Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

FreeSurfer stable v.6 Installation
by Duy Nguyen 17 Feb '17

17 Feb '17

Dear FreeSurfer experts I would like to ask that whether or not I can install the package to the existing FS 5.3 that previously installed on our Linux system? Please forgive if it is an obvious question. Thanks *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme(a)gmail.com <duy.nguyenbme(a)gmail.com>*

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Extract volume, thickness, and surface area from all vertices in a cluster
by Shady Rahayel 16 Feb '17

16 Feb '17

Hi everybody, I compared 2 groups and found a cluster with difference in cortical volume. I want to have a mean value of cortical volume, thickness, and surface area for each subject for this cluster, that I can use for further statistical analysis. What do you recommend? I'm not looking for a value that would only be the one from the peak vertex (I've tried it with mri_segstats already). I'm rather looking for a volume, thickness and surface area value from EACH vertex from the cluster, so that I can have a mean value for each metric if I average them with a basic statistical tool. I searched the forum quite a bit and all the different replies are confusing me. Thank you very much Shady -- *Shady Rahayel* Étudiant au Ph.D. en neuropsychologie R/I Université du Québec à Montréal Centre d'Études Avancées en Médecine du Sommeil Hôpital du Sacré-Coeur de Montréal

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Re: [Freesurfer] Intensity Re-scaling Relative to Full Brain Atlas <Repost>
by Anderson Napolitano 16 Feb '17

16 Feb '17

I am so sorry about that Dr. Greve. The post I made earlier is reference from the following thread: On 02/16/2017 12:28 PM, Anderson Napolitano wrote: > > Thank you Dr. Greve. Just to clarify, the 'inputfile.nii.gz' file in > the command: > > fscalc inputfile.nii.gz div value -o outputfile.nii.gz > ,is the gtm.nii.gz file generated after the command: > mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg > gtmseg.mgz > --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output > located at gtmpvc.output directory? If that's the case, fscalc will > not modify > gtm.stats.dat file corresponding to the image. Wouldn't that be > counter intuitive, > as gtm.stats.dat remains unchanged but we just normalized the image > using the > fscalc command? > Again, thank you Dr. Greve. I really appreciate all the help. > -Anderson >> There is not a flag to do this, but it should be fairly easy. There will >> be a file called aux/global.gmwmcsf.dat. This has the mean value average >> over all GM, WM, and CSF voxels (after PVC). You can use this to scale >> your data like >> fscalc inputfile.nii.gz div value -o outputfile.nii.gz >> You can also use the --scale option when running mri_vol2surf to apply a >> scaling factor when projecting on to the surface On 02/14/2017 02:04 PM, Anderson Napolitano wrote: >>> Hi Experts! >>>? >>> >>> Quick question: is it possible to re-scale intensities relative to the full >>> brain atlas? >>> Details: >>> Per step 3 of the following tutorial: >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer >>> >>> >>> I wanted to re-scale the the intensities relative to the full brain atlas. The >>> command: >>> >>> --no-rescale >>> >>> removes scaling relative to the Pons and the command: >>> >>> --rescale <Ids> >>> >>> rescales the intensities relative to the region determined by Ids. Would >>> listing all the regions on the --rescale command be the right approach to >>> rescale the intensities relative to the atlas? If so, how do I determine which >>> Ids is which? >>> >>> >>> Thank you in advance! >>> >>> >>> -Anderson >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>Douglas N. Greve, Ph.D. >>MGH-NMR Center >>gr...(a)nmr.mgh.harvard.edu >>Phone Number: 617-724-2358 >>Fax: 617-726-7422 >> >>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Talairach Registration Error : recon-all -s
by Antonin Skoch 16 Feb '17

16 Feb '17

Dear Experts, according to the log, Vasudev is using version 5.3-HCP. Therefore I expect that he is running FreeSurfer inside HCP pipeline scripts. The problem is that the use of 6.0 version with HCP pipeline scripts is not currently recommended. see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51416.html Antonin

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Talairach Registration Error : recon-all -s
by Dev vasu 16 Feb '17

16 Feb '17

Dear FreeSurfer Developers, I am incurring Talairach registration error when i was running recon-all -s Error : recon-all -s KON2 exited with ERRORS at Do 16. Feb 16:23:10 CET 2017 Freesurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP Platform: Ubuntu 16.04 recon-all log : see the attachment Kindly let me know the problem with registration. Thanks, Vasudev

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DTI images, mri_glmfit-sim
by Magnús Ingvi 16 Feb '17

16 Feb '17

Hello! I'm toying with some images acquired by following the dt_recon tutorial (fa-tal). I have prepared them for group analysis and run mri_glmfit, and the results look decent. However, I wanted to correct for multiple comparisons using for example mri_glmfit-sim --sim mc-full 100 2 cdbasename --sim-sign abs -glmdir testdir --overwrite And variations of this command. None of them find any cluster, and the output file (cdbasename.sig.cluster.summary) always reports zero cluster, no matter how I change the thresh value. Am I doing something wrong?

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mris_preproc version 6
by Fotiadis, Panagiotis 16 Feb '17

16 Feb '17

Hi Doug and Bruce, I was wondering whether you know where I can download the version 6 mris_preproc! Thanks in advance, Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA, 02114 T: (617) 643-3869

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Intensity Re-scaling Relative to Full Brain Atlas <Repost>
by Anderson Napolitano 16 Feb '17

16 Feb '17

Thank you Dr. Greve. Just to clarify, the 'inputfile.nii.gz' file in the command: fscalc inputfile.nii.gz div value -o outputfile.nii.gz ,is the gtm.nii.gz file generated after the command: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output located at gtmpvc.output directory? If that's the case, fscalc will not modify gtm.stats.dat file corresponding to the image. Wouldn't that be counter intuitive, as gtm.stats.dat remains unchanged but we just normalized the image using the fscalc command? Again, thank you Dr. Greve. I really appreciate all the help. -Anderson

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Volume maps unit in FreeView
by Martin Juneja 15 Feb '17

15 Feb '17

Hi, I have a very simple question. I have cortical volume maps (averaged over 30 subjects). I can view those in FreeView using lh.pial overlaid with lh.mean.volume.mgh file. In overlay > configure option, I had to set the min as 0 and max as 4 to display the average volume. Now the color bar is showing scale between 0 (min as blue color) and 4 (red) as maximum. I am not sure what does this 0 and 4 represent here, what are its units and how the actual volume values 20,000-40,000 mm^3 converted to this range between 0 and 4? Similarly, for surface area, color bar range is between 0 and 0.9 when actual values range around 11000-14000 and for cortical thickness, color bar range is between 1 and 3 when actual values range around 2.1-3 mm. Any help please. Thanks.

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mirroring right-hemisphere cluster dimensions on left hemisphere
by Uquillas, Federico D'Oleire 15 Feb '17

15 Feb '17

Dear FreeSurfer community, We have a cluster that we drew on the surface on the right hemisphere, and we’re interested in extracting cortical thickness values from the contralateral hemisphere. Wondering if there’s a way to transform the dimensions of our cluster from the right hemisphere to the left-hemisphere? Thank you so much for any help you may be able to provide. Best regards, Fred

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Freesurfer February 2017