[Freesurfer] Combining parcellated regions within an atlas?

Hi Freesurfer Experts, I was wondering what the best way of combining regions within a parcellation? For example, in the Schaefer 2017 functional atlas, there are regions such as: 7Networks_LH_DorsAttn_FEF_1 0 118 22 0 7Networks_LH_DorsAttn_FEF_2 0 119 17 0

Re: [Freesurfer] error in segmentHA_T2.sh

Dear Eugenio, Using full path solved the problem, thank you very much! Best Regards Cong > From: "Iglesias Gonzalez, Eugenio" > Subject: Re: [Freesurfer] error in segmentHA_T2.sh > To: Freesurfer support list > Message-ID:

[Freesurfer] license file error

Hi All, I am using Mac OS X Sierra and I downloaded free surfer 6 and when running recon I am getting the following error reading from IM-0001-0001.dcm... -- ERROR: Invalid FreeSurfer license key found in license file

[Freesurfer] Editing brainmask and white matter volumes when erasing dura

Dear experts, After I erasing dura from my brain mask volume, I noticed that the white matter volume still had dura when I clicked on it. Is it usually fine to only edit the brain mask when we’re trying to erase the dura and regenerate the surfaces? The dura on the white matter volume has both

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

Hi Bruce, The aseg.mgz may be precisely what I was looking for. Good to know. Other regions of interest include the following for our project: 17 Left-Hippocampus220 216 20 0 53 Right-Hippocampus 220 216 20 0 415 AIPS_AIP_l

[Freesurfer] Overlaying multiple results onto one surface

Hello, I have been running different analyses through QDEC GUI for different covariates that describe a similar construct, for instance: * Model A: (cortical thickness) ~ (covariate 1) + (nuisance factors) * Model B: (cortical thickness) ~ (covariate 2) + (nuisance factors) *

Re: [Freesurfer] error: dyld: lazy symbol binding failed

Hi Stephan, This probably has to do with SIP being enabled, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, Andrew On Nov 29, 2017, at

[Freesurfer] error: dyld: lazy symbol binding failed

Hello freesurfer experts, when trying to run the local gyrification index I run into an error: >> recon-all -s S01 -localGI ... reading surface from lh.pial... dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from:

Re: [Freesurfer] Creating functional ROI

Hi Doug, I ran the funcroi-config command the same way the tutorial suggested: *"funcroi-config -annot aparc fusiform -analysis eba-fba.native.rh -contrast faces-vs-objects -thresh 2 -sign pos -roi rh.fus.test.roicfg -force"* However, I got this error: *"annotations can only be used with

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

Hi Jessica it depends which ones you mean. Thalamus we label in the aseg.mgz, although for some reason the CMA called it "thalamus proper" so that is the index you should use (10 instead of 9 for left). What other labels do you mean? Bruce On Wed, 29 Nov 2017, Jessica Huang wrote: Hi

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

Hi Bruce, Ah! I found these regions (ex. the thalamus) in the FreeSurferColorLUT.txt lookup table but otherwise not in each subject's aseg/apar/label dir. Would you have any suggestions for how to extract a timecourse for the thalamus or the hippocampus? Did I miss a step? I have labels for the

Re: [Freesurfer] the ordering in ascii txt file

Hi Douglas, Does LIA means the stored intensity changes first from left to right, followed by changing from inferior to superior, and the slowest changing is from posterior to anterior? Best Regards, Yi -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Erroneous output after recon-all: Bad segmentation and surfaces

Hi Bruce and Emma, I am running the latest version of Freesurfer, version 6.0. I will try manually erasing the voxels then and try re-processing the subject. Thank you so much for your help. Best, Arsenije ___ Freesurfer mailing list

[Freesurfer] Postdoctoral position in Machine Learning for 3D Histology

Dear all, We are looking for a postdoc to work on my ERC Starting Grant project "Building Next-Generation Computational Tools for High Resolution Neuroimaging Studies", at the Translational Imaging Group (TIG) at University College London

Re: [Freesurfer] Erroneous output after recon-all: Bad segmentation and surfaces

I would reprocess all the way through first and see if the remaining dura affects the surfaces, then only edit in those locations that it does cheers Bruce On Wed, 29 Nov 2017, Boyd, Emma wrote: Hi Arsenije, If you've already tested out different watershed thresholds and gcut, then yes,

