Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

you would do it in fcseed-config by using -mean instead of -pca On 7/20/18 4:06 PM, Eryilmaz, H. Hamdi wrote: Thanks Doug! One last question: If I wanted to regress out the average signal from the ventricles and the white matter (instead of using the PCA output), could I directly incorporat

[Freesurfer] Resample data for longitudinal comparisons

External Email - Use Caution All, I would like to compare cortical thickness between two timepoints. Timepoint 1 has 1mm^3 data. Timepoint 2 has 0.8mm^3 data. I realize that there are limitations with this change in resolution between timepoints and that no analysis is going to

Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

Thanks Doug! One last question: If I wanted to regress out the average signal from the ventricles and the white matter (instead of using the PCA output), could I directly incorporate that into fcseedcor? Best, Hamdi From: freesurfer-boun...@nmr.mgh.harvard.

Re: [Freesurfer] FreeSurfer License issue

External Email - Use Caution Hi, Here's what I've learned from my attempts (eventually successful), to run freesurfer in docker on a mac: There are three tricks to running the freesurfer *docker* container. 1) You must request a license.txt file from the freesurfer website: h

Re: [Freesurfer] mri_binarize

It was just an oversight on my part when I wrote the program. I've just updated the file in our repository and put a copy here: https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize You can also specify all the structures you want by using the --match flag On 7/20/18 10:00 AM, John Ander

Re: [Freesurfer] Exporting results from QDEC

which results? On 7/20/18 9:11 AM, Avi Gharehgazlou wrote: External Email - Use Caution Hi experts, I want to make plots of my results that I have from QDEC, however, I'm having difficulty exporting values from QDEC. I examined LGI differences between groups, and I want to export my

Re: [Freesurfer] Bug in make_average_subject

where did you get the make_average_subject script? It is not the one that is released with version 6. On 7/20/18 3:46 AM, Raffington, Laurel wrote: External Email - Use Caution Dear Freesurfer Developers, My goal is to build a study-specific pediatric template brain to rerun the

[Freesurfer] Question about Freeview, 20% threshold

Dear FreeSurfer experts, I am currently using TRACULA( from freeSurfer 6.0), and on the freeview visualization of merged files of the probability distributions of the tracts, I don't understand the thing about the "20% threshold". Indeed, on the tracula tutorial, it is written that the tracts a

[Freesurfer] mri_binarize

External Email - Use Caution Dear Freesurfer experts, I would like to inquire about the flag --subcort-gm in mri_binarize. It seems that the final product of this flag create a mask include the brain stem which is largely white matter. Why it was included in the subcortical gray

Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

Hi Hamdi, sorry for the delay. Answers below. On 6/26/18 2:50 PM, Eryilmaz, H. Hamdi wrote: Hi Doug and Freesurfers, I am using fcseedcor to compute the correlation between two time courses for each subject in my group. The command that I run is as follows: fcseedcor -s $subject -fsd restin

[Freesurfer] Exporting results from QDEC

External Email - Use Caution Hi experts, I want to make plots of my results that I have from QDEC, however, I'm having difficulty exporting values from QDEC. I examined LGI differences between groups, and I want to export my results, so the LGI values of significant between-group

Re: [Freesurfer] Label numbers for thalamic nuclei

External Email - Use Caution Dear KT, They range from 8100 to 8300. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of

Re: [Freesurfer] Why I have to set the environment every time

External Email - Use Caution Hi Ziqian, have you tried to set the environment by writing export FREESURFER_HOME=/Applications/freesurfer on the .bashrc (if using a Linux distribution) or .bash_profile (in using macOS)? To do so open the .bashrc (or .bash_profile) with an editor,

[Freesurfer] Why I have to set the environment every time

External Email - Use Caution Hi, Every time I wanna use the command of freesufer I have to reset the environment again, otherwise it will remind me “not found the command”. Only after I write “export FREESURFER_HOME=/Applications/freesurfer; source $FREESURFER_HOME/SetUpFree

Re: [Freesurfer] FreeSurfer License issue

External Email - Use CautionApologize, I forgot  to attach the file with the license. Here it is.Best regards,CarolinaCarolina Bonivento 37084 *Cl5ULwBr1to2 FSr/.mH1ADRn2 Il giorno 20 lug 2018, alle ore 10:08, Carolina Bonivento ha scritto:Dear Sir/M

[Freesurfer] FreeSurfer License issue

External Email - Use Caution Dear Sir/Madame, I recently subscribed the FS license (attached) but when I tried to run the 'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I received the following error message: ERROR: Invalid FreeSurfer license key found in li

[Freesurfer] Bug in make_average_subject

External Email - Use Caution Dear Freesurfer Developers, My goal is to build a study-specific pediatric template brain to rerun the recon-all-all. I am encountering the same error while running make_average_subject Freesurfer version 6.0.0 on MacOS High Sierra 10.13.6 as descr

[Freesurfer] Label numbers for thalamic nuclei

External Email - Use Caution Dear Freesurfer Team, I have been using segmentation of thalamic nuclei from the Freesurfer dev version(freesurfer-linux-centos7_x86_64-dev). I see some thalamus labels in FreeSurferColorLUT.txt(#8001-8014), but I can't find label numbers for 25 d