped anatomical nifti file, What’s the difference between '91 x 109 x 91’ and 2mm x 2mm x 2mm? [image1.png] Youssif

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Recon-all creating binary T1.mgz image
by Emily Grossnickle Peterson 21 Mar '17

21 Mar '17

Dear surfers, For several subjects recon-all created a binary brainmask and binary T1.mgz image. Recon-all finished successfully for these subjects and the nu.mgz file looks fine. I have attached a screenshot of what it looks like when I open Freeview. This only happened for 7/82 subjects. Any ideas what might be the issue? Thank you in advance for your thoughts, Emily [image: Inline image 1]

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Freesurfer March 2017