[Freesurfer] FreeSurfer stable v.6 Installation

Dear FreeSurfer experts I would like to ask that whether or not I can install the package to the existing FS 5.3 that previously installed on our Linux system? Please forgive if it is an obvious question. Thanks *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell:

Re: [Freesurfer] FreeSurfer stable v.6 Installation

Dear Zeke Thank you for your help. I am really appreciated. Duy Nguyen *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)90056* *Email: duy.nguyen...@gmail.com * On Fri, Feb 17, 2017 at 2:45 AM, wrote: > If your question is whether you

[Freesurfer] Extract the cortical thickness

Dear FreeSurfer expert I wonder that whether I can use the command aparc2statstable to get the cortical thickness or is it better to get the cortical thickness of a volume defined ROI or is there the easy way to get the most accurate cortical thickness from ROI I am following the pipeline "Volume

Re: [Freesurfer] Extract the cortical thickness

from a group of subjects. Is that what you want? > > > On 03/13/2017 02:01 AM, Duy Nguyen wrote: > > Dear FreeSurfer expert > > > > I wonder that whether I can use the command aparc2statstable to get > > the cortical thickness or is it better to get the cortical thic

[Freesurfer] Qdec 1.5

Dear FS Expert I am doing analysis from the group_analysis_tutorial data to practice and learn. However, I come across the error window like it shows on the attached picture (please see the attachment) when I press the button "Generate Stats Data Table." Please help me how can I can find the file

Re: [Freesurfer] Qdec 1.5

Dear Douglas Thank you for your response. I cannot run asegstats2table and aparcstats2table command outside of qdec. Best regards, Duy Nguyen *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)90056* *Email: duy.nguyen...@gmail.com * On Thu, Mar 23

Re: [Freesurfer] Qdec 1.5

: duy.nguyen...@gmail.com * On Thu, Mar 23, 2017 at 10:23 PM, Douglas N Greve wrote: > need more info > > > On 03/22/2017 09:37 PM, Duy Nguyen wrote: > > Dear Douglas > > > > Thank you for your response. I cannot run asegstats2table and > > aparcstats2table command o

Re: [Freesurfer] Qdec 1.5

to > others in terms of size > > > On 3/24/17 9:11 AM, Duy Nguyen wrote: > > Dear Doughlas > > > > When I tried to run the aparcstats2table command, it shows the following > > error in the terminal window: > > SUBJECTS_DIR : /home/toibigi2007/Desktop &

[Freesurfer] How to visualize the result with mri_glmfit and --table aparc flag

Dear FreeSurfer experts I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doing this? Any help is appreciated! Warmest r

Re: [Freesurfer] How to visualize the result with mri_glmfit and --table aparc flag

)90056* *Email: duy.nguyen...@gmail.com * On Sat, May 13, 2017 at 12:00 AM, Duy Nguyen wrote: > Dear FreeSurfer experts > > I have come across with this issue as I don't know how visualize the > result after mri_glmfit done using --table aparc flag instead of --y. Do I > use Mat

Re: [Freesurfer] How to visualize the result with mri_glmfit and --table aparc flag

Thank you for you quick response Doug Please instruct me how I can read out the output file beta.mgh to get the values from the mri_glmfit output on FreeSurfer. Thank you for your help and warmest regards, Duy Nguyen *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC

[Freesurfer] mri_glmfit-sim output error

Dear FreeSurfer experts, When I try to run mri_glmfit-sim, the output came out like this: cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx

Re: [Freesurfer] mri_glmfit-sim output error

Engineering Department- IU HCMC* *Cell: (+84)90056* *Email: duy.nguyen...@gmail.com * On Mon, May 22, 2017 at 9:57 PM, Douglas N Greve wrote: > Can you add --debug as the first argument and send the terminal output? > > > On 05/19/2017 11:48 PM, Duy Nguyen wrote: > > Dear

Re: [Freesurfer] How to visualize the result with mri_glmfit and --table aparc flag

values. Please sort me out this issue. I am totally confusing. Warmest regards, Duy Nguyen *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)90056* *Email: duy.nguyen...@gmail.com * On Mon, May 22, 2017 at 9:56 PM, Douglas N Greve wrote: > beta = MRIr

[Freesurfer] mri_annotation2label No such file or directory

Dear FreeSurfer experts I am trying to extract the label using standard aparc.annot and will be using mri_mergelabels to create my own lobes to do GLM fit later on for ROI analysis. However, it shows me the error like this when I check there are the files aparc.annot and the file from surf folder.

Re: [Freesurfer] mri_annotation2label No such file or directory

that the annotation is on. Once you have > your label, you can use it for thickness > > On 5/26/17 3:54 AM, Duy Nguyen wrote: > > Dear FreeSurfer experts > > I am trying to extract the label using standard aparc.annot and will be > using mri_mergelabels to create my own lob

Re: [Freesurfer] mri_annotation2label No such file or directory

Fischl wrote: > Hi Duy > > it is Unix permissions you need to check. It looks like the subject's label > dir doesn't exist or couldn't be created. > cheers > Bruce > > > On Sat, 27 May 2017, Duy Nguyen wrote: > > > Dear Doug > > Thank y

[Freesurfer] Unsubscribe Mailing List

Hi Freesurfer Team Please unsubscribe my email from the list Email: duynguyen@gmail.com Thanks -- Sent from Iphone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informa