Re: [Freesurfer] recon-all error

External Email - Use Caution Dear Yujing, Thank you for your reply. 1. Confirmed I am running Freesurfer 6.0. 2. I am running both commands from within the individual subject directory (ID=1003156). The parent folder contains several folders all labelled with

Re: [Freesurfer] License for 5.X versions of FreeSurfer

External Email - Use Caution Responding to you off the list. - R. On Apr 21, 2022, at 15:08, Paul Wighton p...@corticometrics.com wrote:External Email - Use CautionHi Jacob,Can you provide more details on how FreeSurfer was installed, how you are using the license key and

Re: [Freesurfer] Failed to open FS 7.2 on Virtual Machine

External Email - Use Caution Dear R., I have already re-install FS and it worked. Thanks for your attention! Regards, Krystal From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of krystaly Sent: 22 April 2022 08:57:00 To: fsbuild;

Re: [Freesurfer] Failed to open FS 7.2 on Virtual Machine

External Email - Use Caution Dear R., Thank you for your reply. As per advise, I checked that my C drive still has 66.3 GB of free space. Next, when I followed the instructions of how to disable Hyper-V, it has already unchecked. VM is still not working... Would you please

Re: [Freesurfer] License for 5.X versions of FreeSurfer

External Email - Use Caution Hi Jacob, Can you provide more details on how FreeSurfer was installed, how you are using the license key and the errors you are receiving? I just created a docker container with FreeSurfer v5.3.0-HCP (

Re: [Freesurfer] recon-all error

Hi Rebecca, I’m trying to get more information to determine how it core dumped. 1. Can you confirm that you are running Freesurfer 6.0? 2. From which directory, did you run recon-all and dcmunpack? 3. Can you try dcmunpack by passing it full path to dicom directory? Thanks. Yujing

Re: [Freesurfer] ERROR: Talairach failed!

Can you provide the tkregisterfv command line and the terminal output? On 4/21/2022 3:37 AM, Fritze, Stefan wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to computerecon-all -all -subjid XXX -qcache -3T, which works fine with most of my study

Re: [Freesurfer] differences between Freesurfer 6.0 and 6.0-beta

basically, you should not have been using the beta version since it is a beta version. hard to know what the differences were On 4/20/2022 6:21 PM, Paul Wighton wrote: External Email - Use Caution Hi Matt, freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c was compiled from

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

Can you send your mri_gtmpvc command line? On 4/20/2022 12:50 PM, Zhener Zhang wrote: External Email - Use Caution Hello, I have a question regarding the way ROI-wise values are calculated using PETSurfer. We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively

Re: [Freesurfer] recontruction of an elephant brain

HI Malav, did you create the subcortical mass? Have you separated the hemispheres? On 4/18/2022 4:48 PM, Malav Shah wrote: External Email - Use Caution Hi Dr. Greve, I send a gentle reminder, in case the previous mail skipped your attention. with regards, Malav

Re: [Freesurfer] rerunning on 7.2 with edited brainmask using hi-res

Yes, same command On 4/17/2022 10:24 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Can someone confirm? Thx. Jim *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Alexopoulos, Dimitrios *Sent:* Tuesday, April 12, 2022 3:24 PM *To:* Freesurfer

Re: [Freesurfer] Recon process for skull-stripted data

I'm not sure. You can try just passing the skull stripped as input to recon-all. The talairach transform will probably be off, but the rest might work On 4/17/2022 9:09 PM, Muhammed Görünen wrote: External Email - Use Caution Hi, How can I run a recon process if I have just skull

Re: [Freesurfer] Rerunning freesurfer with manual edits and T2 or FLAIR pial refinement

you need to add these flags again On 4/16/2022 11:49 AM, VINCENT KOPPELMANS wrote: External Email - Use Caution I have made manual edits to a subject that was initially run with the -FLAIR and -FLAIRpial input flags. When I want to rerun freesurfer to implement these edits should I

Re: [Freesurfer] Multiple comparison correction

Do you mean the difference between the d,m,h classes? If so, it would be 1 1 -1 -1 0 0 (rest all 0s) 1 1  0  0 -1 -1 ... 0 0 1 1 -1 -1 ... On 4/14/2022 9:50 AM, David wrote: External Email - Use Caution Hi Freesurfer experts,     I'm very sorry to bother you, but I am very confused

Re: [Freesurfer] How to make surfaces below the GM-WM boundary?

Try using mris_expand, eg, mris_expand lh.white -1 lh.subwhite will create a surface 1mm into the WM On 4/14/2022 7:50 AM, Lee Subin Kristine wrote: External Email - Use Caution Dear FreeSurfers, I am interested in sampling values in the superficial white matter (SWM) region, which

Re: [Freesurfer] [Freeview] View Flatmap

in freeview, runsomethiing like freeview -f rh.white:patch=rh.full.flat.patch.3d The rh.white is just there to give freeview a full surfce to load. You will only see your patch On 4/14/2022 4:30 AM, Morgenroth Elenor wrote: External Email - Use Caution Dear Freesurfer Experts, I

Re: [Freesurfer] Beta values (resubmitting)

Yes, first line intercept, 2nd line slope On 4/12/2022 3:44 PM, Laura Willers de Souza wrote: External Email - Use Caution Hey! I'm resending this email because I think it got lost on the list. Hello FreeSurfer Developers, I'm extracting beta values​​from some analyzes and I would

Re: [Freesurfer] parallel make_average_subject

There is not an easy way to do this. Internally, there is a binary that loads all the subjects then creates an average. You need some way to create intermediate files, then combine them together, which we don't support. Why do you want to create an average subject? On 4/11/2022 9:54 AM,

Re: [Freesurfer] mri_glmfit error

You don't have enough members in the classes to fit the model that you have. Eg, class d has 4 members with which you are fitting an offset and 3 slopes leaving you with 0 degrees of freedom. You need to get more subjects or change your model. btw, gender is usually modeled as a discrete

Re: [Freesurfer] Cortical depth at each cortical voxel

Of course! Please let me know if you have any questions about the toolbox. Best, Iman From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Fotiadis, Panagiotis Sent: Thursday, April 21, 2022 12:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical depth at each cortical

Re: [Freesurfer] Cortical depth at each cortical voxel

External Email - Use Caution Hi Iman, That is extremely helpful, thank you very much (also the paper is a great read)! Best, Panos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Aganj, Iman Date: Thursday, April 21, 2022 at 12:06 PM To: Freesurfer support list

Re: [Freesurfer] Cortical depth at each cortical voxel

Hi Panos, You can do such a volumetric analysis using this toolbox: Code: https://www.nitrc.org/projects/thickness Paper: https://onlinelibrary.wiley.com/doi/epdf/10.1002/hbm.20740 You can apply the MLI_thickness function to the gray matter (soft or binary) mask, which returns the layer

[Freesurfer] Cortical depth at each cortical voxel

External Email - Use Caution Hi FS experts, I was wondering whether there was a way to assign each cortical voxel within the T1w (volumetric) scan an index corresponding to its “cortical depth.” I have essentially taken the cortical ribbon .mgz file, assigned each cortical