Re: [Freesurfer] [External] Re: Quick question on tkregister {Disarmed}

?freesurfer-linux-centos6_x86_64-dev-20190118-24cd5b0, so yes the dev version Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew Sent: Wednesday, April 29, 2020 7:48 PM To:

[Freesurfer] vol2subfield single time course from multiple regions

External Email - Use Caution Hi list, vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sf ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol avgwfvol.mgz --o f2subf.nii.gz extracts the time course from each thalamic subregions. If I would like to m

Re: [Freesurfer] [External] Re: Quick question on tkregister {Disarmed}

Hi Victor, what are the contents of /usr/local/freesurfer/build-stamp.txt? Are you using a dev version? Andrew From: on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" Reply-To: FS Help Date: Tuesday, April 28, 2020 at 8:02 PM To: FS Help Subject: Re: [Freesurfer] [External] Re: Qui

Re: [Freesurfer] Questions about pial_lgi {Disarmed}

Doug is saying that you should replace: --out lh.pial_lgi with --out lh.pial_lgi.mgh on your command line cheers Bruce On Thu, 30 Apr 2020, 肖伏龙 wrote: External Email - Use Caution so how to get the pial_lgi.mgh from the pial_lgi file? MailScanner has detected a possib

Re: [Freesurfer] Questions about pial_lgi {Disarmed}

External Email - Use Caution so how to get the pial_lgi.mgh from the pial_lgi file? | | 肖伏龙 | | 邮箱：xiaofulong1...@163.com | 签名由 网易邮箱大师 定制 On 04/30/2020 06:18, Douglas N. Greve wrote: It needs to have an extension, eg, lh.pial_lgi.mgz On 4/29/2020 9:02 AM, 肖伏龙 wrote:

Re: [Freesurfer] mri_glimfit error - help!

There is some rogue character after the "0" in "Class 0". If you run od -c fsgd_file.fsgd It comes out as 312. I have no idea what it is On 4/29/2020 6:21 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution

[Freesurfer] mri_glimfit error - help!

External Email - Use Caution Dear Freesurfer experts, I'm having a persistent error with mri_glimfit. The fsgd file isn't being read correctly, despite following the exact requirements of the wiki. Also, the output mentions this "carriage returns warning", and despite running this

Re: [Freesurfer] recon-all

The log file you send says that the subject was finished without error. Can you send a log file that has your error in it? On 4/29/2020 4:56 AM, jiahui wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute gray matter volume, but for some of my s

Re: [Freesurfer] Questions about pial_lgi

It needs to have an extension, eg, lh.pial_lgi.mgz On 4/29/2020 9:02 AM, 肖伏龙 wrote: External Email - Use Caution hello everyone I have a question about statistics on LGI. for the LGI data, named as lh.pial_lgi, I used mris_preproc as following: mris_preproc --fsgd fsgd.fsgd --cache-i

Re: [Freesurfer] mri_label2vol

It looks like it should work. The only other thing I would suggest is to use --regheader orig.mgz instead of --identity (though I would have thought --identity would have worked). On 4/29/2020 2:12 PM, Mason Wells wrote: External Email - Use Caution Hi Experts, I want to take an ROI

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

Wait but this isn’t the error your first described…? Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Zeng, Qi" Reply-To: Freesurfer support list Date: Wednesday, April 29, 2020 at 17:28 To: Freesurfer support

Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

Dear Qi, The correct syntax is that of your First try, but I’m very surprised you got that error, as we fixed this a while ago… Can you please send me the complete output? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.

[Freesurfer] mri_label2vol

External Email - Use Caution Hi Experts, I want to take an ROI label that I have drawn on the surface and transform this into the volume. I have drawn the label in the T1 anatomical space and I want to keep the label in this space during the conversion. I am currently using thi

Re: [Freesurfer] convert MNI152 coordinates into vertex index

External Email - Use Caution Thank you for the information, Bruce and Thomas! Thomas, I think this utility is perfect! I tried it with fsaverage subject without problems. Do you think I can use this function to calculate the vertex of the fsaverage5 (instead of the fsaverage)? R

Re: [Freesurfer] convert MNI152 coordinates into vertex index

External Email - Use Caution Hi Marina, We do have a utility to convert from MNI152 to fsaverage space: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion Not sure if this is what you need. Regards, Thomas On Wed, Apr 29, 20

Re: [Freesurfer] convert MNI152 coordinates into vertex index

Hi Marina which surface you use depends on why you are trying to find the vertices cheers Bruce On Wed, 29 Apr 2020, Marina Fernández wrote: External Email - Use Caution Hi Bruce, Thank you very much for the information. It is very useful. I'm taking a look at both possib

[Freesurfer] Questions about pial_lgi

External Email - Use Caution hello everyone I have a question about statistics on LGI. for the LGI data, named as lh.pial_lgi, I used mris_preproc as following: mris_preproc --fsgd fsgd.fsgd --cache-in pial_lgi --target fsaverage --hemi lh --out lh.pial_lgi but freesurfer said E

Re: [Freesurfer] convert MNI152 coordinates into vertex index

External Email - Use Caution Hi Bruce, Thank you very much for the information. It is very useful. I'm taking a look at both possibilities. Regarding the second option you gave me: you can just run through the list of vertices and find the one that is > closest to your MNI coord

[Freesurfer] Ubuntu VM password

External Email - Use Caution Hi guys! I have followed the virtual machine setup for virtual box freesurfer installation.but it ask me the password for the developer account. Which is the password? Cheers, Alex___ Freesurfer mailing l

[Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors

External Email - Use Caution Hi, I am trying to use the longitudinal pipeline of the “hippocampal subfields and nuclei of amygdala”. Keep getting error messages when running it longitudinal but with no error message running it cross-sectional. I want to know if there is any way to