Re: [Freesurfer] ICV as covariate for controls vs. patients

External Email - Use Caution Just to add some more info here: The peak location of regions, X1 and X2, which I found without including ICV as covariate are very close with the peak locations I found in Gamma_Without_ICV (~5.15), whereas Gamma_With_ICV is almost all over the brain

Re: [Freesurfer] Matched analysis with 2 controls 1 case weighting

Hi Doug, Thank you very much for your reply and my apologies for this belated response. The two approaches you mentioned were the only ones we could think that might work for a DV like cortical thickness. That being said, we were originally thinking of a repeated measures anova. However,

Re: [Freesurfer] ICV as covariate for controls vs. patients

For noise compare the values in the rstd.mgh file, for effect size look in the gamma.mgh file On 07/24/2018 12:27 PM, Martin Juneja wrote: > > External Email - Use Caution > > Hi Dr. Greve, > > Thanks for your quick reply. Could you please give me more details how > can I check this

Re: [Freesurfer] mris_ca_label seed

External Email - Use Caution Great, thank you! On Tue, Jul 24, 2018 at 12:28 PM, Bruce Fischl wrote: > no, they should be the same > > On Tue, 24 Jul 2018, Rosemary Nicholas wrote: > > >> External Email - Use Caution >> >> Hi Andrew, >> Thanks! >> >> So as long as we

Re: [Freesurfer] mris_ca_label seed

no, they should be the same On Tue, 24 Jul 2018, Rosemary Nicholas wrote: External Email - Use Caution Hi Andrew,  Thanks!   So as long as we set the seed in mris_ca_label the results should be consistent, right?  Would there be any difference to running it this way

Re: [Freesurfer] Convert to .nii in the native space including all changes in the pial surfaces

Hi Sofia you should be able to "reslice like" the rawavg.mgz: mri_convert -rl rawavg.mgz brainmask.mgz brainmask.rawavg.mgz you might also want to specify the interpolation as e.g. nearest with -rt nearest (trilinear is the default I believe) On Tue, 24 Jul 2018, Sofia Rodriguez Penuela

Re: [Freesurfer] ICV as covariate for controls vs. patients

External Email - Use Caution Hi Dr. Greve, Thanks for your quick reply. Could you please give me more details how can I check this whether its because of noise or its because of less CV difference? I am not sure what method/way is the best and commonly used to confirm these

Re: [Freesurfer] Surfaces misaligned "Did not find any volume info. Warning: MatrixInverse failed".

Hi Sofia, Would it be possible to send us the volume and one of the surface files you loaded? Best, Ruopeng On 07/24/2018 12:08 PM, Sofia Rodriguez Penuela wrote: External Email - Use Caution Dear Freesurfer team, After loading a volume in Freeview, we try to load surfaces, but

Re: [Freesurfer] mris_ca_label seed

External Email - Use Caution Hi Andrew, Thanks! So as long as we set the seed in mris_ca_label the results should be consistent, right? Would there be any difference to running it this way (independently) and running it with recon-all? Thanks, Rosemary On Mon, Jul 23, 2018

[Freesurfer] Convert to .nii in the native space including all changes in the pial surfaces

External Email - Use Caution Hello team, We have first fixed non-cortex voxels in the pial surface using the brainmask.mgz volume, and we next corrected pial surfaces that mistakenly included cerebellum by creating a copy of 'brain.finalsurfs.mgz' named

Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

External Email - Use Caution I am using mri_vol2vol --mov L_AIP_mask.nii.gz --targ $FSLDIR/standard/MNI152_T1_1mm_brain.nii.gz --inv --reg $FREESURFER_HOME/average/mni152.mni305.subfov1.dat --o L_AIP_MNI152.nii.gz --interp nearest (I used mni152.mni305.subfov1.dat in my

Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

no idea how to help with the vol2vol problem without a command line and more description of the problem On 7/24/18 6:52 AM, Yagmur Ozdemir 19 wrote: External Email - Use Caution By copying the matrix that comes up in the terminal, then readjusting it, if needed, in a different .dat

Re: [Freesurfer] ICV as covariate for controls vs. patients

your results could have vanished after ICV correction for one of two reasons: the CV difference became less or the values became noisier (or a combination). So check in your data which one of those things happened. On 7/23/18 8:30 PM, Martin Juneja wrote: External Email - Use

Re: [Freesurfer] Aparc.stats based on fsaverage?

Hi Martin no, the stats are all from subject-space segmentations and surfaces. cheers Bruce On Tue, 24 Jul 2018, Martin Steppan wrote: External Email - Use Caution Dear Freesurfer/s, Sorry, it might be a stupid question, since I am a newbie in this field. Is the

Re: [Freesurfer] Aparc.stats based on fsaverage?

The parcellation starts off in fsaverage space. It is mapped through the surface-based registration into the native subjects surface space. There, the boundaries are refined to better fit the individual. The transformation is based on folding patterns which are pretty consistent across the age

Re: [Freesurfer] How to convert label to volume

External Email - Use Caution In --temp /home/zwj/SCH_immune/A00 you seem to be missing the last bit of the file name, like .mgz or .nii. This option passes the template volume you want the output volume to match. For the second question, you can load that annotation and the

[Freesurfer] How to convert label to volume

External Email - Use Caution Dear experts, Could you tell us how to convert label to volume? when I run this command "mri_label2vol --label lh.insular.label --temp /home/zwj/SCH_immune/A001 --identity --o insular.img", errors happened: corRead(): can't open file

Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

External Email - Use Caution By copying the matrix that comes up in the terminal, then readjusting it, if needed, in a different .dat file, I can fix the issue. But I would still appreciate any suggestions on how to use mri_vol2vol with a binarized mask, or what might be

[Freesurfer] Aparc.stats based on fsaverage?

External Email - Use Caution Dear Freesurfer/s, Sorry, it might be a stupid question, since I am a newbie in this field. Is the ?.aparc.stats file somehow based on transformation to fsaverage space? I am aware that this is the case for -qcache, but is this also true for the

[Freesurfer] tkregister2 scripting- help with saving reg.dat

External Email - Use Caution Hello freesurfer experts, I am editing the registration matrix between two volumes (fsaverage's T1 to fit MNI152 from fsl) using tkregister2, and I cannot save the registration because I do not have permission to change the .dat file I originally