Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

segmentation help
by Dilip Puri 11 Apr '17

11 Apr '17

Hi all, I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment HippoCampus. My input file xyz.img and output file will be like xyz_seg.img which contains only hippocampus image it like Grond Truth image for my original input image. Here is sample files including original and segmented mask link <https://drive.google.com/open?id=0B6rH1c6LupG_b3I4WUJ1RWZCbnM>. Even I am very new to FREESURFER so I don't know the procedure to reconstruct the images. Kindly help me.

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Difference in Recon-All Output Between Freesurfer Versions?
by Taylor, Johnmark 10 Apr '17

10 Apr '17

Hello, Recently, I re-ran recon-all with Freesurfer version 5 on some subjects whose surfaces had previously been reconstructed with Freesurfer version 4. As a result, it appears that their surface reconstructions have subtly changed, such that the labels that were specified in the old reconstruction are all messed up in the new reconstruction (since the surfaces that they were once associated with have changed). Did recon-all change between Freesurfer versions, and if so, is there a way to go back to the old algorithm short of simply switching back to Freesurfer version 4? It is possible that I have accidentally changed something else and that's why the surface files are different, but I wanted to see if there were any changes in the reconstruction algorithm between versions that might have caused this. Thank you very much, JohnMark Taylor

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Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation
by Antonin Skoch 10 Apr '17

10 Apr '17

Dear Doug, do you think that it is necessary/useful to rerun -normalization2 -maskbfs -segmentation steps after wm.mgz have been edited (that is what the -autorecon2-wm is used for I suppose)? The wm.mgz is not used in this steps as far as I can tell. In contrast, it seems to me that the documentation is more close to the optimum (the three steps: normalization, mask and segmentation steps are run only when it is needed - in -autorecon2-cp, not in -autorecon2-wm). Antonin I think the stages in the command line help are out of date On 04/08/2017 05:58 PM, Antonin Skoch wrote: > Dear experts, > > I noticed inconsistency between recon-all -help and actual code of > recon-all in -autorecon2-wm option. > According to the recon-all --help the -autorecon2-wm processes stages > 15-23 (fill through make white surfaces) and -autorecon2-cp processes > stages 12-23 (normalization2 throuhgh make white surfaces). But, in > the code both -autorecon2-wm and -autorecon2-cp are equivalently > processing stages 12-23. > > It seems to me that the stages 12-14 are not needed to process again > in -autorecon2-wm (which is used for re-processing after editing wm.mgz). > > Could you please comment on? > > Regards, > > Antonin Skoch

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Mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"
by Harris Hoke 10 Apr '17

10 Apr '17

I’m currently running freesurfer 6.0.0, and I’ve run into the same problem described in this thread on the archives <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43697.html> . Does anyone know if a fix exists? ~Harris

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calculating geodesic distances between vertices
by Burke Rosen 10 Apr '17

10 Apr '17

I am interested in finding the distance between two vertices along the cortical surface. So far I have used two methods: (1) Compute the shortest path with a variant of Dijkstra's algorithm on the white surface. (2) Compute the great circle distance on the sphere surface. (as done by Risk et.al. 2016 Neuroimage) Method (1) is slow and will tend to overestimate distances as the path only goes along mesh edges. Method (2) is very fast and gives a true geodesic but gives a scaled result because the radius of sphere surface is arbitrary; also this method is subject to distortions introduced by the inflation algorithm. My current strategy is to perform a linear regression between the triangle face areas of the sphere and white surfaces. And then apply the coefficients to the sphere surface diameter before calculating geodesic distances. This yields a distance matrix with a similar pattern to the Method (1) at about 62% scale. That scale seems like it might be reasonable. However, the regression only explains ~58% of the variance. My hunch is that the rest is due to inflation distortions. Is there a better way of scaling the sphere surface? Or a way to inflate in such a way that inter-vertex distances are preserved? Or, more generally, what is a good method of computing geodesic distances on freesurfer surfaces. Thank you, Burke Rosen

3 2

FreeSurfer : About ROI analysis
by Lisa Delalande 10 Apr '17

10 Apr '17

Hello, As a PhD student, I often use Freesurfer software and more precisely QDEC. A great question arises in connection with my last work. After drawing ROIs, I extricated values thanks to a " .levels" and a creation of a "stat" folder for each participant (aparcstat2table). My question is : can I make a correlation between a behavioral score and the value of "average SURFACE" obtained for each participant thanks to the command above-mentioned considering that my ROI has been drawn from clusters detected with a correlational analysis between THICKNESS (and not surface) and a behavioral score on QDEC ? Many thanks in advance for your assistance, and I am looking forward to hearing from you. Marine

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-autorecon2-wm: Inconsistency between recon-all code and documentation
by Antonin Skoch 10 Apr '17

10 Apr '17

Dear experts, I noticed inconsistency between recon-all -help and actual code of recon-all in -autorecon2-wm option. According to the recon-all --help the -autorecon2-wm processes stages 15-23 (fill through make white surfaces) and -autorecon2-cp processes stages 12-23 (normalization2 throuhgh make white surfaces). But, in the code both -autorecon2-wm and -autorecon2-cp are equivalently processing stages 12-23. It seems to me that the stages 12-14 are not needed to process again in -autorecon2-wm (which is used for re-processing after editing wm.mgz). Could you please comment on? Regards, Antonin Skoch

2 1

create mask from cluster number?
by lindsay hanford 10 Apr '17

10 Apr '17

Hello Freesurfer Developers, The main point of my post is to determine whether its possible to create a mask from a cluster ID run using a subset of the sample, and then use that mask to extract cortical thickness values from a model run with the full sample. I am running a pretty basic cortical thickness- behavioural correlation analysis with two groups using fsgd. Because I have a relatively small sample size (just over 40 participants in each group) I wanted to restrict my analysis to only regions that showed a relationship within the HC group. I ran the model using mri_glmfit: mri_glmfit --y HC.43.rh.10.mgh --fsgd Behav.fsgd --C v1.slope.mtx --surf fsaverage rh --cortex --glmdir MCCB.HC.43.rh Behav.fsgd setup: GroupDescriptorFile 1 Title MaineffectofGroup Class HC Variables BehavMC Input 128 HC -5 Input 132 HC 8 Input 192 HC -10 Input 193 HC -6 ... v1.slope.mtx: 0 1 *quick side question - in the past I was curious to see if this could test positive and negative relationships. I tried two different contrasts: 0 1 and 0 -1 to test the positive and negative relationships, respectively, however the results were the direct inverse of each other... it didn't show negative slope relationships. I am curious if its possible to test for negative relationships in freesurfer? How would you set up that contrast? next, I used mri_surfcluster to generate image and table files: mri_surfcluster --in HC.43.rh/v1.slope/sig.mgh --subject fsaverage --hemi rh --surf pial --annot aparc --thmin 2 --ocn HC.43.rh/v1.slope/results.ocn.mgh --sum HC.43.rh/v1.slope/results.sum.txt my results.sum.txt file shows a number of clusters ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 3.719 163035 270.33 57.7 -34.6 -21.5 234 inferiortemporal 2 3.499 22608 217.35 33.2 -48.2 -15.1 230 fusiform 3 3.170 2804 93.01 42.1 22.1 23.9 132 rostralmiddlefrontal Would it be possible to create a mask defined by say "ClusterNo 1"? Once the mask is created, I want to use it to extract the cortical thickness values for all participants (including those that weren't used to create the mask).. Is this possible? Can that be done using mri_segstats? Let me know if you require any other details. Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 Thank you in advance, Lindsay

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dimension mismatch between source and mask
by Maria Hakonen 10 Apr '17

10 Apr '17

Dear Freesurfer experts, I have tried to mask fMRI data with grey matter mask as follows: mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz However, I am getting an error " dimension mismatch between source and mask". Could someone please let me know how to solve this problem? Best, Maria

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Ventricle-to-Brain Ratio
by Gullickson, James 10 Apr '17

10 Apr '17

Hello all, I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go about this using the aseg.stats output (using asegstats2table), but am running into inconsistencies. The basic calculation for VBR is: (Total Ventricular Volume/Total Brain Volume) * 100 i.e. Bigler, E. D. (2013). Traumatic brain injury, neuroimaging, and neurodegeneration. *Frontiers in human neuroscience*, *7*, 395. What is the best way to get Total Ventricular Volume (TVV) and Total Brain Volume (TBV) for this calculation? I have tried several ways, which lead to different values: TVV = left lateral ventricle + left inf lateral ventricle + right lateral ventricle + right inf lateral ventricle + 3rd ventricle + 4th ventricle + 5th ventricle + choroid plexus which gives me a different result than TVV = BrainSegVol - BrainSegVolNotVent and for TBV TBV = TotalGrayVol + CorticalWhiteMatterVol which differs from TBV = BrainSegVolNotVent Thank you for your help, James Gullickson

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Freesurfer April 2017