Re: [Freesurfer] mris_label2annot gives wrong label

can you send your command line and full terminal output? On 8/19/2019 9:24 PM, Rachel S wrote: External Email - Use Caution Hi Greve, Thank you for your prompt reply. I tried removing --l before. But it gave Mapping unhit to unknown Found 123407 unhit vertices None of the vertices

Re: [Freesurfer] mris_label2annot gives wrong label

External Email - Use Caution Hi Greve, Thank you for your prompt reply. I tried removing --l before. But it gave Mapping unhit to unknown Found 123407 unhit vertices None of the vertices were labeled. What could be the problem? Thank you. Best regards, Rachel Greve, Douglas

Re: [Freesurfer] Help with using family as random effect in sibling study

I'm not sure I understand. Can you elaborate? On 8/19/19 2:43 PM, Hopkinson, Casey E wrote: > Hello! > > I am trying to generate significance maps for a paired-difference > analysis of cortical thickness using multiple pairs of siblings, and > was wondering if there is a way to incorporate the

Re: [Freesurfer] mris_label2annot gives wrong label

You should remove the --l argument. That is incompatible with --ldir. On 8/19/19 5:50 PM, Rachel S wrote: > > External Email - Use Caution > > Hi Freesurfer community, > > I was trying to use mris_label2annot to generate annotation file, my > commands are: > > mris_label2annot --s p6 --h

[Freesurfer] mris_label2annot gives wrong label

External Email - Use Caution Hi Freesurfer community, I was trying to use mris_label2annot to generate annotation file, my commands are: mris_label2annot --s p6 --h rh --a t500 --ldir $SUBJECTS_DIR/p6/label/regenerated_rh_500 --nhits nhits.mgh --ctab

[Freesurfer] Help with using family as random effect in sibling study

Hello! I am trying to generate significance maps for a paired-difference analysis of cortical thickness using multiple pairs of siblings, and was wondering if there is a way to incorporate the family ID as a random effect/covariate in Freesurfer. Is it possible for the family ID for each

[Freesurfer] BIDS Steering Group nominations

External Email - Use Caution Hi FreeSurfer! We are announcing the nomination period for our fellow colleagues (or self-nomination) to the BIDS Steering Group! The BIDS Steering Group is proposed within our governance

Re: [Freesurfer] mri_robust_template in FMRIprep rotation should not scale error

External Email - Use Caution Hi Martin, Have you had a chance to take a look at this? Is there any other information you’d need? Thanks, Dylan On Thu, Aug 15, 2019 at 8:39 AM Dylan Nielson wrote: > Thanks for taking a look at this Martin. I've uploaded the files to my >

[Freesurfer] autorecon3 with T2_min parameter

External Email - Use Caution ?Hi, When calling recon-all autorecon3, with the -T2pial flag, and a -T2_min value specified via expert options file, I noticed that this parameter is passed to the first call of mris_make_surfaces, which looks, for example, as follows:

Re: [Freesurfer] Fwd: eTIV and brainmask mismatch on Philips data

Hi Agnieska, sorry for the delay. It looks like the contrast is slightly different than FS expects. I ran it with the -3T flag (which changes the talairach atlas), and it seemed to run fine on that subject. Try it out. best doug On 8/19/2019 1:23 AM, Agnieszka Sabisz wrote: External

Re: [Freesurfer] question about qdec

External Email - Use Caution Dear Dr.Dougla, Thanks for your reply! I also feel confused, that SUBJECTS_DIR is set on the the path :/usr/local/freesurfer/subjects and my subjects are indeed on this path. -- Original -- From:

Re: [Freesurfer] question about qdec

It looks like your SUBJECTS_DIR is set to the wrong place. It should be set to the folder where ever your subjects (eg, PT1_01) are On 8/19/2019 4:45 AM, 310913949 wrote: External Email - Use Caution Hi FS Experts, I meet some problem when I use QDEC for Group analysis. When

Re: [Freesurfer] volume data from part of the brain

Did you check the registration (tkregister-sess)? My guess is that the partial field of view messed up the registration. If so, you can probably get around this by adding -init-header to preproc-sess On 8/19/2019 8:11 AM, Hang Zeng wrote: External Email - Use Caution Hi Freesurfers,

Re: [Freesurfer] help for calculating the correlation

If there is no interaction between F/R and Active, then there should not be any theoretical difference between the two analyses, except that FR combined will be slightly more powerful since it has one more degree of freedom. You should first use the uncombined model to look for an interaction,

[Freesurfer] volume data from part of the brain

External Email - Use Caution Hi Freesurfers, when I collected the fMRI data, I set the slices to cover part of the brain (only cover the occipital and the temporal lobe). The anatomy scan was of course whole brain. After analysing the data with the pipeline (preproc mkanalysis

[Freesurfer] question about qdec

External Email - Use Caution Hi FS Experts, I meet some problem when I use QDEC for Group analysis. When I click Generate Stats Data Tables, it report the errors as follows: dec/gender.levels Female Male done. Reading discrete factor levels from config

Re: [Freesurfer] Fwd: eTIV and brainmask mismatch on Philips data

External Email - Use Caution Dear Doug, I uploaded the data by ftp in Windows 10 on 1st Aug. I hope You can see a tar file. The file's name is HTN_Con_096 and it contains the subject's folder after recon_all. Do You need any other data? All the best czw., 1 sie 2019 o 11:44