Re: [Freesurfer] Erroneous output after recon-all: Bad segmentation and surfaces

Hi Arsenije, If you've already tested out different watershed thresholds and gcut, then yes, the next step would be to manually erase these voxels and reprocess. The ventricle labeling is a separate problem - which version of FreeSurfer are you running? Best, Emma - Emma Boyd

Re: [Freesurfer] mri_convert partial support of nrrd file format for diffusion MRI data

no sorry, we have not tried to support nrrd in years, so I'm not surprised that it does not output bvals/bvecs On 11/29/17 8:10 AM, Michael Dayan wrote: Hi, I was pleasantly surprised when I discovered that mri_convert could convert the nrrd file format (to NIFTI in my case). However for

Re: [Freesurfer] Error with mri_vol2surf

Hi Elena can you send us the exact command you ran and the full screen output as text (not a snapshot)? thanks Bruce On Wed, 29 Nov 2017, Elena Theißen wrote: Hello, I am new to freesurfer and have a problem following the step ,mri_vol2surf‘ as described in your tutorial ,cortical

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

I’ve tested a few different (large) sets of subject data and still been unable to replicate this problem, so tough to say what’s causing it. Are you using the make_average_subject 6.0.0-patch? Have you also tried running the command with a subgroup containing the other 56 subjects (maybe it’s a

Re: [Freesurfer] Merging two groups

if you have two dirs, dir1 and dir2, with a set of subjects in each (subjects1 and subjects2), you would do: cd $dir2 foreach s ($subjects1) ln -s $dir1/$s end then all your subjects will be listed in dir2 that should do the trick On Wed, 29 Nov 2017, Ramesh Babu wrote: Dear Bruce,

Re: [Freesurfer] Surface-based kernel operations

Hi Victor the sphere files are lh.sphere and rh.sphere in the surf dir. You could write out the metric tensor (or first fundamental form) of the mapping to compute Euclidean distances from spherical coordinates, or probably just use the 3D euclidean distances on the sphere as the sampling is

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

Hi Jessica not sure I understand, but I don't think so. If we didn't label it in the aseg/aparc/label dir then how would you find it? Or do you mean manually draw it? That is possible. Bruce On Wed, 29 Nov 2017, Jessica Huang wrote: Hi Freesurfer Experts, Can I extract time courses for

[Freesurfer] Error with mri_vol2surf

Hello, I am new to freesurfer and have a problem following the step ,mri_vol2surf‘ as described in your tutorial ,cortical thickness of a Volume-defined ROI‘. During step 3 I always received the error: Could not read (path to) as type 24 The file is a .nii I checked my FS version (6) and

[Freesurfer] mri_convert partial support of nrrd file format for diffusion MRI data

Hi, I was pleasantly surprised when I discovered that mri_convert could convert the nrrd file format (to NIFTI in my case). However for diffusion MRI data, while it displays the diffusion gradients information on the terminal, it does not create the associated bval and bvec files. After looking

[Freesurfer] TRACULA and the IFOF

Dear TRACULA experts I am wondering wheter someone has already implemented the tractography of the inferior fronto-occipital fascicle (IFOF) into TRACULA? if yes, we are interested in this implementation. Regards Jürgen Hänggi

Re: [Freesurfer] error in segmentHA_T2.sh

Hi Cong, This totally looks like a problem with absolute/relative paths. Can you please try again, but using the full path to the T2? Something like: segmentHA_T2.sh control004 /Users/cong/data/subjects/control004/mri/T2.nii T2 1 If this works, let me know and I’ll fix the code. Cheers, /E

[Freesurfer] error in segmentHA_T2.sh

Dear freesurfer experts I am trying segment hippocampal and amygdala subregions in dev version(freesurfer-i386-apple-darwin11.4.2-dev-20171024), the segmentHA_T1.sh works well. However, when I try to add a T2 propeller sequence it doesn’t work. I am sure the T2.nii file is in mri folder,

Re: [Freesurfer] Merging two groups

Dear Bruce, Thank for your reply. I am getting confusion in creating symlink. ln -s /usr/local/freesurfer/subjects/fsaverage /mnt/backup_data/freesurfer_analysis/subjects/ ln -s /usr/local/freesurfer/subjects/fsaverage /mnt/backup_data/freesurfer_analysis/subjects/fsaverage Please let me know

Re: [Freesurfer] Surface-based kernel operations

Thanks Bruce and Doug! Bruce, I think the option of the sphere is the one that better fits my needs, since I need to perform conv operations + derivatives. How should address this issue? I am not very familiar with sphere files (nor metric tensors) and do not know how to open/where to find those