Re: [Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution Hola Miguel Ángel, First, you need to run the T1 through recon-all normally, as you have already done. Next, you run the subfield module with the highres T2 as input - no recon-all on the T2 required, as it's used in a different way. Cheers Eugenio S

Re: [Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution Thanks for your reply Eugenio. You have mentioned like "No recon-all on the T2 required, as it's used in a different way". May I know the actual purpose of using T2 images for reconstruction process. Why we should not T2 images as input for recon-all

Re: [Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution Sorry if I didn’t explain myself properly. T2 scans of the whole head can be used by recon-all to improve the segmentation of the pial surface, but: a) They are not required (you can use the T1 alone); and b) Cannot be run through recon-all independe

Re: [Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution Hi, What would be the command for hippocampal subfields using only the T2 images? This? recon-all -s -hippocampal-subfields-T2 I tried but obtained the following error pcpb3846:~ lab1-rmn$ recon-all -s /Applications/freesurfer/subjects/4235

Re: [Freesurfer] FSGD design for multi-centre study

External Email - Use Caution Hi, Sorry for coming back to this, but I'm still confused about the issue of having unbalanced classes. I thought that I could not remove the class as you suggested since this would mean that the contrast positive and negative values would no longer

Re: [Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution It depends on the version, but yes, in 6.0 it’d be that command. The file name of the additional scan should be an existing nii/nii.gz/mgz file, though (right now you just have “T2”). Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Tran

Re: [Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution Hi Eugenio, In my error free surfer say that cannot find the file, It´s necessary put the additional scan in a specific folder? I have this organization in the free surfer subjects directory 4235_T2 (main folder) mri (subfolder) orig (sub

Re: [Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution recon-all –sd /Applications/freesurfer/subjects -s 4235_T2 -hippocampal-subfields-T2 /Applications/freesurfer/subjects/4235_T2/mri/orig/T2.mgz T2_3D_SAG -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group Universi

[Freesurfer] Register individual functional volume to MNI152

External Email - Use Caution Hi all, I’m having some trouble getting an an accurate registration between an individual functional volume and MNI152 space. Presently, I’m using the commands: bbregister --s MNI152_FS --mov volumeInFunctional --reg mniDir/filename2mni.lta --init

Re: [Freesurfer] Longitudinal data from different sequences and scanners

External Email - Use Caution Martin, Thanks for the feedback. Given our data set (1mm^3 timepoint1 and 0.8mm^3 timepoint 2), what would be the best way to salvage this data and look for longitudinal changes? Would it be possible to upsample/downsample the images so that they are t

[Freesurfer] Freeview surface annotation outline line thickness

External Email - Use Caution The freeview flag "annot_outline=1" is great for viewing results for significant clusters from mri_glmfit-sim. Is there a way to make the outlines thicker? With the default thickness, the outlines are difficult to make out in a multipanel figure. (The

Re: [Freesurfer] transforming functional volumes to MNI without resampling

External Email - Use Caution Hi Doug, funcVol is an individual functional resting state scan. We are doing some clustering analyses and trying to visually compare the clustering across subjects (I would be a bit sketched out trying to quantify the overlap between subjects due t

Re: [Freesurfer] Freeview surface annotation outline line thickness

Hi Kayle, There is no such option. I'll put it on my list for future improvement. Best, Ruopeng On 05/04/2018 01:09 PM, Kayle Sawyer wrote: The freeview flag "annot_outline=1" is great for viewing results for significant clusters from mri_glmfit-sim. Is there a way to make the outlines thick

Re: [Freesurfer] fmriprep to fsfast interface

Hello, I just wanted to follow up on this again. Is there any way to transform functional data (already in T1 space) to tal space directly? Something like passing an identity registration matrix to mri_vol2vol or another command that would apply the tal transform without a registration? If n

[Freesurfer] Problems at exporting recon-all outputs

External Email - Use Caution Hi Freesurfer developers, After having executed the recon-all in several subjects I tried to export all measures of the Destrieux atlas (area, volume, curvind, foldind, gauscurv, meancurv, thickness and thicknesstd) but I got an error because in some