Re: [Freesurfer] How to convert a surface label to .nii

My guess is to use mri_label2vol instead, and a mri_convert to convert to nii.gz I hope this helps. Marc. On Thu, Feb 11, 2016 at 3:17 PM, Afzal, Afsana wrote: > Hi, > > How can I convert a surface .label file

Re: [Freesurfer] FreeSurfer MRI segmentation

Hi Maheen you can look at the aseg.mgz or use the surfaces to create various compartments with mris_fill, but sulcal CSF is pretty hard to accurately detect with only a T1 cheers Bruce On Thu, 11 Feb 2016, Maheen Siddiqui wrote: Dear FreeSurfer Users,  I have a T1 weighted MRI scan and

Re: [Freesurfer] Basal Ganglia Segmentation

I definitely meant to type *Dear in my email. Cheers, Maryam On Thu, Feb 11, 2016 at 2:57 PM, Syeda Wajiha Maryam wrote: > Fear Freesurfer Experts, > > I have a feeling this question has been asked already but I'm still > confused about it. Is there a way to extract the

Re: [Freesurfer] Basal Ganglia Segmentation

sure, we segment putamen, pallidum and caudate as part of the aseg.mgz (and nucleus accumbens, although that is less well-defined) On Thu, 11 Feb 2016, Syeda Wajiha Maryam wrote: > Fear Freesurfer Experts, > > I have a feeling this question has been asked already but I'm still confused > about

[Freesurfer] Basal Ganglia Segmentation

Fear Freesurfer Experts, I have a feeling this question has been asked already but I'm still confused about it. Is there a way to extract the basal ganglia structure using freesurfer? Thanks in advance for your help! Regards, Maryam ___ Freesurfer

Re: [Freesurfer] Processing of young children using Freesurfer

yes, something wrong with the installation but it's outside of my expertise. Zeke: can you take a look? thanks Bruce On Thu, 11 Feb 2016, Zoellner, Frank wrote: Hi, did you find a hint why my installation of freesurfer is not processing the data at that stage ? It seems to be a general

[Freesurfer] How to convert a surface label to .nii

Hi, How can I convert a surface .label file to a .nii format? I'm using mri_label2label in the following way but the output is always in .label not .nii: mri_label2label --srclabel dlpfc-lh.label --outmask dlpfc-lh_mask.nii --s fsaverage --trglabel dlpfc-lh_mask.nii

[Freesurfer] comparison between two hemisphere in single subject

Hello, I want to compare the two hemisphere in one subject (thickness for example). should I use? surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi then what? how can I compare the two hemisphere of one subject? Regards, Ashkan -- -- Ashkan

[Freesurfer] FreeSurfer MRI segmentation

Dear FreeSurfer Users, I have a T1 weighted MRI scan and have run the recon-all command on it. For my steps moving forward I need to have 4 layers of tissue i.e. 4 segmentation files - GM, WM, CSF and extra cerebral tissue. Which of the outputs from recon-all will give me the segmentation? I

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii --dph /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Thank you for your response. Do I need to run the glm_fit-sim command to make the csd file? I feel this would be inappropriate for my data since I already ran the LME model. Second, is there an argument to make an output file that can be visualized via freeview? In other words, how can I view

Re: [Freesurfer] Processing of young children using Freesurfer

This is a known issue with the VirtualBox installation of freesurfer and is related to the mni tools. The mri_nu_correct stage will fail when subjects directory is in a shared folder between the host machine and the VirtualBox environment. Only known solution is to import the entire subject

[Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST

I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii --reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz When I open using freeview the f.nii.gz and the RIGHT_ROI they are fine overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably

[Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST

I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii --reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz When I open with freeview the f.nii.gz and the RIGHT_ROI they are fine overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably

[Freesurfer] Freeview to mark only one specific area

Hello Freesurfer experts, I want either a 2D or 3D picture of one of my subjects image, but with only one colored area. For example, I would like to mark the lh_lateralorbitofrontal_area. It seems that the tool to visualize images in Freesurfer is freeview, however I can't find the label for

Re: [Freesurfer] comparison between two hemisphere in single subject

Follow the further instructions in https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi ie, mris_preproc (which will sample into the common space (fsaverage_sym) and compute the difference) and mris_fwhm, if you want to smooth it. The result will be on fsaverage_sym. If you want to map it back to

Re: [Freesurfer] Processing of young children using Freesurfer

Ok thx for the info. Yours Frank > Am 11.02.2016 um 17:29 schrieb Z K : > > This is a known issue with the VirtualBox installation of freesurfer and is > related to the mni tools. The mri_nu_correct stage will fail when subjects > directory is in a shared folder

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

How was the phase nii created? On 02/11/2016 11:12 AM, Joseph Dien wrote: > MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag > /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii > > --dph >

Re: [Freesurfer] Permission denied error with mri_surfcluster command

On 02/11/2016 11:19 AM, Jennifer Legault wrote: > Thank you for your response. Do I need to run the glm_fit-sim command > to make the csd file? I feel this would be inappropriate for my data > since I already ran the LME model. No, look in $FREESURFER_HOME/average/mult-comp-cor/fsaverage.

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

using spm_read_vols I confirmed that the min and max of the phase difference file is indeed -4096 and 4092 respectively. Further troubleshooting epidewarp.fsl indicates that the script is correctly branching to "# Input is phase difference and magnitude” It then executes the following

Re: [Freesurfer] How to convert a surface label to .nii

yep, that's right. Thanks Marc! On 02/11/2016 09:44 AM, Marc Ramos wrote: > My guess is to use mri_label2vol > instead, and > a mri_convert to convert to nii.gz > > I hope this helps. > Marc. > > > > > On Thu, Feb 11, 2016 at 3:17 PM,

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

yes, that is the problem. Where did that phase image come from? You can use fslmaths to simply rescale it to 0-4095, then it should work On 02/11/2016 11:34 AM, Joseph Dien wrote: > using spm_read_vols I confirmed that the min and max of the phase > difference file is indeed -4096 and 4092

Re: [Freesurfer] Permission denied error with mri_surfcluster command

That's very useful, thank you. In terms of FWHM, I am examining gray matter volume, not cortical thickness, and was previously instructed by Martin Reuter not to smooth these data. Do you think it would make sense then to just use the fwhm01? And in terms of the voxel-wise threshold, is there a

[Freesurfer] wm-hypointensities variables

Greetings, I am wondering if there is some information regarding the meaning of "wm-hypointensities" and "non-WM-hypointensities" variables from the aseg.stats file, ie, what features are included in these variables and how FS computes them. I checked previous posts that have the same issue

Re: [Freesurfer] wm-hypointensities variables

you can turn this off with the -nowmsa flag I believe in recon-all. The labels are for damaged white matter and damaged gray matter, which can be tough to distinguish based only a T1. We have some (not-yet-distributed) tools that do pretty well on this if you have other contrasts like

Re: [Freesurfer] Permission denied error with mri_surfcluster command

by "volume" do you mean a VBM-type analysis or do you mean the volume that comes out of FS (thickness*area)? If you are going to use a clusterwise correction, then you have to have a FWHM measurement. You can try analyzing it in mri_glmfit with --osgm just to get the FWHM out of it. You