[Freesurfer] Virtualbox: developer's password

External Email - Use Caution Hi, I am trying to set-up Freesurfer (fs_ubuntu_18_04_06) from Oracle VM Virtualbox. Could you send me the developer's password useful for login? Thanks for your help Regards Francois ___ Freesurfer mailing li

Re: [Freesurfer] [External] Re: white matter measurements for labels/annotations

You'll have to create an annotation first (maybe with mris_label2annot), then use mri_surf2volseg to create the segmentation. Look at the command line to create wmparc.mgz On 2/4/2022 10:03 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution Yes but i

Re: [Freesurfer] classes for GLM analysis

It is probably not going to work very well if you have some classes that only have one member. You can eliminate members of classes that only have a few members. If you really need to have those cases, there are hybrid ways to analyze the data (but you can't use an FSGD at that point) On 2/6/2

Re: [Freesurfer] Recon-all reconstructed image coordinates

On 2/7/2022 5:29 PM, Salar Dini, Elaheh wrote: External Email - Use Caution Thank you so much. This actually worked well. Just two simple follow-up questions: 1. Do I assume right that this solution doesn't work on aparc+aseg? Correct, that will not work 1. 2. If I want to

Re: [Freesurfer] Longitudinal Stream Error

I'm not sure what the error is as I cannot find an actual error below. If the error is in the base creation, then send the log file for that. On 2/8/2022 10:47 AM, Willett, Andrew Sunday wrote: This is my first time seeking support here so I apologize if I am not familiar with the community's

Re: [Freesurfer] Freesurfer with machine learning

How about this? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI On 2/8/2022 2:02 PM, REEM ABU BAKR BAHATHIQ wrote: External Email - Use Caution Hi everyone, Now that I have done the recon all preprocessing on my structural MRI data, I want to extract the volume and

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

Re: long run  time. Sorry, permutation will not work with PVR. Re: mean thickness. Use the eres.mgh from you osgm analysis instead of the raw thickness map (lh.thickness.fwhm10.mgh) On 2/8/2022 4:12 PM, Dhungana, Asim wrote: Dear Freesurfer experts, I am trying to run a GLM analysis comparing

Re: [Freesurfer] FW: Problems with recon for manually fixed Talairach

I'm a bit puzzled by this. Are you saving the xfm file to talairach.xfm? In the log file, it clearly says: INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talai

Re: [Freesurfer] rm: no match

can you send a log file? On 2/9/2022 5:11 AM, REEM ABU BAKR BAHATHIQ wrote: External Email - Use Caution Hi all, I use a supercomputer to process my data When I run "recon-all –qcache", and after two days of processing there are a lot of Error messages saying "rm: No match." (althou

Re: [Freesurfer] Creating masks on a MNI averaged brain

On 2/9/2022 5:18 AM, Lin Qiu wrote: External Email - Use Caution Dear Freesurfer experts, My analysis is in FSL. But I wish to use the more detailed segmentaHA_T1.shavailable in Freesurfer. I wish to avoid the time & resource to ‘recon-all’ all my participants’ T1 images, and onl

Re: [Freesurfer] Building a model

Sorry, I don't understand the R terminology. in the FSGD, you will have (4+1)*3 = 15 columns to the design matrix (4=2x2=number of classes, 3 = no of continuous variables). Each column will mean something. How many columns will you have in your R analysis and what will they mean? If you can mak

Re: [Freesurfer] [Help needed] recon-all log error

you did not point out the lines that worry you. At the end, it says "finished without error", which means that you should not visually check your results. On 2/9/2022 6:28 PM, HYE JUNG YOUN wrote: External Email - Use Caution Good day, I hope this email finds you well. I’d love you

Re: [Freesurfer] ventricular volumes - freesurfer 6 vs 7

I'm pretty sure you will have some systematic differences between them, though they might be small. So off the top of my head, I'd recommend against it. On 2/10/2022 12:56 PM, Anik Dar wrote: External Email - Use Caution Hi All, I have some datasets processed with freesurfer 6 and o

[Freesurfer] How to measure correlation using FreeSurfer

External Email - Use Caution Dear FreeSurfer experts, I am trying to find the correlation between the regional cortical thickness and volume with different clinical measures of a neurodegenerative condition. I am using DK atlas to get the cortical measures and establish the correl

[Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare cortical surface area among three groups while controlling for estimated total intracranial volume (eTIV), as described on the Surface Based Group Analysis tutorial ( https://secure-web.cisco.com/1

[Freesurfer] DICOM file organization

External Email - Use Caution Dear Freesurfer experts, There are a bunch of RAW DICOM files in my dataset. I recognize that the name of the images begins with Z, i.e. “Z01”, “Z02”… “Z8568”. After converting them into NIfTI format with mricron, it yields the name in this format: