Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

External Email - Use Caution I would like to know what other modification I should make to my script to run --grf (volume analysis): - mris_preproc ?? - mri_glmfit (--surf in white) - mri_glmfit-sim ?? Thanks. Diogenes Bispo diogenesdi...@gmail.com Em sáb., 29 de mai. de 2021

Re: [Freesurfer] mris_fix_topology taking ages

The topology error labels might be be created if it did not finish. YOu can try just loading the brain.mgz, the wm.mgz, and the orig.nofix and see if you can find a big topo error On 5/31/2021 11:16 AM, Ellen Ji wrote: External Email - Use Caution Dear experts, mris_fix_topology has been runn

Re: [Freesurfer] Acquisition/pipeline question

On 5/30/2021 10:27 AM, Massieh Moayedi wrote: External Email - Use Caution External Email - Use Caution Hi, We’re collecting multiecho T1s. We have individual T1 images with different echoes, and the RMS files. I’ve run freesurfer using both the RMS files, and the multiple

Re: [Freesurfer] extract % signal change in FSFAST analysis

The ces.nii.gz file will contain the percent with respect to the mean signal in the brain. The cespct.nii.gz will contain the percent with respect to the mean time series of the voxel. On 5/30/2021 9:42 AM, Star Xi wrote: External Email - Use Caution Hi, dear FS experts,      I'm try

Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

You can't use the --grf option with surfaces On 5/29/2021 2:14 AM, Diógenes Bispo wrote: External Email - Use Caution Hi Freesurfer team. I made the following command: #!/bin/tcsh setenv study $argv[1] foreach hemi (lh rh)   foreach smoothing (10)     foreach meas (volume)         mr

Re: [Freesurfer] FW: mri_convert changing orientation but lose last coronal slice

No, not  easily. I think the field of view must be lower in that dimension and so it is cropping. On 5/28/2021 3:23 PM, Melissa Marie Rundle wrote: External Email - Use Caution Hi, I am using mri_convert to change the orientation of an image in its native space from LPS  to PSR. E

Re: [Freesurfer] FW: WM or Pial edits to correct surfaces

On 5/28/2021 2:17 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution External Email - Use Caution Greg, Additional clarification. Are these 2 options runs independently - i.e. separate tests? Not sure what you  mean here For example, add CPs to brain.mgz and

Re: [Freesurfer] (no subject)

How did you create the sig.mgh that you are trying to overlay? On 5/28/2021 11:16 AM, Francisca Ferreira wrote: External Email - Use Caution Dear Experts, I have extracted subcortical vols corrected for intracranial vols using asegstats2table and I  ran mri_glmfit using the following

Re: [Freesurfer] PVC to calculate myelin maps

Yes, you can use PETsurfer. I would apply it to the ratio On 5/28/2021 10:25 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I saw that the correction of partial volume effects can be u

Re: [Freesurfer] Choosing projfrac/projdist and checking mri_vol2surf output

On 5/28/2021 9:25 AM, M Pope wrote: External Email - Use Caution External Email - Use Caution Hi, Thanks for this. Using mri_surf2vol as a QC hadn't occured to me and is a nice solution. I feel again using --fillribbon is the best way to project the surface to the volume f

Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

Not sure, can you try this cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log and send the file nucor.log On 5/28/2021 7:51 AM, liub wrote: External Email - Use Cauti

Re: [Freesurfer] tkregister2 problem on its GUI

Try using tkregisterfv instead (it takes all the same command line args but uses freeview On 5/28/2021 2:13 AM, 张威 wrote: External Email - Use Caution Hello Freesurfer developers, I am attempting to manually register a cerebral blood flow images to a T1 weighted images via the comm

Re: [Freesurfer] Questions about geting a license file

External Email - Use Caution Hello Nana, Your browser should display a “CAPTCHA” box at the bottom of the freesurfer license page just above the button where you click “I AGREE”. If you do not see the CAPTCHA box in your browser then it is probably blocking some javascript that w

Re: [Freesurfer] about the root password of virtual box ubuntu 710 clone

External Email - Use Caution Hello Wu, Sending the info to your posted email. - R.. On May 31, 2021, at 03:49, HuiNing Wu wrote:External Email - Use CautionDear all,I'm using freesurfer virtual box ubuntu 710 clone.However, I didn't fi

[Freesurfer] mris_fix_topology taking ages

External Email - Use Caution Dear experts, mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice from the thread here https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E

[Freesurfer] Questions about geting a license file

External Email - Use Caution Dear Sir: I met registration error when I provided all the personal information to register the copy of FreeSurfer and obtain the license.txt key file, is there any way for me to get the license file? The error figure is attached and thank you

[Freesurfer] myelin maps

External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I would like to perform a correction of partial volume effects to create the maps (Shafee, Buckner & Fischl, 2015)*, instead of creating the maps using HCP Pipel

[Freesurfer] about the root password of virtual box ubuntu 710 clone

External Email - Use Caution Dear all, I'm using freesurfer virtual box ubuntu 710 clone. However, I didn't find the root password to enter sudo mode... Would you please let me know what it is or where it is? With best regards, Wu ___ F