Re: [Freesurfer] Fixing of Morphometry Stats and Global Measure of Volume: Longitudinal analysis

External Email - Use Caution Thank you Doug, I'll do that! Best, Diana On 20/5/19 20:54, Greve, Douglas N.,Ph.D. wrote: > You will not need to run the entire stream again. Did you run it in > high-res mode? If the volumes are conformed (eg, orig.mgz is 1mm, > 252^3), then you d

Re: [Freesurfer] mris_label2annot empty Annot

External Email - Use Caution Hi Thank you for your response, here is the terminal output: It does create a new annot, but it's empty. bw Michal cwd /Applications/freesurfer/subjects/Alldata6V/bert cmdline mris_label2annot --s bert --h lh --ctab label/aparc.annot.a2009s.ctab --a m

[Freesurfer] Mri glmfit sim error

External Email - Use Caution -- Forwarded message -- From: *abedi...@citymail.cuny.edu * < abedi...@citymail.cuny.edu> Date: Tuesday, May 21, 2019 Subject: To: "amibedi...@gmail.com" Hi Freesurfer developers, While running the mri glmfit sim command for a smooth

Re: [Freesurfer] Mri glmfit sim error

You have applied a lot of smoothing, and the tables don't go up that high. Usually people will apply 5-10mm of smoothing. If you really want that much smoothing, you should use permutation. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 5/21/2019 10:09 A

Re: [Freesurfer] Mri glmfit sim error

External Email - Use Caution Hi Dr Greve, Is it not possible to use Monte Carlo for 30 FWHM? Best, Amrita On Tuesday, May 21, 2019, Greve, Douglas N.,Ph.D. wrote: > You have applied a lot of smoothing, and the tables don't go up that high. > Usually people will apply 5-10mm of

[Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy

External Email - Use Caution Dear FreeSurfer Community, In processing high-resolution (0.7 mm^3 isotropic) and low resolution (1.0 mm^3 isotropic) versions of the same data we have received conflicting volume data in our aseg.stats file. Below is the relevant excerpt from those

[Freesurfer] Job ad: MRI physicist

External Email - Use Caution The Center for Biomedical and Brain Imaging (CBBI) is a core imaging facility at the University of Delaware dedicated to scientific research. It is equipped with a Siemens Prisma 3T MRI scanner, Bruker 9.4T small bore MRI scanner, TMS, and MRI-compat

[Freesurfer] Reminder: OHBM 2019 Brain-Art Competition is open for submissions! {Disarmed}

External Email - Use Caution The OHBM Brain-Art SIG

[Freesurfer] Postdoctoral fellowship in cognitive neuroscience at UCSF

External Email - Use Caution The ALBA Language Neurobiology laboratory or the UCSF Memory and Aging Center has an open postdoctoral position in cognitive neuroscience. Directed by Dr. Maria Luisa Gorno Tempini, the ALBA lab conducts cutting-edge research on the cognitive and neu

Re: [Freesurfer] Mri glmfit sim error

The problem is that it is not 30, it's 53. The FWHM is computed from the residuals. I don't know what your underlying data is, but it is very smooth. You can try not smoothing at all and see if it gets down to 30. You're probably better off using permutation  as it is more accurate. On 5/21/19

Re: [Freesurfer] problem with mri_surfcluster

yes, I often use voxel and vertex interchangeably On 5/21/19 10:58 AM, Barletta, Valeria wrote: > I see, that makes sense. > But why are you mentioning voxels? Shouldn't they be vertices since my > mask is registered to the surface? (I used vol2surf to do it) > ---

Re: [Freesurfer] mris_label2annot empty Annot

I cannot replicate this. Can you look in the input labels and verify that they are not empty? Also, the "&" may be causing problems with the unix shell. Try using one that does not have an ampersand to see if it works. On 5/21/19 4:31 AM, Michal Tanzer wrote: > > External Email - Use Ca

[Freesurfer] number of vertices

External Email - Use Caution Hi, How can I check how many vertices an image of my subject has? Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Segmenting internal capsule

Those region numbers are just a placeholder. We don't segment the capsules. I can't find intcapseg, but it was very crude anyway. On 5/20/19 10:06 PM, Chinappen, Dhinakaran Maheswaran wrote: > Dear Freesurfer community experts, > > We're looking to segment the internal capsule using T1 data. We f

Re: [Freesurfer] number of vertices

mris_info lh.orig will do it On 5/21/2019 6:45 PM, Sam W. wrote: External Email - Use Caution Hi, How can I check how many vertices an image of my subject has? Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] number of vertices

do you mean of one of the surfaces derived from the image? If so, you can use mris_euler_numer or mris_info cheers Bruce On Wed, 22 May 2019, Sam W. wrote: External Email - Use Caution Hi, How can I check how many vertices an image of my subject has? Best regards, Sam

Re: [Freesurfer] FreeSurfer High Resolution vs. Low Resolution Volume Discrepancy

External Email - Use Caution Dear Gaurav Verma, this should fix your issue: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Verma, Gaurav Gesendet: Dienstag, 21. Mai 2019 17:34 An: freesurfer@n