[Freesurfer] Tcsh-error with Freesurfer

Dear Sir / madam, I'm a last year student of Medical Imaging (from Hoge school Universiteit Brussel, HUB). In January i'm defending my thesis. My subject is MRI and Alzheimer's disease. With volumetry I want to show that the Hippocampi have a smaller volume then normal patients. I used the p

[Freesurfer] Fwd: LGI path problem

From: Linn Mittlestein Date: Fri, Oct 18, 2013 at 1:30 PM Subject: LGI path problem To: freesurfer@nmr.mgh.harvard.edu Hi, I am trying to compute lgi measures, and I think my problem lies in the fact that the matlab path is not set correctly; it is calling an older version of matlab however I ne

[Freesurfer] Accuracy

Hello, After run the recon-all instruction, I wanted to extract the paracentral and precentral gyrus in a accurate way. Does anyone knows how can I get extract these areas? Thank you Vicente ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu htt

Re: [Freesurfer] Accuracy

Hi Vicente what do you mean by "extract"? They are both labels in the Destrieux parcellation I believe (?h.aparc.a2009s.annot in the subject's label dir). These can be converted to a volume with mri_aparc2aseg I believe, or Doug has some tools for extracting specific labels from the parcellatio

[Freesurfer] Maybe wrong registration

Hello to everybody, I made a script to extract some structures from a T1 image. The code extract precentral and paracentral gyrus, putamen, nucleus caudate and accumbens. First of all convert from annotation to label, after that I used tkregister (maybe this can be the focus of the problem) to ge

Re: [Freesurfer] Tcsh-error with Freesurfer

Hi Philippe, See link below regarding the error you are getting, although recon-all is probably failing because you need to pass not only the path but one dicom file which is part of the T1-weighted scan. If you run the command below in the directory where you copied the dicom files, you will

[Freesurfer] Segmentation and Surface Errors

Hi Guys, I'm having an issue with a brain involving both inaccurate surfaces and incorrectly segmented voxels. Basically, a sulcus is being skipped over by the main surface where and a bunch of basically empty space is being segmented as white matter. I've edited the segmentation myself by removin

[Freesurfer] Manually drawing surfaces

Is this possible? jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-

[Freesurfer] running recon-all for FSL-based ROIs

Hello FS experts, I am interested in utilizing the functional ROIs made by the Greicius lab out of Stanford (found here). However, these ROIs were made using FSL and the coordinate system for them is not responding to simple resampling commands (su

[Freesurfer] Extremely intense grey matter being omitted

FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas? I fear it may believe they are dura because of the

Re: [Freesurfer] Problem in final analysis

fsaverage is already part of the distribution. I don't understand from your email what the problem is. doug On 10/21/2013 10:03 AM, car...@van-vlodrop.de wrote: > > Hi Doug, > > > I have already run: > > > recon-all -s subject -qcache -target avgsubject for each subject > > > Is it the same fi

Re: [Freesurfer] running recon-all for FSL-based ROIs

If you are trying to get them into fsaverage/mni305 space, then use $FREESURFER_HOME//average/mni152.register.dat doug On 10/21/2013 10:58 AM, Paul Beach wrote: > Hello FS experts, > > I am interested in utilizing the functional ROIs made by the Greicius > lab out of Stanford (found here >

Re: [Freesurfer] Longitudinal Freesurfer & TRACULA quality control

Dear Anastasia, The spikes (problem 5) are also inside the brain accross all volumes so I will have to exclude this time point and thus the subject from the analysis. I checked also again all of the other volumes: Unfortunately, the volumes I would delete are not evenly distributed between gro

Re: [Freesurfer] running recon-all for FSL-based ROIs

It is not done with recon-all. Use mri_label2vol to map your ROIs to fsaverage space using the registration below doug On 10/21/2013 11:54 AM, Paul Beach wrote: > Hi Doug, > > Thank you for the response. > > You'll have to pardon my ignorance here, but how would I integrate > this into the ac

[Freesurfer] "command not found" - unable to set up freesurfer

Hi, I have just downloaded and I thought installed freesurfer on a Debian system (Debian 3.2.51-1 x86_64 GNU/Linux). However when I go to test the install by typing in freeview (or any other command) in the terminal window I get the following: % freeview freeview: Command not found. Before doin

Re: [Freesurfer] Pial surface interhemispheric overlap

Hi Jon that's pretty bad. Is the aseg also incorrect there? If so, try correcting it and rerunning cheers Bruce On Mon, 21 Oct 2013, Jon Wieser wrote: > > > > Hi Freesurfer experts > I recently created surfaces with recon-all, and found that in the straight > gyrus in the medial inferior front

