Re: [Freesurfer] Extra-axial CSF and TCV GM

On 11/19/18 7:34 AM, Crocetti, Deana wrote: External Email - Use Caution Hi Folks, 1) Can I derive a measure of extra-axial CSF. I realize this must be generated in order to create the boundary between the skull and dura but not sure if this is saved in as one of the labels. Do you

Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

On 11/16/18 7:34 PM, YAN Chao-Gan wrote: External Email - Use Caution Dear freesurfer experts, I have a pretty naive question but would like to confirm. When we use --3spaces option in multiple comparison correction, does that mean we set the Cluster-wise threshold (cwp, not Cluster

Re: [Freesurfer] FDR correction

High p-values (i,e close to 1) mean non-significance. I don't know how to do a power analysis with FDR. On 11/19/18 1:16 PM, Laura Ferrero wrote: > External Email - Use Caution > > Hi, > I performed an statistical analysis comparing autism group with control group > using volume/area

Re: [Freesurfer] Gray Matter Manual Edit Reverting

Hi David does this not work in freeview? Can you describe to Ruopeng (ccd) exactly what you tried? cheers Bruce On Mon, 19 Nov 2018, David S Lee wrote: External Email - Use Caution Hello Experts,  I am currently using FreeSurfer version 6.0 to make manual edits to T1w

Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

External Email - Use Caution Dear Douglas, Thanks a lot for your reply! That's very clear! Best, Chao-Gan On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > > > On 11/16/18 7:34 PM, YAN Chao-Gan wrote: > > External Email - Use

Re: [Freesurfer] Map image in MNI onto fsaverage

You can follow the instructions here for the case where you are not using kinetic modeling. You don't need to do the PVC either https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer This command in particular, you just need to generate the registration and supply you input as the --mov

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

I can' tell what is going wrong there. Can you run it with --debug as the first option and send the output? BTW, the MC correction for LGI is probably not very accurate. I would recommend using permutation. See here

Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

Hi June - Circling back to this to see if it was resolved. If you're just using the publicly available data, there should be 3x96 directions, with 3 different b-values. Which set of 96 are you using? a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf

Re: [Freesurfer] How to automate recon-all command for multiple subjects

External Email - Use Caution I'm trying to run this code but it's not working. What should be $i in the code? On Mon, Nov 19, 2018 at 9:15 PM Bruce Fischl wrote: > or you could do that all on a single line: > > recon-all -i $SUBJECTS_DIR/$i/ -s $i -all > > cheers > Bruce > > On

Re: [Freesurfer] How to automate recon-all command for multiple subjects

External Email - Use Caution I have a folder, lets name xyz which contains .nii file. Now I want to run recon-all for all the files in that folder. Please let me know how I can do that. On Tue, Nov 20, 2018 at 11:40 AM Vivek Sharma wrote: > I'm trying to run this code but it's

[Freesurfer] Error tkmedit

External Email - Use Caution Dear Free Surfer experts, I am trying to load my brainmask and the T1 to make editions but I have a problem I do not know how to solve. I would much appreciate your helping here. Best regards, Rosalia *Problem: *

[Freesurfer] How to automate recon-all command for multiple subjects

External Email - Use Caution Hi, I'm using freesurfer to generate head surfaces using MRI file. I want to execute recon-all command for number of subjects, but unable to run it. The script I'm using is: for i in `cat *subs.txt*` do recon-all -s $i -all -qcache done subs.txt

[Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

External Email - Use Caution Dear Freesurfer Developers, I'm trying to run mri_glmfit-sim to correct for multiple comparisons but am receiving the following error: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir

Re: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview

External Email - Use Caution Thanks Eugenio, I'll do that. Much appreciated. best regards Erik Postdoctoral Research Fellow Dept. Of Psychiatry Royal College of Surgeons in Ireland ERC Building Beaumont Hospital Dublin & Dept. Of Psychiatry Trinity College Institute of

[Freesurfer] Extra-axial CSF and TCV GM

External Email - Use Caution Hi Folks, 1) Can I derive a measure of extra-axial CSF. I realize this must be generated in order to create the boundary between the skull and dura but not sure if this is saved in as one of the labels. 2) To generate a measure for Total Cerebral

Re: [Freesurfer] How to automate recon-all command for multiple subjects

External Email - Use Caution HI Vivek, you probably need 2 steps, first registration, second recon-all. Something like: ... do recon-all -i $SUBJECTS_DIR/$i/ -s $i recon-all -all -subjid $i I didn't check if the scrips runs. That's the general structure. Best, Alex Le

Re: [Freesurfer] How to automate recon-all command for multiple subjects

or you could do that all on a single line: recon-all -i $SUBJECTS_DIR/$i/ -s $i -all cheers Bruce On Mon, 19 Nov 2018, Alex Hanganu wrote: External Email - Use Caution HI Vivek, you probably need 2 steps, first registration, second recon-all. Something like: ... do    

Re: [Freesurfer] Error tkmedit

Hi Rosalia tkmedit is deprecated - can you try freeview? Also, check to make sure that your SUBJECTS_DIR is set properly (it looks like it is /home/ms_naroa/subjects and it probably should be ~/Escritorio/subjects_controls) cheers Bruce On Mon, 19 Nov 2018, Rosalia Dacosta Aguayo wrote:

[Freesurfer] Gray Matter Manual Edit Reverting

External Email - Use Caution Hello Experts, I am currently using FreeSurfer version 6.0 to make manual edits to T1w images. In an earlier version 5.3, when GM has been erroneously removed, I used the "clone tool" to bring back voxels based on the original T1w. However, this tool

[Freesurfer] FDR correction

External Email - Use Caution Hi, I performed an statistical analysis comparing autism group with control group using volume/area and thickness measures. I found significant differences in some regions but they were not significant after FDR correction. The majority of p-values

[Freesurfer] Pial edition and Intensity Normalization / Control points

External Email - Use Caution Dear Free Surfer team, I have edited the pial surface and I am running: -autorecon-pial. This process is taking its time. Then I will look for intensity normalization and control points. Then I will have to run recon-all -autorecon2-cp -autorecon3.

[Freesurfer] Research Associate Position: Molecular Imaging in Neurodegenerative Disease, Johns Hopkins University

External Email - Use Caution Research Associate Molecular Brain Imaging in Neurodegenerative Disease A full-time opening is available for a Research Associate in the Department of Psychiatry and Behavioral Sciences and Radiology and Radiological Sciences at Johns Hopkins

[Freesurfer] Map image in MNI onto fsaverage

External Email - Use Caution Dear Freesurfer experts, I have the mean PET images for a number of subjects in MNI152 space. For visualization purposes, I would like to map this mean image onto brain surface. How can I do it. I appreciate any suggestion you may provide. Thanks!

Re: [Freesurfer] Segmentation fault

External Email - Use Caution Update - Segmentation fault I think I have finally found the issue. The bvec files I uploaded actually contained only zeroes for each bvec value, and that made it impossible for Tracula to function properly. This was a result of the original files

Re: [Freesurfer] Pial edition and Intensity Normalization / Control points

1. Yes, this should be fine. Frequently control points help the pial surface cheers Bruce On Mon, 19 Nov 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear Free Surfer team, I have edited the pial surface and I am running: -autorecon-pial. This process