[Freesurfer] mris_calc erroe in recon-all

Hi list, I have a problem during recon-all #@# Surf Volume lh Thu Sep 12 08:25:31 CEST 2013/Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/surf\n mris_calc -o lh.area.mid lh.area add lh.area.pial \n mris_calc: Sorry, but I seem to have encountered an error. While checking

[Freesurfer] updating the tables and volumes associated with aseg.mgz

Hi, I'm seeking some advice on updating the tables and volumes associated with aseg.mgz. I have completed the cortical analysis on a number of subjects and now would like to review and edit (if needed) aseg.mgz My strategy is to not cause any changes to the surfaces already completed and invo

[Freesurfer] Fwd: talairach transforms

-- Forwarded message -- From: swathy p.s Date: Wed, Sep 11, 2013 at 1:47 AM Subject: talairach transforms To: freesurfer@nmr.mgh.harvard.edu after motiioncor was runned sucessfully,getting error with talairach.comand was as given bellow [root@ml freesurfer]# recon-all -talairach

[Freesurfer] reconall question

Hello FreeSurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages for that subject as an input file, may I just keep the three mgz files (001.mgz, 002.mgz and 003.mgz) in the orig

[Freesurfer] t-statistics map using tksurfer

Dear all, Is there a way to visualize vertex wise t-values (t-statistics), instead of p-values, on a vertex map when you are doing group analyses? I successfully generated the p-maps using mri_glfmfit, but I am wondering if vertex-wise maps that represent t-values can be also generated and vis

Re: [Freesurfer] Could not find .mat

no, you'll need to figure out which series to give an a file from, but it will figure out the other files in the same series. Also, please cc the list so that others can answer Bruce On Wed, 11 Sep 2013, Pedro Rosa wrote: > Hi, > Thanks for your help. > Is freesurfer able to select T1-w dicoms

[Freesurfer] rerunning recon-all

I have a somewhat strange question and hopefully someone can help me out. I have a few hundred subjects that have all been run through recon-all, and have gone through some QA. In some of the cases control points have been added or brain masks have been modified etc, and recon-all has been reru

Re: [Freesurfer] Could not find .mat

Hi Pedro you are *far* better off avoiding the analyze format. If you must convert, try nifti, but in general we prefer starting with the dicoms directly. If you give recon-all a *single* image file in the correct (T1-weighted) dicom series we will figure out the other ones cheers Bruce On Wed

[Freesurfer] Could not find .mat

Hi, I am finding a warning at recon-all when creating the folders: INFO: could not find /Path/subject.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. INFO: if not valid, please provide the information in /Path/subject.mat file What are the co

[Freesurfer] z-scores versus raw_age for correction in GLM_FIT or qdec

Dear Douglas, attached you´ll find the two y.fsgd file from the analysis run in GLM_FIT. the results are completely different (the z-score converted age produces a believable result, while the result correcting with raw age scores seems completely wrong. best regards Olof y.fsgd_raw_age Descrip

Re: [Freesurfer] mri_tesselate: max vertices 1000000 exceeded

To comment further on this. It appears that - at least in our data - the talairach registration fails frequently (i.e. in more than 60% of the cases) as a result of the larger field inhomogeneities at high field. A good work-around is to use FLIRT for doing the registration. So just use FLIRT to r

Re: [Freesurfer] [martinos-tech]

Suzanne, p<0.005 is the same whether its voxels or vertices. The liberal nature of 20 voxels is vague to begin with as there is two things contributing to how liberal 20 voxels are: (1) voxel size - 20 1mm isotropic voxels is quite different from 20 3mm isotropic voxels; (2) The number of voxels y

Re: [Freesurfer] TALx coordinates

Hi Doug, It's pretty awesome. So accordingly, MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1 The l

[Freesurfer] FS versions

Dear FS team, I'm using the web portal Neugrid (https://neugrid4you.eu/it) for the analysis of my T1w MRI data with FreeSurfer. In particular, I'm using the *reconall -all*. My question is about possible problems arising from different FS versions. The version provided by Neugrid is the Freesurf

[Freesurfer] mri_annotation2annotation?

Hi all, I know I can use mri_label2label and then mris_anatomical_stats -l to obtain the label-based cortical thickness for each individual subject. I also know that there is a tool called mri_annotation2label. But is there a way to convert annotation to each individual subject, so that I can

[Freesurfer] ASeg Stats is done twice?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi. I try to get information about the progress of my subjects out of the log files, writing a script that reports about the progress and sends progress messages. For that I try to get the individual stages as progress indicator from the recon-all.log

Re: [Freesurfer] TALx coordinates

Hi Gari, The transformation actually consists of a 3 x 3 matrix and a 3 x 1 translation vector. The use of a 4 x 4 matrix allows the representation of an affine transformation as a matrix multiplication (http://en.wikipedia.org/wiki/Affine_transformation#Representation). --Thomas On Wed, Sep 11,

Re: [Freesurfer] TALx coordinates

Hi Doug, just a very naive question about coordinate change: why do we need the fourth component? I mean, shouldn't be the transformation matrix 3x3 instead of 4x4 for a coordinate change in 3D space? thanks! Gari On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve wrote: > Hi Yang, I've computed

Re: [Freesurfer] [martinos-tech]

Hi Doug, Thanks for your reply. I know how to run mri_glmfit-sim. What I'd like to do is to apply a more liberal threshold to my data to examine the clusters that fall outside of the MC-corrected threshold. To do this I applied the mri_surfcluster command with a vertex-wise threshold of p < .005,