Re: [Freesurfer] Co-ordinate systems in FS

Add --no-fixmni to the mri_surfcluster command On 8/4/17 3:03 PM, Martin Juneja wrote: Hi Douglas, When I checked the summary created by FreeSurfer by running FS commands: For cortical gyrification I get (here co-ordinates are in TalX TalY and TalZ): # ClusterNo Max VtxMax Size(mm^2)

Re: [Freesurfer] label2annot issue

Doug, did you receive my files? I received an email explaining that the mail is too big and I need to wait for an authorisation from the moderator. Thank you, Redwan On Aug 4, 2017 10:34 AM, "Redwan Maatoug" wrote: > Thank you very much Doug, I really appreciate your

Re: [Freesurfer] ROI labeling?

Sorry, I meant that I would somehow want to merge all of these masks together into one. Not changing the values in the masks, but somehow combining them. Also, with the mri_glmfit --label flag, is it possible to have multiple labels listed (like one label per subject)? Sort of like a frame mask

Re: [Freesurfer] Co-ordinate systems in FS

Hi Douglas, When I checked the summary created by FreeSurfer by running FS commands: For cortical gyrification I get (here co-ordinates are in TalX TalY and TalZ): # ClusterNo Max VtxMax Size(mm^2) *TalX TalY TalZ * NVtxs WghtVtx Annot 1 -2.108 44783 1067.81-28.3

Re: [Freesurfer] Co-ordinate systems in FS

How do you know one is MNI and one it Tal? can you send a summary of your commands? On 8/4/17 2:09 PM, Martin Juneja wrote: Hi FreeSurfer experts, I am trying to correlate my behavioral data with whole brain cortical measures using cortical measures as IVs and behavioral data DV. Somehow

[Freesurfer] Co-ordinate systems in FS

Hi FreeSurfer experts, I am trying to correlate my behavioral data with whole brain cortical measures using cortical measures as IVs and behavioral data DV. Somehow the significant clusters I get from cortical thickness, area and volume are in MNI co-ordinates but significant clusters from local

Re: [Freesurfer] Optseq2 onset times

those are not concerning, you can just round to the nearest TR On 8/4/17 12:32 PM, Ruthie Shaffer wrote: Hi, I’m using Optseq2 to generate stimulus / jitter schedules, and, depending on the TR used, in the output timing files I see several event onset times very close to the correct time,

Re: [Freesurfer] label2annot issue

Yes, send me two label files and the ctab again. On 8/4/17 12:49 PM, Redwan Maatoug wrote: Hi Douglas, I tried to rename the parcel files and in the ctab but it does not change anything. I have the feeling that sometime label2abnot can read the colors because as you can see in the

Re: [Freesurfer] label2annot issue

Hi Douglas, I tried to rename the parcel files and in the ctab but it does not change anything. I have the feeling that sometime label2abnot can read the colors because as you can see in the screenshots there is some colors on the brain. If I give you the files could you help me to follow the

[Freesurfer] Optseq2 onset times

Hi, I’m using Optseq2 to generate stimulus / jitter schedules, and, depending on the TR used, in the output timing files I see several event onset times very close to the correct time, but slightly off (for example, something like 124.7999, instead of 124.8).  I’ve used the following command

Re: [Freesurfer] Pineal gland volume?

Yes, you will need to choose an index and then pass the color table to mri_segstats with --ctab to make sure it appears in the output. On 8/4/17 10:25 AM, Bruce Fischl wrote: Hi Rotem sorry, we don't label the pineal gland, but yes you can label it in the volume yourself using freeview. I

Re: [Freesurfer] Pineal gland volume?

Hi Rotem sorry, we don't label the pineal gland, but yes you can label it in the volume yourself using freeview. I think if you add it to the color lut file it will be included in the stats, but perhaps Doug can comment Bruce On Fri, 4 Aug 2017, Rotem Saar wrote: Dear Freesurfer experts,

Re: [Freesurfer] output with input matrix size and referential

it seems to works thanks. On Wed, Aug 2, 2017 at 6:20 PM, Douglas Greve wrote: > Try adding --to-scanner to the mris_convert command. I think you'll need v6 > > > On 8/2/17 12:02 PM, pierre deman-kibleur wrote: > > yes, it's what i wanted to say. > > On Aug 2, 2017

Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256

Dear FS experts, I want to reconstruct white and pial surface using both -hires and -T2pial options. My T1 and T2 image resolution is .85mm^3. But [recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial -all -cw256] command is not working as I emailed below.. Is there any

[Freesurfer] Pineal gland volume?

Dear Freesurfer experts, I wondered if its possible to extract the volume of the *pineal gland* using the basic cortical + sub-cortical segmentation (recon-all)? I could not find the volume of this ROI in the output. If the volume output for this ROI is available - please guide me where to look