Re: [Freesurfer] aparcstats2table

External Email - Use Caution Hi, Can I use the below command to extract the cortical thickness using Destrieux Atlas from longitudinally preprocessed subjects? aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas thickness \ --parc aparc.a2009s \

Re: [Freesurfer] Cannot allocate memory

External Email - Use Caution Hello Bruce thank you for your quick reply, Where should I look to get all these files? The idea to check them is to confirm that the MRI went wrong at some point, right? Thanks, Gabriel Tapia www.Partage3D.fr

Re: [Freesurfer] Cannot allocate memory

Hi Gabriel, that is a huge defect and generally means something major has gone wrong. Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix over the wm.mgz file to see what is wrong (usually something like a big chunk of skull is left over and connected to the surface,

[Freesurfer] Cannot allocate memory

External Email - Use Caution Hello dear Freesurfer developers, nice to e-meet you and thank you for working on this open source software! I am trying to produce a 3D file of a brain. The command I am trying to run is recon-all and here is the error I get: *CORRECTING DEFECT 57

Re: [Freesurfer] Which FDG-PET file to use for PETSufer?

External Email - Use Caution Thank you very much Douglas for the information. Kate On Mon, Feb 24, 2020 at 2:44 PM Douglas N. Greve wrote: > what are those three? The same data just oriented in a differeent way? If > so, then it does not matter as long as the orientation info

Re: [Freesurfer] Which FDG-PET file to use for PETSufer?

what are those three? The same data just oriented in a differeent way? If so, then it does not matter as long as the orientation info is correct. Load one into freeview to assure that the cor view actually shows up as cor, etc. One thing you will not be able to check is whether there is a

Re: [Freesurfer] samseg permissions error

Hi Andrew, Thanks for pointing this out, it looks like the permissions of our fsaverage subjects have all changed since yesterday! Will fix this now Best, Andrew From: on behalf of "Russo, Andrew William" Reply-To: FS Help Date: Monday, February 24, 2020 at 10:51 AM To: FS Help Subject:

[Freesurfer] Which FDG-PET file to use for PETSufer?

External Email - Use Caution Hi FreeSurfer Users, I would like to perform PET analysis using PETSurfer and I have the following FDG-PET NIfTI files below: 1. TRANSAXIAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii 2. SAGITTAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii 3.

[Freesurfer] Pre-release (beta) version of FreeSurfer v7 now available

You can now download and install the beta version 7 of FreeSurfer. See this page https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1 The purpose of this beta is for users to install and run FreeSurfer on some of their data sets using

[Freesurfer] Registration error

External Email - Use Caution Hi, I'm trying to learn to use Freesurfer to see if I can use it for some academic work on TBI. I downloaded it to a spare laptop at home, and filled out the registration form, and I got a message that stated "Registration Error: Spammer. Go

[Freesurfer] samseg permissions error

Hello Freesurfer Developers, I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do not have permission to access the directory /usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory? ValueError: file

Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

External Email - Use Caution Hi Bruce, Thank you very much Bruce. Kate On Mon, Feb 24, 2020 at 8:50 AM Bruce Fischl wrote: > Hi Kate > > the .lta format is for a linear registration (in ascii). YOu can just cat > it to see the contents - it is not a PET image (which will be

[Freesurfer] skull stripping problem

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm

Re: [Freesurfer] Apply transformation

External Email - Use Caution Hello all, is it possible to transform a binary mask (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) and change a final FOV by specifying a diffusion reference image? Or the transform can be applied only

Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

Hi Kate the .lta format is for a linear registration (in ascii). YOu can just cat it to see the contents - it is not a PET image (which will be stored in .mgz or .nii). mri_convert or mri_vol2vol can be used to apply the registration and/or change the output format (if you specify file.nii or

Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

External Email - Use Caution Hi Douglas, Is there a way to save the registered PET image in NIfTi format instead of .lta? Kate On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve wrote: > Not sure what you are trying to do. An lta file is a matrix and nifti is a > format for

Re: [Freesurfer] cluster size threshold

You need to find the correct CDF file, eg, if the final FWHM is 12, it would be in $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm12/abs/th30/mc-z.cdf To get the FWHM look in glmdir/fwhm.dat and round down in the mc-z.cdf file, find the row where the MaxClustCDF drops below

Re: [Freesurfer] Version Beta 7.0

We have not released stable 7 yet. Technically we have not released 7beta yet but only because I need to make the announcement and write up some docs. On 2/24/2020 2:46 AM, Victor Montal Blancafort wrote: External Email - Use Caution Freesurfer developers, I have seen from the

Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary

Try setting -max XXX where XXX is the maximum allowable thickness. It is default to 5, so try something large On 2/21/2020 11:36 AM, CiRong Liu wrote: External Email - Use Caution Dear experts of the freesurfer, I was trying to create the white matter and pial surfaces of the 

Re: [Freesurfer] Optseq2 help needed

By default, optseq2 assumes that you want to perform an FIR analysis where you get an average for each post-stimulus time point so that you can create a waveform. This is in contrast to assuming the shape to the hemodyn respnse where you only estimate a single value (the amplitude). By

Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

Not sure what you are trying to do. An lta file is a matrix and nifti is a format for storing images. On 2/21/2020 7:52 AM, Kate Marvel wrote: External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks,

Re: [Freesurfer] surfreg function

it is ok to spec -surfreg, but is not necessary in this case mris_preproc will change the name when you spec a target subject (eventhough the says that the default is sphere.reg) On 2/21/2020 6:20 AM, Marina Fernández wrote: External Email - Use Caution Hi Doug, Thank you for your

Re: [Freesurfer] GLM DOSS questions

On 2/21/2020 4:01 AM, Ferraro, Pilar wrote: External Email - Use Caution Dear Freesurfer experts, I’ve just completed a GLM analysis in Freesurfer and I’d like to be sure that all the steps I’ve performed are the right ones. My analysis is looking at age related changes in

Re: [Freesurfer] Extract specific LGI and Volume values

Try using freeview On 2/18/2020 8:17 PM, Tien Pham wrote: External Email - Use Caution Thank you for your email. I tried to load the label with qdec and freeview and both were not worked. When i tried with qdec, It said '' load the surface first '' then I did but It did not work and

[Freesurfer] cluster size threshold

External Email - Use Caution Dear experts, To perform a Monte Carlo based cluster correction, I have run the following line: mri_glmfit-sim --glmdir glmdir --mczsim 3 abs --cwp 0.05 --2spaces --a2009s I need to figure out which is the minimum number of voxels required for a