Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)

Hi Daniel I don't think we can help you with why Surf Ice is failing (at least I can't). What are the features that freeview doesn't have? I'll leave question 2 for Doug cheers Bruce On Wed, 23 Jan 2019, Daniel Leopold wrote: External Email - Use Caution Hello FS experts

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

Based on the output below, it looks like there are problems with running one of the freesurfer binaries. Can you run mris_fwhm ? Just type the command and return and see what happens. /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT

Re: [Freesurfer] FSFAST poor registration

Can you tar up the anatomical and functional analyses and send them to me through our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu On 1/23/19 5:57 AM, Keri Woods wrote: > > External Email - Use Caution >

Re: [Freesurfer] correction for multiple comparison: simulation vs grf vs cache

Hi John, I would recommend that you use permutation. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm In terms of the threshold, "not going higher than .01" means using between 0 and .01 (eg, don't use .05). For permutation, you can use whatever thershold you

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

Version 6 does not work very well with such high-res data. I created a patch for the HCP that you can download from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp This works in version 6. Just follow the instructions in the README. I ran it on your data, and it looks pr

Re: [Freesurfer] move statistical map onto the cerebellum surface

You will have to put the cerebellar surface in fsaverage/surf/lh.cerebellum Note use "lh" even if it is the entire cerebellum as FS commands generally require a hemisphere. The run mri_vol2surf specifying --hemi lh --surf cerebellum On 1/23/19 10:04 AM, john Anderson wrote: > > External E

Re: [Freesurfer] move statistical map onto the cerebellum surface

External Email - Use Caution Hi Dr Greve, I appreciate your guidance very much. I followed your suggestion. I put lh.cerebellum in fsaverage and I ran mri_vol2surf. as follows: mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf cerebellum --mni152reg --o grf_onto_

Re: [Freesurfer] move statistical map onto the cerebellum surface

It should only do that if you have specified a projection fraction. Is that your full command line? Can you send the full terminal output? On 1/24/19 4:56 PM, john Anderson wrote: > > External Email - Use Caution > > Hi Dr Greve, I appreciate your guidance very much. > > I followed your s

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

External Email - Use Caution Hi Doug, The data I sent was generated using the development version, freesurfer-linux-centos7_x86_64-dev-20180807-df586ca. I downloaded the patch and will rerun the scans using version 6. Thanks, François On 1/24/19, 3:40 PM, "Greve, Douglas

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

The dev version has the same problem :( On 1/24/19 6:37 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > External Email - Use Caution > > Hi Doug, > > The data I sent was generated using the development version, > freesurfer-linux-centos7_x86_64-dev-20180807-df586ca. I downloaded the patch

[Freesurfer] How to extract cortical features of a ROI

External Email - Use Caution Dear Freesurfer Experts, I want to extract cortical features of a ROI that I drawn manually on the rawavg.mgz in Freesurfer, but i don't know how to do that. I think maybe first the lesion mask should be registered to the standard templates