Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

External Email - Use Caution Got it :) filling the unassigned vertices with 'unknown' using tksurfer solved my problem. cheers, Joerg > Hi Bruce, > this did not change anything. But I tried the process of mris_ca_train, > mris_ca_label with lh.oasis.chubs.annot and this work

[Freesurfer] GLM twin design

External Email - Use Caution Dear FS List, I wanted to check if my GLM design for a surface based analysis is sound. I am new to FS so please don’t skip over details. I have 3 groups of monozygotic twins: low-risk, high-risk, ill. Twin pairs may be present in the same group (e.g

[Freesurfer] DPABISurf: A Surface-Based Resting-State fMRI Data Analysis Toolbox

External Email - Use Caution Dear Colleagues, We are pleased to announce the release of DPABISurf! DPABISurf is a surface-based resting-state fMRI data analysis toolbox evolved from DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on fMRIPprep 1.3.0.post3 (Esteban

Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

are they currently labeled 0? Where did you get your color LUT from? On Wed, 6 Mar 2019, Jörg Stadler wrote: External Email - Use Caution Hi Bruce, this did not change anything. But I tried the process of mris_ca_train, mris_ca_label with lh.oasis.chubs.annot and this worked fine. A c

Re: [Freesurfer] extracting cortical parcellation

External Email - Use Caution Hi Bruce, Thanks for your comment! I used mri_annotation2label to existed lh.aparc.annot file in label folder and got the labels. but the labels' text file contain 0 in fifth column. I need to create atlas from my own data including surface parcellati

[Freesurfer] curved reformat image....

External Email - Use Caution Hi: How can I get in an automatic way curved reformat images (for example, see paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009174/) Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology C

Re: [Freesurfer] extracting cortical parcellation

Hi Atena what were you hoping would be in the fifth column? What are you hoping to create your own annotation files from? Can you give us a bigger picture of what you are trying to achieve? cheers Bruce On Wed, 6 Mar 2019, Atena Rezaei wrote: External Email - Use Caution   

Re: [Freesurfer] Choroid plexus analysis

External Email - Use Caution Hi Ben - Although I have not worked on this myself, it is my belief that FS quantifies the CP fairly accurately. The volumes of the CP are being used in understanding etiology and pathogenesis of psychiatric disorders such as Schizophrenia. The lab I

Re: [Freesurfer] citing freesurfer

There was not freesurfer specific publication from dt_recon. It is really basic, so any publication that talks about fitting tensors to the diffusion data will do. On 3/4/19 12:30 PM, Daniel Callow wrote: > > External Email - Use Caution > > Hello, > > How should I go about properly citi

Re: [Freesurfer] Whitening/weighting matrix in FSFAST

Whitening is done by default (you can turn it off with -nowhiten to mkanalysis-sess). It uses an AR1 model. On 3/4/19 12:46 PM, Zhi Li wrote: > > External Email - Use Caution > > Hello Freesurfer Experts, > > May I ask if there is a whitening/weighting matrix used to give > weighted leas

Re: [Freesurfer] Group analysis

On 3/4/19 10:11 AM, Hengameh Marzbani wrote: > > External Email - Use Caution > > Hi Freesurfers, > > I want to do group analysis on four groups and use the volume values > in aseg,stats. > 1- Is it correct that each subcortical segmentation is based on a > "volumetric segmentation atla

[Freesurfer] mri_segstats issue with hippocampal subfields

External Email - Use Caution Hello, I am trying to extract stats from the hippocampal subfield volumes that I have warped to diffusion space. mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz --targ /Volumes/DANIEL/dti_freesurf/diffusion_recons/$

Re: [Freesurfer] Whitening/weighting matrix in FSFAST

External Email - Use Caution Thank you very much. I would like to whiten the data. May I know the details of the whitening process used in FSFAST? If I could get the whitening matrix (maybe from the source codes)? Best regards, Lizhi On Wed, 6 Mar 2019 at 11:54, Greve, Douglas N

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt The first number should be the one you are looking for. On 3/6/19 12:26 PM, Daniel Callow wrote: > > External Email - Use Caution > > Hello, > > I am trying to extract stats from the hippocampal subfield volumes > t

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

External Email - Use Caution Hi Doug, Thank you for your reply! Unfortunately when I run the same code as before but by calling to /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt instead of /Applications/freesurfer/FreeSurferColorLUT.txt and using the a

Re: [Freesurfer] extracting cortical parcellation

External Email - Use Caution Hi Bruce, I am going to extract the cortical parcellation file with its color table from freesurfer then import that in the other interface to detect and visualize the somatosensory (3b broadmann ) area. Therefore, I need the fifth column with some val

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

External Email - Use Caution Never mind. I see that I can use those to id #'s to call from FreeSurferColorLUT.txt. I assume that those Id's are consistent for both left and right hippocampus. Thanks for the help! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* E

Re: [Freesurfer] unable to map surface to fsaverage4

This is a bug in mris_preproc. I have created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc Copy this to $FREESURFER_HOME/bin (after making a backup of the one that is there) let us know if this works On 3/2/19 8:57 AM, Chenfei YE wrote: > > External E

Re: [Freesurfer] projfrac question

Hi Doug I re-analyzed one of my subjects from the very beginning with -projfrac 0.2. But still, in mri_vol2surf, the projfrac is 0.5 (copied below). Could you please let me know what I'm doing wrong? Here is my command: preproc-sess -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface fsav

[Freesurfer] (no subject)

Hello - I'm wondering how to generate a label in FreeSurfer from peak activation in a cluster? Is there a specific command? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] extracting cortical parcellation

Hi Atena the vertex indices are stored in the first column. You should be able to use them to look up into any overlay you want cheers Bruce On Wed, 6 Mar 2019, Atena Rezaei wrote: External Email - Use Caution Hi Bruce, I am going to extract the cortical parcellation fil

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

Hi Daniel left and right hippocampus have different indices (17 and 53) cheers Bruce On Wed, 6 Mar 2019, Daniel Callow wrote: External Email - Use Caution Never mind. I see that I can use those to id #'s to call from  FreeSurferColorLUT.txt. I assume that those Id's are co

[Freesurfer] PETSurfer: Equivalence between surfaces un gtmseg space and native surface?

