[Freesurfer] run preproc-sess wrongly and some other question about FSFAST

External Email - Use Caution dear experts, I try to run FSFAST with a block design paradigm. there a few question i can figure out on my own. the 1st question: the directory structure was set as: -meridian --sess01 --bold -001 -002

Re: [Freesurfer] run preproc-sess wrongly and some other question about FSFAST

On 1/3/19 5:07 AM, xi star wrote: > > External Email - Use Caution > > dear experts, > I try to run FSFAST with a block design paradigm. there a few question > i can figure out on my own. > the 1st question: > the directory structure was set as: > -meridian >      --sess01 >            -

Re: [Freesurfer] Extracting cortical thickness from a significant cluster in an independent sample

Can you include the full command line (no $variables) and the full terminal output? On 1/2/19 4:22 PM, Tamara Sussman wrote: > > External Email - Use Caution > > Thanks for your response - yes, I should have included this > information before. :) > > $label was set to a label I made by 1

Re: [Freesurfer] Which T1 volume to use for coregistration with PET volume

I doubt it would make much difference. If your PET has lots of extracerebral uptake, then I might use something that has not been skull stripped (eg, orig.mgz, T1.mgz, nu.mgz). If it does not  have much extracerebral, then using brain.mgz is probably better. On 12/31/18 10:53 AM, Bruce Fischl w

Re: [Freesurfer] FSGD file

The contrast is not correct for your design. Your design matrix will have 3 columns, one for HC, one for CMT, and one for rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a DOSS kind of way. If you want to test for a difference in thickness-meylin slopes between the two groups

Re: [Freesurfer] Which T1 volume to use for coregistration with PET volume

External Email - Use Caution Thank you Douglas for this clarification. So, correction of inhomogeneities and intensity normalization would have no positive effect on the PET/MR coregistration ? Best, Matt > Le 3 janv. 2019 à 20:04, Greve, Douglas N.,Ph.D. a > écrit : > > I d

Re: [Freesurfer] map parcellations into DWI space?

you might try this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 On 12/30/18 1:45 AM, Yerong Li wrote: > External Email - Use Caution > Dear FreeSurfer experts: >  I am trying to map ./mri/aparc.a2009s+aseg.mgz and > ./mri/aparc+aseg.mgz into DTI file. >  Let's say, we

Re: [Freesurfer] -qcache error

Does that file exist? If not, check to see whether that subject finished or whether there was an error On 12/20/18 2:37 PM, 塩浜 直 wrote: > External Email - Use Caution > > Hello FreeSurfer Developers, > > I'm attempting to do group analysis for cortical thickness map using Qdec GUI. > We'

Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047

Hi Jeongson, I took a look at your data, thank you for uploading it. Your recon is likely failing because your case has a large pathology that is causing your white matter surface to be topologically incorrect. I recommend filling in that whole area on the wm.mgz mask and re-running the rest o

Re: [Freesurfer] Extracting cortical thickness from a significant cluster in an independent sample

External Email - Use Caution Thanks so much for your suggestion, Douglas. Here is the whole input and output: Tamara-Posner-lab:~ posnerlab$ mri_segstats --slabel /Volumes/Pegasus_tsussman/data/ALFF_Analysis/FreeSurfer/LowVsNormHgb_T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.Superi

Re: [Freesurfer] Extracting cortical thickness from a significant cluster in an independent sample

The first command does not work because --slabel requires three options and it is interpreting "--i" and "/Volumes...mgh" as those two so it thinks you have not included. It is probably better to use something like mri_segstats --seg ocn.mgh --excludeid 0 --avgwf test.dat --sumTest_SupParietal.

Re: [Freesurfer] Extracting cortical thickness from a significant cluster in an independent sample

External Email - Use Caution Thank you so much, Douglas, it works!! On Thu, Jan 3, 2019 at 3:10 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > > The first command does not work because --slabel requires three options > and it is interpreting "--i" and "/Volumes...m

[Freesurfer] Diagnosing a recon error

Dear Experts, I was wondering if someone might be able to help diagnose a recon error. I used the following command to initiate recon: recon-all -subject RMD002 -i /ncf/anl/anl01/MultiMode/Data/structural/T1_MEMPRAGE_5_RMD002_e1.nii -T2 /ncf/anl/anl01/MultiMode/Data/structural/T2_SPACE_6_RMD00

Re: [Freesurfer] Diagnosing a recon error

Do you have access to the stderr output from this process? On 1/3/19 3:55 PM, Maksimovskiy, Arkadiy wrote: > > Dear Experts, > > I was wondering if someone might be able to help diagnose a recon error. > > I used the following command to initiate recon: > > recon-all -subject RMD002 -i > /ncf/anl

[Freesurfer] MRI sequence parameter difference and effect on cortical thickness values

External Email - Use Caution Dear experts, For our study, we are planning on combining two different datasets to examine cortical thickness. There is a slight difference in the inversion time (400 vs 650) and flip angle ( 8 vs 11) between the two datasets. I know that free surf

Re: [Freesurfer] map parcellations into DWI space?

External Email - Use Caution Yes, this is super-helpful. Thank you so much. Yerong Quoting "Greve, Douglas N.,Ph.D." : > you might try this page > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 > > On 12/30/18 1:45 AM, Yerong Li wrote: >> External Email - Use

Re: [Freesurfer] -qcache error

External Email - Use Caution Hi Dr. Greve, I found out the reason why it does not work. That was because the subjects' folder does not include lh white.K. Thank you so much! Tadashi Shiohama -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesu