Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

Re: [Freesurfer] Overestimation of volume in Hippocampus
by Antonin Skoch 27 Feb '17

27 Feb '17

Dear Michel, by default in the recon-all the input images are resampled to 1x1x1mm3. To disable this and retain your resolution, you have to add -hires flag (and adapt the mris_inflate -n parameter). This could improve the segmentation results, however I would not expect that it is the reason of volume overestimation you are refering to. I am not expert at hippocampal anatomy, therefore I cannot comment on your results. But I am guessing, maybe the hippocampal atlas in FreeSurfer includes some portions which have not been included in the MCI studies you refer to? Maybe you can find answer in the Hippocampal subfields paper: http://www.nmr.mgh.harvard.edu/~iglesias/pdf/subfieldsNeuroimage2015preprin… Antonin Dear Antonin, I did use the T2 scan for the T2pial refinement during the recon-all however I actually already preformed the hippocampal subfields and when i looked at the txt file generated from that the results are quite similar. I used the multispectral segmentation. I didn't not use the -hires flag but what does this flag exactly do if i may ask?Sincerely, Michel Hu ________________________________ Van: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> namens Antonin Skoch <a...(a)ikem.cz> Verzonden: maandag 27 februari 2017 12:31 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus Dear Michel, Given your resolution 0.8x0.8x0.8, did you run recon-all with -hires flag? What did you used T2 image for? As a -T2pial refinement? T2 image is not used for hippocampal segmentation in standard recon-all stream. But pay attention that with -hires you also have to alter default value for mris_inflate, as specified here http://freesurfer.net/fswiki/SubmillimeterRecon In my case -n was not enough, I would recommend -n 50 (more does not do any harm). In any case, I would recommend to try hippocampal subfields module. https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields This should be more precise than "standard" aseg segmentation and given you have also 3D T2, multispectral T1 and T2 segmentation can be used. Antonin Skoch Dear Shane, I have checked the aseg.mgz and in only one I would say the segmentation failed however the others look fine and I'm taking the measurements from the text file that is generated from the aseg.stats. Should I redo the recon-all with a different input? I have always given freesurfer T1 and a T2 scan to process both having a resolution of 0.8x0.8x0.8 mm. Sincerely, Michel Hu ________________________________ Van: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> namens Shane S <shane.schofi...(a)yahoo.com> Verzonden: maandag 27 februari 2017 11:15 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus Hi Michel Hu, Yes, that’s too large for MCI or even controls for that matter I think. Have you checked the aseg.mgz? I generally find that the hippocampus is well segmented, even in patients with a lot of atrophy. Are you taking the measurements with the asegstats2table? Sincerely, -- Shane S On 27 February 2017 at 10:12:09, Michel Hu (a...(a)live.nl<mailto:a...@live.nl>) wrote: Dear Shane, I apologize for not being clear. The reported value is of only one half of the hippocampus. I have only run 4 subjects of the 75 however they all have a reported value of between 6000 to 10000 mm^3 summed together for the hippocampus. Sincerely, Michel Hu ________________________________ Van: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> namens Shane S <shane.schofi...(a)yahoo.com> Verzonden: maandag 27 februari 2017 11:00 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus Hi Michel Hu, Is that a summed value of left and right hippocampus? That seems normal to me since averaged total hippocamppal volumes for MCI have been typically reported at around 2500-3500mm3. Thanks, -- Shane S On 27 February 2017 at 09:44:27, Michel Hu (a...(a)live.nl<mailto:a...@live.nl>) wrote: Dear Freesurfer experts, I have run several subjects through the recon-all pipeline including the hippocampal segmentation with freesurfer 6.0 on Ubuntu 16.04. However when looking at the text file with the volumes it seems that all the numbers are bigger than normal as all my subjects have MCI and freesurfer reports them having all over 5000 mm^3. I was wondering if the problem could lie somewhere in the recon-all process? Thank you for your time Sincerely, Michel Hu

2 1

Re: [Freesurfer] Overestimation of volume in Hippocampus
by Antonin Skoch 27 Feb '17

27 Feb '17

Dear Michel, Given your resolution 0.8x0.8x0.8, did you run recon-all with -hires flag? What did you used T2 image for? As a -T2pial refinement? T2 image is not used for hippocampal segmentation in standard recon-all stream. But pay attention that with -hires you also have to alter default value for mris_inflate, as specified here http://freesurfer.net/fswiki/SubmillimeterRecon In my case -n was not enough, I would recommend -n 50 (more does not do any harm). In any case, I would recommend to try hippocampal subfields module. https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields This should be more precise than "standard" aseg segmentation and given you have also 3D T2, multispectral T1 and T2 segmentation can be used. Antonin Skoch Dear Shane, I have checked the aseg.mgz and in only one I would say the segmentation failed however the others look fine and I'm taking the measurements from the text file that is generated from the aseg.stats. Should I redo the recon-all with a different input? I have always given freesurfer T1 and a T2 scan to process both having a resolution of 0.8x0.8x0.8 mm.Sincerely, Michel Hu ________________________________ Van: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> namens Shane S <shane.schofi...(a)yahoo.com> Verzonden: maandag 27 februari 2017 11:15 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus Hi Michel Hu, Yes, that’s too large for MCI or even controls for that matter I think. Have you checked the aseg.mgz? I generally find that the hippocampus is well segmented, even in patients with a lot of atrophy. Are you taking the measurements with the asegstats2table? Sincerely, -- Shane S On 27 February 2017 at 10:12:09, Michel Hu (a...(a)live.nl<mailto:a...@live.nl>) wrote: Dear Shane, I apologize for not being clear. The reported value is of only one half of the hippocampus. I have only run 4 subjects of the 75 however they all have a reported value of between 6000 to 10000 mm^3 summed together for the hippocampus. Sincerely, Michel Hu ________________________________ Van: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> namens Shane S <shane.schofi...(a)yahoo.com> Verzonden: maandag 27 februari 2017 11:00 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus Hi Michel Hu, Is that a summed value of left and right hippocampus? That seems normal to me since averaged total hippocamppal volumes for MCI have been typically reported at around 2500-3500mm3. Thanks, -- Shane S On 27 February 2017 at 09:44:27, Michel Hu (a...(a)live.nl<mailto:a...@live.nl>) wrote: Dear Freesurfer experts, I have run several subjects through the recon-all pipeline including the hippocampal segmentation with freesurfer 6.0 on Ubuntu 16.04. However when looking at the text file with the volumes it seems that all the numbers are bigger than normal as all my subjects have MCI and freesurfer reports them having all over 5000 mm^3. I was wondering if the problem could lie somewhere in the recon-all process? Thank you for your time Sincerely, Michel Hu

2 1

Overestimation of volume in Hippocampus
by Michel Hu 27 Feb '17

27 Feb '17

Dear Freesurfer experts, I have run several subjects through the recon-all pipeline including the hippocampal segmentation with freesurfer 6.0 on Ubuntu 16.04. However when looking at the text file with the volumes it seems that all the numbers are bigger than normal as all my subjects have MCI and freesurfer reports them having all over 5000 mm^3. I was wondering if the problem could lie somewhere in the recon-all process? Thank you for your time Sincerely, Michel Hu

2 4

Re: [Freesurfer] Fw: PETsurfer mri_coreg problem
by Antonin Skoch 26 Feb '17

26 Feb '17

Dear Paul, LTA means transformation matrix stored in .lta format. This matrix can encode transformation between various coordinate spaces. What coordinate systems transform this .lta from and to is specified by string in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or RAS2RAS. Most typically the type is vox2vox. The explanation of coordinate systems is specified for example here: http://freesurfer.net/fswiki/CoordinateSystems http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm The output of freeview is only info, not error, indicating that your .lta is not of type vox2vox. I personally still use tkregister2 for checking of registration, since the freeview does not contain full functionality for checking transformations (see the warning). Therefore I have no experience with tkregisterfv and consider tkregister2 still as a "gold standard". However, if you use tkregisterfv for checkning transformation between volumes and the output is only "info", I would guess that everything is OK and you do not need to be bothered. Btw, does the alignment of the images seem reasonable? How does it look in tkregister2? Regards, Antonin

3 2

PETsurfer mri_coreg problem
by miracooloz＠gmail.com 26 Feb '17

26 Feb '17

2 2

CORTICAL THICKNESS
by Flavia Arduini 26 Feb '17

26 Feb '17

Hi everyone, I segmented with Mantis, a toolbox of spm, MRI T2-weighted images of infants . Now I have to compute cortical thickness. How can I do it with Freesurfer? I know there's the recon-all function that segments and does this but is based on T1-weighted images. There is a way to be able to adapt? Thank you and I hope someone can help me. Flavia Arduini

1 0

Re: [Freesurfer] Mindboggle official software release and publication!
by Antonin Skoch 26 Feb '17

26 Feb '17

Dear experts, I was wondering what is your opinion on the fact, that, according to the mindboggle paper http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.10053… it is beneficial to use ANTS volume-based gray matter segmentation to refine gray matter segmentation in FreeSurfer. I am not expert in ANTS but looking at the ANTS code it seems to me that the ANTS routine does not do anything more than the volume-based nonlinear registration to the template and intensity and probabilistic atlas-based voxel labeling. Therefore, the method is in principle identical to GCA volume-based labeling (mri_ca_register and mri_ca_label, part of recon-all) in FreeSurfer which also produces cortical gray matter mask, far not so precise as the segmentation based on pial and white surface estimation. I think that FreeSurfer pipeline for estimation of white and pial surfaces is much more sophisticated and precise than any method using volume-based registration and volume-based labeling by intensity and anatomical priors. The FreeSurfer gray matter underestimation showed in figure 2 of the paper http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.10053… seems to me like either partial-volume effect or skull-strip error (which cuts out part of gray matter) which can be corrected by proper inspection and manual correction of brainmask.mgz. In contrast, the errors in presented ANTS gray matter segmentation in figure 2 are much more severe, spanning not only the blue encircled region. I would very appreciate your expert opinion on this. Regards, Antonin Skoch Announcing the official release of Mindboggle (http://mindboggle.info) open source software <http://mindboggle.info/software.html> and data <https://osf.io/ydyxu/> for analyzing the shapes of brain structures from human MRI data (processed through FreeSurfer and optionally through ANTs). The release coincides with a publication in PLoS Computational Biology that documents and evaluates the software:Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B, Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350 <http://doi.org/10.1371/journal.pcbi.1005350> Cheers, @rno

1 0

Disastrous Soft Error
by Rockers, Elijah D. 25 Feb '17

25 Feb '17

Hello all, I recon-all'd ~40 different subjects. I have been going through all the images to make sure they were processed correctly. Most required no no editing and recon-all did a very good job. But for one scan in particular, it looks like Freesurfer thinks the top of the spinal cord is the brain. Several vertebrae are very nicely segmented... :P Just wondering if you have any suggestions for reprocessing this subject? The error is reproducible with default recon-all settings. Subject has some pathology in the white matter which might be causing the problem? Screenshot of T1.mgz + lh.pial at the following link: http://imgur.com/a/uwyaq Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 3

Re: [Freesurfer] lh.white.H , Failed to create
by Antonin Skoch 25 Feb '17

25 Feb '17

Dear Vasudev, on what filesystem does your working directory reside? According to the path to your data it seems that you use some external drive, probably with non-unix-like filesystem. The error most probably means, that your filesystem does not support symbolic links. Regards, Antonin Dear all , I have been incurring lot of problems while running recon-all on ubuntu 16.04 , recon-all throws following error : " #@# Curv .H and .K lh Sa 25. Feb 04:09:16 CET 2017 /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/surf mris_curvature -w lh.white.preaparc total integrated curvature = 8.913*4pi (112.005) --> -8 handles ICI = 172.8, FI = 1966.7, variation=30317.492 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Function not implemented " Could you please let me know why this error is occurring . Thanks Vasudev

1 0

lh.white.H , Failed to create
by Dev vasu 25 Feb '17

25 Feb '17

Dear all , I have been incurring lot of problems while running recon-all on ubuntu 16.04 , recon-all throws following error : " #@# Curv .H and .K lh Sa 25. Feb 04:09:16 CET 2017 /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/surf mris_curvature -w lh.white.preaparc total integrated curvature = 8.913*4pi (112.005) --> -8 handles ICI = 172.8, FI = 1966.7, variation=30317.492 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Function not implemented " Could you please let me know why this error is occurring . Thanks Vasudev

1 0

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Freesurfer February 2017