Freesurfer May 2018

freesurfer@nmr.mgh.harvard.edu

117 participants
167 discussions

Non-parametric correlation between FC and neuropsychological/volumetric outcomes
by stdp82＠virgilio.it 08 May '18

08 May '18

Hi list, which the best way to perform a whole-brain correlation of the FC assessed by FS-FAST with the volumetic or neuropsychological outcomes? Please note that my question is specifically addressed to those factors (neuropsycholgical scores or volume of seed) did not show a normal distribution and that cannot be trasformed. Thanks Kind regards Stefano

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N3 kernel decrease
by Rebecca Ray 07 May '18

07 May '18

External Email - Use Caution Hello, I am working on T1 images from multi-sites. One site in particular is producing T1s that have small to large areas of temporal cortex being excluded from segmentation. It seems that there may be an issue with inhomogeneity of the bias field and subsequent over correction. I have 2 scans from each person and the 2nd scan is worse. The second scan from one subject refuses to finish the freesurfer pipeline. It seems to boom out right before segmentation. I was told to decrease the bias field correction smoothing kernel but have not found where to do that on the Wiki. How do I add that syntax? Thanks. Rebecca

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Re: [Freesurfer] transforming functional volumes to MNI without resampling
by David Beeler 07 May '18

07 May '18

External Email - Use Caution Hi Doug, Ok so if I am understanding correctly, SPM or FSL will be better at registering functional data to CVS or MNI space for group analyses than freesurfer will be because they have the capability of doing nonlinear registrations. If that's the case I may give SPM a shot and compare the results. But if I were to use freesurfer to do this registration, is there something better than the following commands?: bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --bold mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg --no-resample --nearest Adding --12 to bbregister and using the same mri_vol2vol as above actually makes the transformation much worse, is there something I'm missing? I will use SPM if I have to, but I feel like there is probably something smarter I could be doing with freesurfer. And for clarification, is the --12 flag in bbregister making the registration affine (ie accounting for translation, rotation, scaling, and sheers)? Thanks again for your help, much appreciated! DB ------------------------------------------------------------------------ Douglas N. Greve wrote: If that is really what you want to do, you should use a tool appropriate for this type of analysis (eg, SPM and FSL have non-linear intersubject registration) ------------------------------------------------------------------------ On 05/04/2018 01:13 PM, David Beeler wrote: > > > Hi Doug, > > funcVol is an individual functional resting state scan. We are doing > some clustering analyses and trying to visually compare the clustering > across subjects (I would be a bit sketched out trying to quantify the > overlap between subjects due to individual differences in anatomy, > etc, but just looking at it might give us a clue on what is going on). > We do all our analyses in the individual subject's native space, but > it's hard to see what the similarities / differences are. > > If not bbregister, what would be the correct way to align all subjects > to a common space? > > Thanks, > DB > ------------------------------------------------------------------------ > Douglas N. Greve wrote: > What is funcVol? An individual functional? If so, then use --12 (12 dof > to account for scaling). In general, we don't recommend doing cross > subject registration with BBR as it is really not appropriate for that > kind of thing. > ------------------------------------------------------------------------ > On 05/03/2018 01:30 PM, David Beeler wrote: > > Hi, > > I'm trying to register and transform some raw functional data > (108x108x72x175, 2mm iso voxels) to MNI space, while keeping the low > res dimensions. > > I have tried: > bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl > --bold > mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg > --no-resample --nearest > mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg > --no-resample > > And this looks pretty good, but not perfect... the functional data is > oriented correctly but the brain seems to be a centimeter or two > smaller in multiple dimensions, see: > > http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png > > I'm not too surprised since the MNI brain is blurry and oddly round, > but presumably there is a way to do this transformation more > accurately. I've run mri_cvs_register for this subject using the --mni > flag: > > mri_cvs_register --openmp 8 --mni --mov $subjID --outdir $mniDir > > And for other applications I use this m3z file to transform volumes > between MNI orig.mgz and individual subject orig.mgz, but is there a > way to use it to transform functional data to MNI space while keeping > the functional dimensions? > > I could do: > > mri_vol2vol --mov funcVol --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz > --reg register.dof6.lta --nearest --o template-in-anat.nii.gz > > mri_vol2vol --noDefM3zPath --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz > --mov template-in-anat.nii.gz --m3z > $mniDir/final_CVSmorph_tocvs_avg35_inMNI152.m3z --o > template-in-MNI-m3z.nii.gz --nearest > > But not only is this unideal because it requires upsampling the > functional data to 256x256x256, it also gets these funky wavy distortions: > > http://web.mit.edu/dsbeeler/www/images/m3z-mni.png > > > Any thoughts are appreciated, thanks! > > -DB > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Query regarding creation of atlas directly from probabilistic information
by Mageshwar Selvakumar 07 May '18

07 May '18

External Email - Use Caution Dear All and Bruce, This mail is on top of the query I had a couple of weeks back where I misinterpreted that I had binary mask of each structure as individual nifti volume files but on closer look, the nifti files had the probability that the structure is present at that certain location. On looking into the freesurfer website, I came across this documentation of creation of Atlas, https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas SurfaceLabelAtlas - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas> Overview. This document provides an overview of two related topics: How the FreeSurfer pipeline automatically labels a subject's regions (producing an annotation file) by comparing the subject's curvature data to an "atlas" ("gcs") file. surfer.nmr.mgh.harvard.edu In this documentation the process is done by looping through N subjects to get the probability information, and these subjects are registered to the registration template derived from average of reference templates. I would like to know if I could use these probability information directly and since the atlas information is already in the MNI152 space, can I use the registration template which is already available with freesurfer, and if yes, can someone guide me on which registration files I must use. Secondly, I tried using mri_vol2surf and tried to convert the volume data to a surface data before creating labels, but on doing so I had errors when creating labels from the surface files. To convert into volume I ran the below code: *mri_vol2surf --mov ID076_LL_PHGa_l_HvOx_prob.mgz --ref ID076_LL_PHGa_l_HvOx_prob.mgz --out ID076_LL_PHGa_l_HvOx_prob_surf.mgz --hemi lh --mni152reg --projdist-max -2 0 .1 --reshape --interp nearest* Then I to convert this surface file into label I ran *mri_cor2label --i ID080_CPuP_l_HvOx_prob_surf.mgz --l area1.label --id 076* And I got the error *Found 0 label voxels ERROR: found no voxels matching id 76* But the process runs fine if I run the mri_cor2label on the volume file. It would be nice if someone can help me out on where I'm going wrong here. Thank you, Kind regards Mageshwar Selvakumar, M.Sc Department of Pharmakologische Bildgebung und Bildanalyse Friedrich Alexander Universität Erlangen Nürnberg Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898

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Motion Parameter on the Cortical Surface
by Pfannmoeller, Joerg Peter 07 May '18

07 May '18

Dear all, in fMRI analyses the translation of the the brains center and the rotation of the associated coordinate system are determined. Did anybody of you ever write a tool to determine the corresponding motion of the cortical surfaces? What I mean is the total shift due to translation and rotation for each time point in the fMRI time series and for each point on the white matter or pial surface. Yours Joerg

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vertex wise cortical thickness within ROIs
by Fujiwara, Hisako 07 May '18

07 May '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute absolute cortical thickness for each vertices within anatomical ROIs using apac.annot. I have successfully output the whole brain vertex wise cortical thickness using: mris_convert -c <subject>/surf/?h.thickness <subject>/surf/?h.org <subject>/surf/?hthickenss.asc Since this creates huge numbers (> e.g., 140,000) for each hemisphere for each participants, I would like to narrow out focus on the specific ROIs for relevant to our study? Is this achievable to add options to do? Thank you for your help in advance. Best regards, Hisako

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fmriprep to fsfast interface
by Boggess, Matthew Jozsef 07 May '18