Re: [Freesurfer] Manually drawing surfaces

you can't manually draw them, which would be extremely difficult to do and maintain topology, but there is a surface repositioning tool in freeview you can try out. cheers Bruce On Mon, 21 Oct 2013, Jonathan Holt wrote: > Is this possible? > jon > >

Re: [Freesurfer] Extremely intense grey matter being omitted

why are they so bright? Are they that way before intensity normalization (e.g. in the orig.mgz)? On Mon, 21 Oct 2013, Jonathan Holt wrote: FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that shou

Re: [Freesurfer] Segmentation and Surface Errors

Hi Jon yes, we'll need images or just upload the subject as we can't diagnose it from only this information. If I had to guess, I would think it's an incorrectly fixed topological defect. See if the ?h.orig.nofix surface has the sulcus that is missing from the ?h.orig surface. If so, you'll n

[Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

Hello, I am running into a tracula error very early in the preprocessing steps. I have data that was already somewhat preprocessed (reconstruction, eddy correction and magnetic field inhomogeneity correction) that I'm trying to use as an input. I have turned off those steps in the tracula configu

[Freesurfer] Tracula Error

Hello, I am running into the following error when I try to run trac-all: set: No match. ERROR: must specify as many DWI dicoms as subjects I have taken my script and examined it line by line and have made several attempts at debugging it. I was wondering if you had any suggestions? Attached

Re: [Freesurfer] "command not found" - unable to set up freesurfer

Hi Laura, So the 'freesurfer' command works but all other other freesurfer commands (e.g. tkmedit, freeview) return "Command not found."? Can you please provide me with the out of the 'echo $PATH' command? Thanks. -Zeke On 10/21/2013 12:34 PM, Laura Taylor wrote: > Hi, > > I have just download

Re: [Freesurfer] Pial surface interhemispheric overlap

HI bruce thanks for the info the aseg was ok, except that the Right and Left cerebral cortex lables were in adjacent voxel in the region. I modified aseg.mgz so that they didn't touch. by eraseing some of the segmentation in the space between the hemispheres. At which stage do I restart the re

Re: [Freesurfer] Pial surface interhemispheric overlap

yes, I think you could probably run -autorecon2-cp -autorecon3, but I'm not positive On Mon, 21 Oct 2013, Jon Wieser wrote: > HI bruce > thanks for the info > the aseg was ok, except that the Right and Left cerebral cortex lables were > in adjacent voxel in the region. I modified aseg.mgz so th

[Freesurfer] QDEC

Freesurfer, I want to make sure I am setting up my group analysis correctly. I have 2 groups, one a control population and the other a patient population , that I am wanting to see where there are differences controlling for age. I set the group as the fixed factor and I demeaned the ages and

Re: [Freesurfer] medial wall crossing the surface: repost

Not always, but yes, in some instances the aseg crosses. > - Original Message - > From: Bruce Fischl > Sent: 10/18/13 01:22 PM > To: silve...@gmx.com > Subject: Re: [Freesurfer] medial wall crossing the surface > > Does the aseg cross as well? > > > > On Oct 17, 2013, at 10:07 PM, "si

Re: [Freesurfer] medial wall crossing the surface: repost

Try fixing the aseg and rerunning Cheers Bruce > On Oct 21, 2013, at 6:23 PM, "silve...@gmx.com" wrote: > > Not always, but yes, in some instances the aseg crosses. > > >> - Original Message - >> From: Bruce Fischl >> Sent: 10/18/13 01:22 PM >> To: silve...@gmx.com >> Subject: Re: [Fre

Re: [Freesurfer] medial wall crossing the surface: repost

Thanks Bruce for your response, I'll fix aseg where it is incorrect, but what about the instances where the aseg is correct and the pial surfaces cross? Other than needing to update aseg.stats, are there any other concerns with the 'hemisphere' approach I described below? Thanks again, Paul

[Freesurfer] ill conditioned matrix with covariates that are unequal between groups

Hello freesurfers, I'm trying to run mri_glmfit between groups analysis (patients vs. controls) with gender, age, medication (continuous), and duration of illness as covariates. The problem is, only the patients have medication and duration of illness values - by virtue of being control participan

[Freesurfer] result is L-R fliped in native space

Dear Freesurfer： I am now working in converting cortical labels from freesurfer to volumetric masks. First i gained the registration matrix by bbregister, then applied those matrix to tranform ROI labels into native space using label2vol. However, when i got the final .NII results, both of the