Freesurfer

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30064 discussions

Version 6.0 - ?h.white.preaparc vs. ?h.white for determining the need to edit brainmask.mgz, wm.mgz, add control points, etc.
by Mira Michelle Raman 04 Sep '17

04 Sep '17

Hi, My main question to the 6.0 experts is: Is the lh.white.preaparc close enough to the lh.white to determine whether editing is needed (brainmask.mgz, wm.mgz,control points) or do we need to run the full pipeline and get ?h.white? Here's the reasoning behind this question. In previous versions of Freesurfer we have run -autorecon1 -autorecon2, then checked surfaces, made edits if needed, and then only after we were satisfied with the surfaces we ran -autorecon3. Primarily we have done this for 2 reason, first is to save processing time, on both the initial pass and running -autorecon2-cp or -autorecon2-wm. We also use this as a quality control method, in which ONLY subjects whose surfaces have been verified, have been through -autorecon3, those that haven't, don't have stats files, and thus can't get inadvertently included with finished data. If ?h.white.preaparc doesn't topologically differ from the ?h.white could we use it for determining what edits to do? if it does differ obviously we will have to run the whole pipeline. Thank you in advance for your guidance. Sincerely, Mira _______________________________________________ Mira Michelle Raman Lead Scientific Programmer The Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd, Ste. 1356

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Using Total Cortical White Matter Volume as a "whole brain" covariate
by Mehta, Chintan 04 Sep '17

04 Sep '17

Dear FreeSurfer Developers, I am using FreeSurfer 5.3 to analyze whether a risk factor explains variation in brain structures related to surface area, mean thickness, and subcortical volumes. Documentation suggests using estimated Total Intracranial Volume (eTIV) as a covariate to adjust for brain size in analyses of surface area and volumes: (https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV) Previous posts have also suggested using BrainSegNotVent or Total Gray Matter Volume as covariates as a "whole brain" covariate, with the choice of covariates representing different hypotheses regarding local vs. global atrophy. However, it seems to me that using BrainSegNotVent or Total Gray Matter Volume as covariates could lead to a significant loss in power in detecting effects on area/thickness measures from a risk factor associated with atrophy across many regions. On the other hand, eTIV may suffer from not accounting accounting for local atrophy (in addition to heightened measurement error, as frequently alluded into previous posts). But still, a normalization covariate is needed to account for differences in brain size need to be accounted In the analysis of cortical surface area or mean cortical thickness among normal populations, could it make sense to use cortical white matter volume as the "whole brain" covariate? In normal populations, cortical white matter volume is significantly correlated with surface area, mean thickness, and gray matter volumes but its value is not derived from the gray matter structures. My understanding is that FreeSurfer sets cortical surface area as the area at the boundary of white and gray matter. As a covariate in models of cortical surface area or mean thickness, white matter volume could side-step the loss in power in detecting effects lead to both global atrophy in gray matter volume while also partly adjusting for total brain differences. Cortical white matter volume is not a standard "whole brain" covariate in the literature (in the way eTIV or Total Gray Matter Volume are). However, am I misunderstanding how FreeSurfer computes these Cortical White Matter that makes it unsuitable as a "whole brain" covariate? Thank you. Best, Chintan

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Cerebellum Segmentation
by José Gómez-Feria Ferreiro 04 Sep '17

04 Sep '17

Dear Freesurfer, I have been doing some MRI segmentations using the "mri2mesh" command (which does "recon all"). However, I noticed the cerebellum segmentation is not correctly done. It considers the cerebellum as white matter but it also has grey matter. Is there a way to make a more precise segmentation of the cerebellum? Best regards, José Gómez-Feria Ferreiro MD/PhD candidate Grupo de Trastornos del Movimiento. Lab 104 Programa de Investigación de Neurociencias Instituto de Biomedicina de Sevilla (IBiS) Hosp.Univ. Virgen del Rocío/CSIC/Univ. de Sevilla Avda. Manuel Siurot s/n. 41013 - Sevilla (España)

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volume registration; volume connections;
by Daniel van de Velden 04 Sep '17

04 Sep '17

Dear Freesurfer-Team, I am trying to study volume based neuronal activities via a Spatio Temporal Clustering Test. Therefore I need to morph my subjects to an average subject. I couldn't find a non-linear morphing command to perform this. Is there any function and can I extract to resulting morphing map that was used to morph the subjects ? Something like the /'hemisphere'.sphere.reg/ files, which are automatically created by the 'recon-all' function. Additionally is it possible to extract the volume neighboring connection from a /'hemisphere'.volume/ file ? For further information: I am going to use mne-python to perform the Spatio-Temporal-Clustering. They are extracting the vertice connections via a function ( /_get_subject_sphere_tris(subject_from, subjects_dir)/ ) from the /'hemisphere'.sphere.reg/ files. Can I also do this for volume data files created by FreeSurfer. Looking forward to your reply. I am glad to any kind of corporation, I really want this study to work, since the results will be very interesting. Yours sincerely, Daniel van de Velden

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Pial surface volume
by Fereshte 04 Sep '17

04 Sep '17

Hello FreeSurfer developers Is it possible to have the volume of pial surface in FreeSurfer?

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recon-all error: ERROR! FOV=272.000 > 256
by juhyoung Ryu 03 Sep '17

03 Sep '17

Hi experts, I'm trying to surface reconstruction using high-resolution T1 and T2 data using freesurfer version 6 So I typed like this: recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all and that excited with errors like this; \n**************************************** ERROR! FOV=272.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. ****************************************\n So I added -cw256 flag and run the command line again (recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all -cw256). But the result is same. I'd appreciate any suggestion. Thank you, Juhyoung

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Run stats for both hemisphere?
by Xianwei Che 03 Sep '17

03 Sep '17

Dear freesurfer experts, I am wring to ask a stupid question, which I did not find the answer in the mailing list. I am going to run stats on the thickness data as described in the tutorial, do I have to run separately for each hemisphere? If I am not wrong, we have to specify the hemi in the data assembling stage. Are we able to run once for both hemis in the glm and correction stage? If not, I am a little confused in the correction stage, which we specify the --2spaces in the simulation. As indicated in the tutorial, this is for adjusting p for both hemis. Another question is about subcortical areas. Do we have to run stats for the cortical and subcortical areas separately? Thanks *-------------* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia

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Freesurfer tutorial
by Esteban, Eva(GE Healthcare) 03 Sep '17

03 Sep '17

Good afternoon, I am new to Freesurfer and following the instructions to find out the Cortical Thickness of a Volume-defined ROI(http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness), everything goes well until step 4. Even if I try to use -reshape-factor 7 as suggested, it reshapes it to 6 and so the next step gives an error because the segmentation is shaped to 7. Would anyone mind giving me some guidance on how to do it? Many thanks, Eva

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Continuous co-variate by continuous co-variate interaction effects
by Timothy Hendrickson 03 Sep '17

03 Sep '17

Freesurfer experts, I have created a design matrix in order to test for whether there is an interaction effect between two continuous co-variates controlling for a categorical variable. So I have one categorical variable with two levels, and two continuous co-variates. My design matrix is as follows: 0 0 1 1 0 0 0 0 0 0 1 1 Is this correct? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

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-refeventdur in mkanalysis-sess?
by Tori Williams 03 Sep '17

03 Sep '17

Hi FreeSurfer Team, I was wondering if you could provide a bit more clarification on what the "-refeventdur" flag is referring to in the mkanalysis-sess command? The description in the help screen states it should be the "duration (sec) of reference event for scaling." I am unsure what the "reference event" is. I couldn't find any additional info on the listserv, and the two examples I saw from tutorials used a value of "4" and another used a value of "16". Any clarification is greatly appreciated! Because the help for the flag is listed under the "Assume a shape" header, does it have something to do with the HRF? Thanks so much! Tori -- Victoria J. Williams, PhD Clinical Research Fellow Interdisciplinary Brain Center Massachusetts General Hospital Harvard Medical School Department of Neurology 149 13th Street Charlestown, MA 02129

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