Re: [Freesurfer] tkmedit

yes! On Wed, 15 Jun 2016, kojima_masaki_m...@yahoo.co.jp wrote: Hi Bruce Thank you for useful advice. I referred to FreesurfuerWiki and tried to use tkmedit to check whether recon is accurate or not. Now I am trying to use freeview. Is it possible to do these procedure with freeview instead of

Re: [Freesurfer] tkmedit

Hi Bruce Thank you for useful advice. I referred to FreesurfuerWiki and tried to use tkmedit to check whether recon is accurate or not. Now I am trying to use freeview. Is it possible to do these procedure with freeview instead of tkmedit? Regards, Kojima - Original Message - >From:

[Freesurfer] concerting surface format

Hi there is there a way to convert .mesh (BrainVisa) to the Freesurfer surface format? mri_convert doesn't seem to do it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___ Freesurfer mailing

Re: [Freesurfer] Combining cross sectional and longitudinal analyses

Hi William, either way is fine, as long as you don't mix results from cross and long processing in your analysis. Since all images need to go through the cross sectional stream anyway, I think actually (2) will be less processing (and potentially less QC and editing). Best, Martin On

Re: [Freesurfer] Coregister the CT image and MRI image

Hello Hari, In order to use mri_coreg on Mac, you will need to download the "Development Version" of freesurfer. See the following page under Development Version: https://surfer.nmr.mgh.harvard.edu/fswiki/Download Once downloaded, uncompress the .tar.gz file to some directory on your

Re: [Freesurfer] SAVE REG in tkregister2

When you run that command, are you in a folder where you have write permission? On 6/8/16 10:05 AM, Hao wen wrote: tkregister2 --mov template.nii --s fbirn-anat-101.v4 \ --regheader --reg myregister.dat --surf ok, here it is

Re: [Freesurfer] output file from running mri_glmfit-sim

On 6/8/16 9:51 AM, Yu Sun Chung wrote: Hi, all, While working on gyrification data using Freesurfer, I have a question to confirm one of output files. First, I did run mri_glmfit using age x IQ itneraction. fsgd file in which I included intracranial volume and gender to covary out. then, I

Re: [Freesurfer] Define the design matrix by myself

When passed to mris_preproc, the fsgd file is only to specify the subjects. Using the fsgd file for both mris_preproc and mri_glmfit assure that the order of the subjects is the same On 6/14/16 6:10 AM, Hao wen wrote: Hello: To make it more clear! I thought from FSGD file in mris_preproc,

Re: [Freesurfer] Define the design matrix by myself

remove the 1st column and it will be ok On 6/14/16 6:24 AM, Hao wen wrote: It turned out this is not possible, I got this error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.34551e+07 here is my design matrix: 1 AD CN age male female 1.000

Re: [Freesurfer] Segmentation fault in mri_convert

Hello Christopher, Perhaps you could upload a data set for which mri_convert is segfaulting so that we can take a closer look? http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange -Zeke On 06/13/2016 02:19 PM, Christopher Finuf wrote: > I'm trying to convert the dicom to the original

Re: [Freesurfer] fs development version

Go to the indicated by the link, fill out the form, and license key will be emailed to you. -Zeke On 06/13/2016 06:56 PM, shi yao wang wrote: > Dear Experts: > I set up FS development version. > And now it shows error message: > >

Re: [Freesurfer] swapped dimensions?

Hi Ruopeng, I am very sorry since I think you would like to figure out why freeview did not take my DICOM's, but due to privacy issues I have deleted the DICOM's after the recon -all (on the niftis) was completed without any errors. Basically when I selected the files, nothing happened, while

Re: [Freesurfer] swapped dimensions?

Would it be possible to send us a file? Best, Ruopeng > On Jun 14, 2016, at 8:52 AM, Marja Caverlé wrote: > > Hi Bruce, > > I did not get any error message, the page just remained empty after selecting > the files. Maybe my files were the reason why it didn't work. >

Re: [Freesurfer] swapped dimensions?

Hi Bruce, I did not get any error message, the page just remained empty after selecting the files. Maybe my files were the reason why it didn't work. Best, Marja On Tue, Jun 14, 2016 at 10:50 PM, Bruce Fischl wrote: > freeview works fine with most dicoms. Do you

Re: [Freesurfer] tkmedit

Hi Kojima tkmedit has been deprecated. Can you try using freeview instead? cheers Bruce On Tue, 14 Jun 2016, kojima_masaki_m...@yahoo.co.jp wrote: Hi.  I have this error, when I was doing tkmedit PSY1001fs/Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/brainma sk.mgz

Re: [Freesurfer] swapped dimensions?

freeview works fine with most dicoms. Do you get an error message? On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, When I wanted to view them in freeview, simply nothing happened. Freeview did not load the files, so I assumed it did not work with dicoms, that's why I converted them.

Re: [Freesurfer] Define the design matrix by myself

It turned out this is not possible, I got this error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.34551e+07 here is my design matrix: 1 AD CN age male female 1.000 0.000 1.000 74.300 0.000 1.000; 1.000 0.000 1.000 73.700

[Freesurfer] Interpretation of QA tools results

Dear FS experts, Could you explained me how to interpret results from the QA tools. Please find attached the recon_checker summary log. 1) How to know there is a problem according to results below: *checking subcortical label: Left-Cerebral-Exterior, 0 +/-* *checking subcortical label:

Re: [Freesurfer] Define the design matrix by myself

Hello: To make it more clear! I thought from FSGD file in mris_preproc, it will regard the group and gender as class, so in the X.dat will be gender*group; will not be possible to have the seperate columns for gender and group? do I understand it correctly? Or the FSGD file used in

[Freesurfer] QA Tools : All in errors for aseg outliers detection

Dear FS experts, I tried to run the QA Tools on a subject with the following command: *${QA_TOOLS}/recon_checker -s 207043_M0_2010-10-07 -outputFOF ${SUBJECTS_DIR}/FOF -gen-outputFOF -gen-asegLUT ${SUBJECTS_DIR}/AsegOutliers* But I got all errors concerning the detection of Aseg outliers:

Re: [Freesurfer] tkmedit

Thank you for quick reply. I finished preprocessing and tried to check imagies, but tkmedit does not work. Please let me know how to do. Kojima - Original Message - >From: "kojima_masaki_m...@yahoo.co.jp" >To: "freesurfer@nmr.mgh.harvard.edu"

[Freesurfer] tkmedit

Hi.  I have this error, when I was doing tkmedit PSY1001fs /Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/brainmask.mgz -aux /Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/wm.mgz -surfs ERROR: Assertion failed: (!c->out.queue_len), function

Re: [Freesurfer] Define the design matrix by myself

Yes, actually, I just want to know what does that mean when we use *, for example Gender*Group, does this mean group and gender has a interaction? So what i want to know, if we can create design matrix like this: X = 1 + age + gender + group, I dont want the interact between group and gender