07 May '18

Hello, I've been working on taking the outputs of the fmriprep BOLD preprocessing tool (https://fmriprep.readthedocs.io/en/latest/index.html) and coercing them into the fsfast structure so that first levels can be run with mkanalysis-sess and selxavg3b-sess. It's been a bit trickier than anticipated and I was hoping to get some help verifying my current approach (attached to this email). Question 1: fmriprep outputs the preprocessed BOLD data in the T1 space (mni305 is not an option). However, the typical spatial normalization workflow uses a registration matrix from the bold to T1 to transform to talairach. Is there a way to do this transformation without having to specify a registration matrix given the functional data is already in the T1 space? My current approach is to use mri_convert with the --apply_transform flag pointing to the talairach.xfm registration matrix in the subject's recon folder, but I am not sure if this is a reasonable workaround. Question 2: fsfast normally calculates the global mean value of the raw data to be used for intensity normalization. However, with fmriprep I only have access to the preprocessed data in T1 space. Would extracting the global mean value for intensity normalization from the preprocessed BOLD in T1 space be valid? Question 3: Is there a way to do first levels in the native subcortical space? If so, what is the filename structure expected (maybe mni305.2mm gets replaced with the subject name as with the surface data)? I've only seen examples transforming to mni305 space, but ideally an option would be to just transfer the preprocessed BOLD in T1 space and run first levels staying in the native T1 space. Thanks for your help! Matt

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wmparc.mgz transformation
by Rongxiang Tang 07 May '18

07 May '18

External Email - Use Caution Dear All, I would like to transform individual wmparc.mgz into MNI space for each of my subjects. I have tried using this command:mri_vol2vol --targ /data/mri/wmparc.mgz --mov /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --inv --reg /usr/local/freesurfer/subjects/fsaverage/mri/transforms/reg.mni152.2mm.dat --o test.mgz However, when I compare this output file with my FSL normalized functional data (MNI space), they didn't really match well - not a one-to one exact match (orientation slightly different), although the dimension and space are all in MNI 2mm. Do I need to use bbregister or other commands to transform it better? Thanks!Catherine

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Complete CSF value computation
by M Janani 07 May '18

07 May '18

External Email - Use Caution Hi Team, We would like to compute the CSF value from the MRI data. We have both T1 and T2 weighted images. Have processed the T1 images and obtained the CSF value(summation of ventricular system and CSF value). But it's very low since it doesn't include the sulcal CSF value. We are interested in computing the complete CSF value. Any help from your people end would be really grateful. Regards, Janani ::DISCLAIMER:: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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(Follow-Up) Interaction Contrast
by David S Lee 07 May '18

07 May '18

External Email - Use Caution Dear Douglas, Thank you for your guidance. I am following-up on your response with regards to setting up DODS matrix to test interaction between two continous covariates. If I understand your recommendation correctly (please correct me if I am wrong), I am averegaing slopes for the new interaction covairate (age*weight), while regressing out slope estimates for age and weight. I am curious to know why regressing out the two original covariates is recommended. Thanks for your time! David _____________________________________________ You need to put in age, weight, AND age*weight. If you have two classes and use DODS, then the contrast would be 0 0 0 0 0 0 0.5 0.5 On 4/13/18 8:02 PM, David S Lee wrote: Hi Douglas, Thank you for your reply. To follow up, I am setting up GLM analysis with 1 categorical variable and 1 continuous variable (age X weight). Myfsgd looks like this: /GroupDescriptorFile 1/ /Title Cortical Thickness Interaction between Age and Weight/ /Class class1 plus blue/ /Class class2 circle green/ /Variable Demean Age X Demean Weight/ /Input001Class1500/ /Input002Class2433/ /.../ I want to test for an interaction between age and weight while controlling forgroup. Instead ofputting-inage and weight separately, I multiply them to test for interaction. Can you tell me if following contrast vector will correctly test for this? /0 0 0.5 0.5/ / / Thank you for your time, / / -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115 <tel:%28608%29%20890-1115> _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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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Freesurfer May 2018