[Freesurfer] Mapping input volume (fa.nii) to hippocampus segmentation volume

External Email - Use Caution Hello Freesurfers, I am trying to segment the hippocampus into its subfields and take the FA values from each subfield area. I am able to segment the hippocampus using the command (segmentHA_T1.sh) and I was also able to perform the dt-recon function

Re: [Freesurfer] Importing atlas with mris_register: "hips not supported"

External Email - Use Caution Hello, I just wanted to follow up as I'm still dealing with this issue and would love any help at all with making this analysis work. Thanks so much, Jasmine From: Jasmine Cakmak Sent: Tuesday, October 31, 2023 3:59

Re: [Freesurfer] About Mean LGI value

External Email - Use CautionDear. Dr. Greve,Thank you for your response.I attached both “*h.aparc.pial_lgi.stats” and “*h.aparc.mean_pial_lgi.stats” files.For example, in left hemisphere, mean LGI value is 3.0761 (SegId 1, Seg0001, is it correct as mean LGI value?), while the

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

Can you send the command line, all the terminal output, and your fsgd file? On 11/3/2023 11:51 AM, Ludmila Midrigan wrote: External Email - Use Caution Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error: "error:

Re: [Freesurfer] About Mean LGI value

How different are the values? Those two stats files are created with different programs, so there could be some small differences. But if you're seeing large differences, then that is something else. If the latter, then send both stats files. On 11/3/2023 9:14 AM, 笹林大樹 wrote:

Re: [Freesurfer] Group analysis question

So you are trying to predict the neuropsych battery from brain measurement? This is not how mri_glmfit is usually used, but it is just a GLM so it is possible. You'd have to set up a table for the --table input. You can try running asegstats2table to get an example table, then you'd just set

Re: [Freesurfer] dt_recon question

On 10/30/2023 9:50 PM, Mirsol Choi wrote: External Email - Use Caution Hi there, I am currently going through the dt_recon tutorial on your website and I just have a quick question regarding the recon-all and dt_recon commands on freesurfer. For me to process dt_recon, my

Re: [Freesurfer] SynthSEG continued developments

My experience is that it is extremely robust with respect to defacing (and even skull stripping). On 10/30/2023 12:02 PM, Iglesias Gonzalez, Juan E. wrote: Dear Dawn, Integrating the hippocampal subfields into SynthSeg in on the to-do list, but it’s tricky due to differences in resolution.

Re: [Freesurfer] PETsurfer kinetic modeling

There is not an easy way to do this yet. If you have your segmentations in the conformed anatomical space, you can merge them with gtmseg.mgz with something like mri_vol2vol --interp nearest --mov yoursegs.mgz --targ gtmseg.mgz --o yoursegs-in-gtmseg-space.mgz mergeseg --src gtmseg.mgz --merge

[Freesurfer] Unsubscribe Mailing List

External Email - Use Caution Hi Freesurfer Team Please unsubscribe my email from the list Email: soleymani.yunus@yahoo.comThanksYunus Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University