[Freesurfer] Import tract files from other programs

Good morning, For our project, we are studying tracts that from two deep brain nuclei spread to the cortex. Our aim is to find the coordinates of the cortical targets and compare them across individuals to assess the variability of these projections. We used the recon-all command for preprocess

[Freesurfer] Longitudinal processing with different FS versions

Dear Freesurfers, We are running a longitudinal study with 4 time points. The first two time points were processed and edited with the 5.3 version of Freesurfer and the other two time points with FS6. I assume we have to re-run the first two time points with the new versión, but is there a way to

Re: [Freesurfer] Longitudinal processing with different FS versions

Susanna carino!! On Fri, Apr 13, 2018 at 10:21 AM, Susanna Carmona Cañabate < susannacarm...@gmail.com> wrote: > Dear Freesurfers, > > We are running a longitudinal study with 4 time points. The first two time > points

Re: [Freesurfer] Surface Problem

Dear freesurfer, I saw the issue below online and wondered whether it got solved? I have the “if: Missing file name.” error when testing my installation with recon-all -i sample-002.nii.gz -s bert -all attached my recon-all file. Thank you for your help and best regards, Laeitita --

Re: [Freesurfer] Import tract files from other programs

Hi Samantha - You display a .trk file that was generated in any possible tool, as long as that tool preserves the image orientation information in the header of the .trk file. If that info is not there, there is no way for freeview to guess how to display everything in the same space. Best, a.y

[Freesurfer] mri_vol2surf: issue with registration

Hi , I am facing an issue when I try to compare two network-based maps, one of which has been registered on a surface while the other one has not. If anyone has tried doing something similar and has any thoughts about it please share your suggestions, I highly appreciate it. I have two sets of ne

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

On Di, 2018-04-10 at 16:09 +0200, Kaushal, Mayank wrote: > I appreciate your providing the pros and cons associated with both > options. > > Lets say for now we want to pursue option 2. > > My understating is that since you recommend not to include ‘visit’ > and 'time_from_baseline’ in the same mod

[Freesurfer] LGI for the lobar annotation

Good night, does anyone know if it is possible to calculate the lGI for the ?h.lobesStrict.annot? And if it yes, how can I do it? I've already tried to use: *mri_segstats --annot subjxx/label/lh.lobesStrict.annot --i $SUBJECTS_DIR/subjxx/surf/lh.pial_lgi --sum lh.lobesStrict.annot.pial_lgi.stats

[Freesurfer] mri_anatomical_stats with lobeStrict annot for multiple subjects

Good night, I would like some help to extract mri_anatomical_stats with lobeStrict annot for multiple subjects in a table format, with the results for all subjects there. I've already tried aparcstats2table and I don't got how to insert the lobeStrict annot there. Thank you very much, Fernanda Mo

Re: [Freesurfer] LGI for the lobar annotation

that should work, except the command line is not quite right On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes wrote: Good night, does anyone know if it is possible to calculate the lGI for the ?h.lobesStrict.annot? And if it yes, how can I do it? I've already tried to use: /mri_segstats --

[Freesurfer] Visualizing Single anatomical ROI on FreeView

Hi, I am attempting to view single anatomical ROI (say Right-Hippocampus) overlaid on MRI image using freeview.How can I achieve this? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

Re: [Freesurfer] Visualizing Single anatomical ROI on FreeView

you can use mri_extract_label on the aseg.mgz to pull out just the label you want, then load it and the MRI into freeview (if that is what you mean) cheers Bruce On Fri, 13 Apr 2018, Srinivasan, Dhivya wrote: > Hi, > > I am attempting to view single anatomical ROI (say Right-Hippocampus) >

Re: [Freesurfer] Visualizing Single anatomical ROI on FreeView

Or simply uncheck every item in the look up table except the one you want to show. > On Apr 13, 2018, at 5:15 PM, Bruce Fischl wrote: > > you can use mri_extract_label on the aseg.mgz to pull out just the label > you want, then load it and the MRI into freeview (if that is what you > mean) >

Re: [Freesurfer] Visualizing Single anatomical ROI on FreeView

BTW, that only applies to the dev version. Ruopeng > On Apr 13, 2018, at 5:18 PM, Ruopeng Wang wrote: > > Or simply uncheck every item in the look up table except the one you want to > show. > >> On Apr 13, 2018, at 5:15 PM, Bruce Fischl wrote: >> >> you can use mri_extract_label on the as

Re: [Freesurfer] Visualizing Single anatomical ROI on FreeView

There is also an "All" button that if you uncheck will uncheck all of them; then you can go check the one(s) you want On 4/13/18 5:22 PM, Ruopeng Wang wrote: > BTW, that only applies to the dev version. > > Ruopeng > >> On Apr 13, 2018, at 5:18 PM, Ruopeng Wang wrote: >> >> Or simply uncheck ev

Re: [Freesurfer] mri_anatomical_stats with lobeStrict annot for multiple subjects

If you look in the recon-all.log file, you will find the call to mris_anatomical stats used to generate the aparc.stats files. Just modify it select your annotation and output stats file name On 4/13/18 4:26 PM, Fernanda Hansen P. de Moraes wrote: Good night, I would like some help to extrac

[Freesurfer] Group Analysis Contrast (Follow-up)

Hi Douglas, Thank you for your reply. To follow up, I am setting up GLM analysis with 1 categorical variable and 1 continuous variable (age X weight). My fsgd looks like this: *GroupDescriptorFile 1* *Title Cortical Thickness Interaction between Age and Weight* *Class class1 plus blue* *Class cl

[Freesurfer] how to use annotation file in FSFAST for seed based analysis

Hello, I am trying to use Glasser’s parcellation to create a correlation matrix that compares all parcels to all parcels. I am new to FSFAST, but so far I have gotten the data preprocessed and ready to go. But I am unsure how to proceed. I have rh and lh annotation files of the parcellation in f