Re: [Freesurfer] the problem about XL defect detected...

External Email - Use Caution Hi， I am sorry. In my recon_all folder, there isn't lh.white, rh.white,lh.pial and rh.pial files, so I can run below command freeview -v topo_defect_before/mri/brainmask.mgz \ topo_defect_before/mri/wm.mgz:colormap=heat:opacity=0.4:visible=0 \ -f topo_

[Freesurfer] Labels in nii files

External Email - Use Caution Hello, I have a t1w.nii file and a segmentation.nii file. For the latter, I was wondering how I could join labels together and create new labels. Best, Maxime ___ Freesurfer mailing list Freesurfer@nmr.mg

Re: [Freesurfer] Labels in nii files

External Email - Use Caution C5dyzZczzzvSent from my Samsung Galaxy smartphone. Original message From: Vidal Maxime Date: 12/04/2019 11:54 (GMT+00:00) To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Labels in nii files     External Email - Use Ca

[Freesurfer] Time course thalamic subregions

External Email - Use Caution Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS. I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i

Re: [Freesurfer] Using Custom Atlas for Segmentation of Brain Surfaces

External Email - Use Caution Thank you very much for both of your answers. I haven't been able to download the Power parcellation from BALSA webpage, even though I registered to the site, it doesn't allow to download, so I sent an email to the technical team. Once I download it I w

[Freesurfer] Fwd: Fw: mriglmfit error

External Email - Use Caution Hi Dr Greve, Is the idea behind removing one column for the NS 1 column in the design matrix meant to remove the columns for females? And how do we know which of the two columns for the Ns_1 in the design matrix are for which gender? In the contrast

Re: [Freesurfer] Aparc stats files aren’t being generated

try recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 On 4/11/2019 10:01 PM, Romella Durrani wrote: External Email - Use Caution Hello, I am having problems generating the aparc stats files for all my scans. I have checked the surfaces for all scans and they were all

[Freesurfer] Fw: mriglmfit error

External Email - Use Caution Hi Dr Greve, Is the idea behind removing one column for the NS 1 column in the design matrix meant to remove the columns for females? And how do we know which of the two columns for the Ns_1 in the design matrix are for which gender? In the contrast

Re: [Freesurfer] the problem about XL defect detected...

Use orig.nofix and orig instead On 4/12/2019 4:21 AM, Abby tang wrote: External Email - Use Caution Hi， I am sorry. In my recon_all folder, there isn't lh.white, rh.white,lh.pial and rh.pial files, so I can run below command freeview -v topo_defect_before/mri/brainmask.mgz \ topo_defec

Re: [Freesurfer] Labels in nii files

Try mri_binarize --i seg.nii --replaceonly segno1 segno2 --o newseg.nii which will merge segno1 into segno2 On 4/12/2019 6:54 AM, Vidal Maxime wrote: > External Email - Use Caution > > Hello, > > I have a t1w.nii file and a segmentation.nii file. For the latter, I was > wondering how I c

Re: [Freesurfer] Time course thalamic subregions

You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f

Re: [Freesurfer] Fw: mriglmfit error

No, the idea is to merge the males and females into one column. I just so happens that the female column is all 0s and the females have a 0 in the male column, so you can effectively merge them by just removing the last column. You cannot test for a difference between genders on Ns_1 (which appe

Re: [Freesurfer] Hippocampal subfield version

External Email - Use Caution Hi Eugenio, Thanks! I am able to run it now. Best, Emily From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: Thur

Re: [Freesurfer] Time course thalamic subregions

External Email - Use Caution Thanks!! Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." > ha sc

Re: [Freesurfer] Time course thalamic subregions

Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 1:46 PM, std...@virgilio.it wrote: External Email - Use Caution Thanks!! Using mri_

Re: [Freesurfer] How to convert a functional FSL mask to an anatomical Freesurfer mask

It looks like you are trying to do a surface-based analysis using a mask derived from the volume-based fmri analysis. Is that right? And the fMRI is on the mni152? If so, then you will need to get your mask onto the surface of fsaverage. The easiest way to do that is to run recon-all on the mni

Re: [Freesurfer] mri_segstats

Following my previous question, I have one more question and I appreciate if you could please reply whenever you had time. I extracted time series from a single resting state run using mri_segstats and compared it to the time series extracted from the same run using (fcseed-config & fcseed-sess

Re: [Freesurfer] How to convert a functional FSL mask to an anatomical Freesurfer mask

It looks like you are trying to do a surface-based analysis using a mask derived from the volume-based fmri analysis. Is that right? And the fMRI is on the mni152? If so, then you will need to get your mask onto the surface of fsaverage. The easiest way to do that is to run recon-all on the mni