[Freesurfer] Error "dyld: lazy symbol binding failed..." when some commands run via Matlab [system('fscmd')]

External Email - Use Caution Hello FreeSurfer Developers, I’m attempting to run FreeSurfer commands via Matlab [system(‘fscmd’)]. Some of the commands work but some don’t, though all the commands work well when run in Terminal. Commands work in both Terminal and Matlab: When

Re: [Freesurfer] Recon all hard failure,

External Email - Use Caution Hi Bruce, You are actually right, wh.mgz has some skull left, this is what is problably causing the inflated surfaces to have so many defects. Thanks for the info. Cheers, Vicente Ferrer Predoctoral Researcher BCBL www.bcbl.eu Legal disclaimer/Avis

Re: [Freesurfer] Error "dyld: lazy symbol binding failed..." when some commands run via Matlab [system('fscmd')]

External Email - Use Caution Hello hj23, If you are running the 6.0.0 freesurfer Mac release, then you can try downloading this patch.  You will need to double click on the archive to expand it and then follow the instructions in README.patch.  I think you will also need admin p

Re: [Freesurfer] Error "dyld: lazy symbol binding failed..." when some commands run via Matlab [system('fscmd')]

External Email - Use Caution Hi I can run the command through Matlab now (with FreeSurfer 6.0). Many thanks, Haiyang > On Nov 13, 2019, at 1:50 PM, fsbuild wrote: > > Hello hj23, > > If you are running the 6.0.0 freesurfer Mac release, then you can try > downloading this pa

[Freesurfer] Conference on “Emerging Topics in Artificial Intelligence”

External Email - Use Caution Dear all, We are organizing a conference on “Emerging Topics in Artificial Intelligence”, which will take place from 23-27 August 2020 in San Diego, USA. The aim of this conference is to bring together experts from different fields to discuss new appl

Re: [Freesurfer] Freesurfer6.0 hippocampal and amygdala segmentation-command not found error

Dear Isabella, You need to download the development version to run segmentHA_T1.sh. However, you do not need to rerun your subjects through the development recon-all (in fact, you should *never* do that). If/when you write a paper, you would state that you used FS 6.0 to recon the cases, and the

[Freesurfer] fspalm issue

External Email - Use Caution Hi FreeSurfer community, I’m using fspalm to correct multiple comparisons for vertex-based cortical thickness analysis. It ran successfully and several clusters survived after correction for multiple comparisons. Below is the code I used for permutatio

Re: [Freesurfer] 4D multi-frame parcellation

If you have an anatomical MR that you have run through recon-all, then just use that one instead of bert in your steps below ps. Please remember to post to the FS list and not to us personally On 11/12/19 8:41 PM, an wrote: > > External Email - Use Caution > > Many thanks. > > I got the 4

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

I'll have to leave this one for Kersten as it appears that the LME stuff is generating and inf value On 11/12/19 7:05 PM, Bronwyn Overs wrote: > > External Email - Use Caution > > Hi Douglas, > > Yes I have looked at it in Freeview and I have attached a screenshot > for your reference. >

[Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

External Email - Use Caution -- Forwarded message - From: Dalton Bermudez Date: Wed, Nov 13, 2019 at 1:54 PM Subject: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm To: Dear FreeSurfer Developers, I am attempting to obtain a average

Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

Hi Dalton you need to give us a lot more information. What command did you run? What was the full output? cheers Bruce On Wed, 13 Nov 2019, Dalton Bermudez wrote: External Email - Use Caution -- Forwarded message - From: Dalton Bermudez Date: Wed, Nov 13,

Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

External Email - Use Caution Dear Bruce, This is the command I ran with my own data: recon-all -subjid 00_0086 -i RAW/00_0086/ns_00_0086_3T_T1w_MPR1.nii -i RAW/00_0086/ns_00_0086_3T_T1w_MPR2.nii The whole output can be found in the recon-all.log attached below On Wed, Nov 13, 2019

[Freesurfer] Processor speed/cores vs cache size

External Email - Use Caution Hello, For running recon-all or tracula on a local workstation, is it recommended to go for a higher processor speed/number of cores, or a larger cache size for the processor (Intel Xeon W series). Or is it likely to be a more complex interplay between

[Freesurfer] Spatial smoothing for cortical folding measures

External Email - Use Caution Dear FS experts, Is it necessary to do spatial smoothing for cortical folding measures (curv/sulc/smoothwm.FI.crv/pial_lgi, etc.)? These cortical folding measures are inherently smooth based on the computation methods used. If spatial smoothing is

[Freesurfer] Volume (WM Parcellation) of RightCerebralCortex--Freesurfer 6.0

External Email - Use Caution Dear Freesurfer experts, I am trying to use ADNI MERGE R package to get 'wholebrain' volume. It requires CerebralCortex. The information I get from ADNI merge is "Volume (WM Parcellation) of RightCerebralCortex". But when I ran Freesurfer reconall 6

Re: [Freesurfer] Question about design matrix for surface group analysis

External Email - Use Caution Dear freesurfer experts,we want to analyze the relationship between the cortical thickness and the neuropsychology regressing out the effects of gender and age, but I don't know how to make the design matrix? Is it [0.5 -0.5 0.5 -0.5 0 0 0 0 1 -1 1