External Email - Use Caution Dear Douglas, RBV PVC use the advantage of upsampled gtmseg space at 0.5 mm3 to compute PVCorrected images. Would it be beneficial to project this PVCorrected images onto gtmseg space surfaces to keep this upsampled resolution ? Or would it be equiva

Re: [Freesurfer] PETSurfer: Equivalence between surfaces un gtmseg space and native surface?

I don't think so. The surfaces are at about 1mm resolution, which should be fine for this. The reason that RBV had to be upsampled is that there is no way to represent the different tissue types at a single (big) voxel On 3/6/19 4:46 PM, Matthieu Vanhoutte wrote: > > External Email - Use

[Freesurfer] Gradient Inhomogeneity Correction in Bay3

Dear Freesurfer community, We acquired images in Bay3 and would like to know where the gradient inhomogeneity correction files would be on cluster, if any. We are familiar with the Bay4 procedure for correcting for inhomogeneity and were also wondering if similar steps would be followed for ima

Re: [Freesurfer] recon-all Workflow Help

Sorry Riya, you have to run it all. doug On 3/3/19 11:36 AM, Riya Chatterjee wrote: > > External Email - Use Caution > > Hi, > > I am new to FreeSurfer - I am a high school sophomore trying to learn > more about processing brain MRI's. I have read through most of the > documentation, but

Re: [Freesurfer] Cerebellar Cortex Reconstruction

that mri_tessellate command should have worked. It might be a gifti problem. Can you run it with our standard surface as an output and view it in freeview? On 3/3/19 11:47 AM, Max Crayen wrote: > External Email - Use Caution > > Hi Bruce, > > we are 3D printing brains in our lab, at the

Re: [Freesurfer] Resampling a gifti image to nifti using mri_surf2vol fails

What is actually in the gii file? It is expecting only to read in overlay information (eg, a binary mask with values of 0 or 1 at each vertex). I have not used gifti all that much On 3/4/19 10:55 AM, CAGNA Bastien wrote: > > External Email - Use Caution > > Hi everyone, > I need to conve

Re: [Freesurfer] Gray matter segmentation

Can you tar up and upload the subjects to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when they are there On 3/4/19 4:59 PM, Maxime Perron wrote: > > External Email - Use Caution > > Hi Freesurfer Experts, > > > I was wondering if you have had time to look at my problem

Re: [Freesurfer] How to extract cortical features of a ROI

you can use mri_segstats with the --slabel option On 3/5/19 10:35 AM, Bruce Fischl wrote: > Hi Kan > > you can give the surface-based label to mris_anatomical_stats and it > will constrain it's calculations to the label (where it makes sense): > > mris_anatomical_stats -l ... > > you can probabl

Re: [Freesurfer] Masks in mri_segstats

Only one mask and one threshold is used. If you need to combine masks in some way, you can use fscalc (or mri_binarize). On 3/5/19 12:47 PM, Zhi Li wrote: > > External Email - Use Caution > > Hello Freesurfer experts, > > I would like to use mri_segstats with two different masks and >

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

Your FSGD file is incorrect in several ways. Under "variables" you have "Sex" and list "Male" and "Female". The variables must be numbers, not strings. The variables should also represent continuous quantities, not categories. To handle sex, you should have a total of 6 categories, the 3 that y

Re: [Freesurfer] PETSurfer and thickness data

Procedurally, you would create stacks (eg, mris_preproc) of the thickness and the PET data, then you would use one as the --y input to mri_glmfit and the other as --pvr input (in addition to your fsgd file or design matrix). The PVR is per-voxel regresssor, so it will create a design matrix for

Re: [Freesurfer] projfrac question

This does appear to be a bug. Are you using FS version 6? If so, I put a test in that distriubtion called preproc-sess.test. Can you try running that on a subject and see if you get the desired behavior? On 3/6/19 1:31 PM, Nasiriavanaki, Zahra wrote: > > Hi Doug > > > I re-analyzed one of my sub

[Freesurfer] Creating Labels

Hello, I am wondering how to generate a label in FreeSurfer from peak activation in a cluster - is there a specific command? Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

[Freesurfer] Accounting for family relation in FS

External Email - Use Caution Dear FS List, (apologies for reposting under different title) I wanted to check if my GLM design for a surface based analysis is sound. I am new to FS so please don’t skip over details. I have 3 groups of monozygotic twins: low-risk, high-risk, ill.

[Freesurfer] 回复： unable to map surface to fsaverage4

External Email - Use Caution Yes, it solved my problem. Thank you Greve. Hope next FS version will fix this bug. Best, Chenfei -- 原始邮件 -- 发件人: "Greve, Douglas N.,Ph.D."; 发送时间: 2019年3月7日(星期四) 凌晨2:30 收件人: "freesurfer@nmr.mgh.harvard.edu"; 主题: Re: