[Freesurfer] the -label flag in mri_cnr

External Email - Use Caution Hello! I had a couple of questions about how mri_cnr computes the contrast to noise ratio. From previous posts, a command such as mri_cnr $FREESURFER_HOME/subjects/bert/surf $FREESURFER_HOME/subjects/bert/mri/norm.mgz gives the lh cnr, rh cnr, and t

[Freesurfer] FS6: Mapping data to fsaverage6

External Email - Use Caution Dear FreeSurfer experts, I'm trying to resample cortical thickness data onto the fsaverage6 template subject in FreeSurfer v6. I have copied fsaverage6 into my $SUBJECTS_DIR. I tried the following 2 commands: * mris_preproc --s subject1 --target fsav

[Freesurfer] Problem_mri_watershed

External Email - Use Caution Dear Freesurfer community, using the mri_watershed and -surf to crate inner_skull, outer_skin and outer_skull I get a incorrect inner_skull segmentation, probably due to an erroneous skullstrip. I tried to modify the parameters available but it does no

[Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

External Email - Use Caution Dear Freesurfer experts, When I run "recon-all -autorecon2-wm -subjid post_006" I get the following error: ... # #@# Fill Tue May 26 16:13:33 CEST 2020 /usr/local/freesurfer/subjects/post_006/mri mri_fill

Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

Hi Marina have you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz and the wm.mgz look ok? Bruce On Wed, 27 May 2020, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, When I run "recon-all -autorecon2-wm -subjid post_006" I

[Freesurfer] fs_install_mcr error

External Email - Use Caution Hi all, I have installed FS7 (centOS8 version) on ubuntu 18.04. I try to install MATLAB runtime but it gives an error when I type "fs_install_mcr R2014b": Archive: installer.zip End-of-central-directory signature not found. Either this file is not a

Re: [Freesurfer] Command cannot recognise session from sessid file

Are you in the funcionals  folder when you run your command? If not, you have to specify the session folder with -d /path/to/functionals What is a command line that fails? Try running the command substituting the command name with gestsesspath and adding -debug as the first option On 5/23/202

Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

Are all your subjects skull stripped or just this one? On 5/24/2020 9:08 AM, Schranzer René wrote: External Email - Use Caution Hi Douglas, First of all, thank you for your help. I forgot to mention that I am already using skull-stripped data for the recon-all processing stream. Th

Re: [Freesurfer] Are my slice-time corrected files being used in selxavg3-sess?

What is your mkanalysis-sess command line? You have to specify the STC there; if not, it will run without STC On 5/22/2020 1:35 PM, Mcnorgan, Christopher wrote: External Email - Use Caution Hi all, There was some ambiguity in communication from a previous MR technician regarding

Re: [Freesurfer] Feat to fsfast

Yes. You can try this tutorial, though it has not been run in a while and everything might not work https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer On 5/26/2020 10:27 AM, Alshelh, Zeynab wrote: Hi all, Is it possible to do the first level unsmoothed using feat and the

Re: [Freesurfer] PETsurfer: --usf in gtmseg

yes, that controls how finely the surface-based segmentations are resampled into the volume. The surface is semi-continuous so you can sample them into the volume as finely as you like. 0.5mm seems to work fine. On 5/26/2020 4:33 PM, Julie Ottoy wrote: External Email - Use Caution Hi

Re: [Freesurfer] FS6: Mapping data to fsaverage6

It is probably easier if you don't use mris_preproc and run the resampling yourself, eg, mris_apply_reg --src lh.thickness --streg lh.sphere.reg $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg --streg $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg $SUBJECTS_DIR/fsaverage6/surf/lh.sphere.reg --trg lh.t

Re: [Freesurfer] Problem_mri_watershed

You can try -more or -less when running mri_watershed You can correct is manually to get a better inner skull. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview After fixing you can run mri_binarize with the --surf option Not sure about the outerskull if you are d

Re: [Freesurfer] recon-all misses part of occipital cortex

my guess is that it is a topological defect that was fixed incorrectly. Try looking at this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview You can also run defect-seg to create a segmenttation of the defects and see whether a defect is in that area. run

[Freesurfer] Citation of hard and soft failures

External Email - Use Caution Dear all, I am writing a paper for which I need to introduce the concepts of "hard" and "soft failures", and I am wondering what is the proper way of citing them. I am aware there is plenty of material online (see for example https://fscph.nru.dk/s

[Freesurfer] Registering Mean Diffusivity to Anatomical Space

Hello FreeSurfer users, I have a mean diffusivity map that exists in MNI152 space that I want to register to a subject’s anatomical space. In the end, I want to display the diffusivity on the subject’s surface. I want to ask if this is the correct way to do this: 1) bbregister --s sub-01 --mov

Re: [Freesurfer] Citation of hard and soft failures

Not that I know of, but I think most programmers would know what you mean On 5/27/2020 1:59 PM, Monereo Sanchez, Jennifer (RAD) wrote: External Email - Use Caution Dear all, I am writing a paper for which I need to introduce the concepts of “hard” and “soft failures”, and I am wonde

Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space

I would probably run recon-all on the mni152, and then sample the MD map onto the mni152 surface, then use mris_apply_reg to map it to an individual. Also, Thomas Yeo has some possibly-better tools to do this. On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote: Hello FreeSurfer users, I have a

Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space {Disarmed}

Thanks Doug! When you say sample onto the mni152 surface, you mean to use mri_vol2surf, correct? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On May 27, 2020, at 11:10 AM, Douglas N. Greve wrote: > > I wo

[Freesurfer] mris_register using manual label(s) as guides

External Email - Use Caution Hi FreeSurfer experts, I'm currently working on a brain with a bit of atypical morphology and was wanting to parcellate through the DKT labels, but by using manually drawn labels as guides. The intent here is to fix specific labels to be where they

Re: [Freesurfer] mris_register using manual label(s) as guides

Hi Danny yes, you can specify up to 100 labels. Make sure that the label name is exactly as it appears in the parcellation though cheers Bruce On Wed, 27 May 2020, Danny Kim wrote: External Email - Use Caution Hi FreeSurfer experts, I'm currently working on a brain with

Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space {Disarmed}

Correct. Also make sure to set --projfrac 0.5 to sample in the middle of cortex (or set to some other value depending upon where you want to sample) On 5/27/2020 3:12 PM, Nillo, Ryan Michael R wrote: Thanks Doug! When you say sample onto the mni152 surface, you mean to use mri_vol2surf, corre

[Freesurfer] Problems with freesurfer 7.1.0

External Email - Use Caution Dear Freesurfer experts, I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS Catalina. I found 2 main problems 1. About a 10% of cases failed at the segmentation stage during the recon-all processing (I uploaded one of these

[Freesurfer] LGI and Global GI

External Email - Use Caution HI, I have generated the LGI for a group of pediatric subjects. Is there a way to compute a single Global gyrification index measure for each subject? Jim, The materials in this message are private and may contain

[Freesurfer] Circular/cyclic color map for polar data and threshold-ing question in freeview

External Email - Use Caution Hello freesurfer community, I had asked this question before, however I am unable to reply to that thread. The question still remains unsolved. I am trying to setup a retinotopy pipeline. I have analysed population receptive field data that generates

[Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)

External Email - Use Caution Hi guys, I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my subject, I have run recon-all, then run mri_cvs_register to obtain a brain image registered in MNI152 space. My questions are: 1. In recon-all, is there a way to sp

[Freesurfer] FreeSurfer 7.1 Matlab error, GLIBC_PRIVATE not defined

External Email - Use Caution Hello FreeSurfer Developers, I attemting to run brainstem/ hippocampus/ thalamus segmentation with FS 7.1 and there seems to be a problem with environment variables. Based on comments on other forums, I cannot install GlibC (if this is the case) since

Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)

On 5/27/2020 11:10 PM, Elizabeth Haris wrote: External Email - Use Caution Hi guys, I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my subject, I have run recon-all, then run mri_cvs_register to obtain a brain image registered in MNI152 space. My questions are:

Re: [Freesurfer] FreeSurfer 7.1 Matlab error, GLIBC_PRIVATE not defined {Disarmed}

External Email - Use Caution Hello Alex, I would try unseting LD_LIBRARY_PATH altogether or at least take the matlab paths out of it.  My understanding is freesurfer commands don't need matlab paths in LD_LIBRARY_PATH to use matlab after you have setup the freesurfer environment