Re: [Freesurfer] Permutation simulation cluster include vertices below cluster-forming threshold

External Email - Use Caution I just checked and 3.0+log10(0.5) gives me 2.69, which is exactly the lowest value I saw in *.sig.masked.mgh. Thanks for the explanation! Best, Fengdan > On Jun 5, 2020, at 1:07 PM, Douglas N. Greve wrote: > > The reason is that you specified a sig

Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

External Email - Use Caution thanks, the subj I sent you the logfile has a cut on the posterior part, I uploaded a similar case 098_S_4275_20181221.tar.gz Is there any way to run gtmseg regardless? Thanks Am Fr., 5. Juni 2020 um 20:01 Uhr schrieb Douglas N. Greve < dgr...@mgh.har

Re: [Freesurfer] samseg with subfields {Disarmed}

External Email - Use Caution Thank you Doug. it is not run by default * When I ran “samseg2recon –s subject” after running samseg, it did not do anything different, am I missing anything? Yes, a lot of file names changed. You should look at the seg.stats file * We did

Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

Removing the -U ;-) Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Zeng, Qi" Reply-To: Freesurfer support list Date: Friday, June 5, 2020 at 16:02 To: Freesurfer support list Subject: Re: [Freesurfer] Get hi

Re: [Freesurfer] samseg with subfields {Disarmed}

On 6/5/2020 3:54 PM, Sneha Pandya wrote: External Email - Use Caution Dear Dough, Is samseg2recon run by default when we run just samseg command? After samseg is completed it displays towards the end samseg2recon run time in sec and hours, right before computation time of samseg as

Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

External Email - Use Caution Thanks. I was wondering If there is another way around to get the amygdala mgz. Best, Qi On Fri, Jun 5, 2020 at 2:44 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Yes 😊 the amydala labels are in the 7000 range and the

Re: [Freesurfer] samseg with subfields {Disarmed}

External Email - Use Caution Dear Dough, Is samseg2recon run by default when we run just samseg command? After samseg is completed it displays towards the end samseg2recon run time in sec and hours, right before computation time of samseg as below. If it is called by samseg com

Re: [Freesurfer] mz3 for freesurfer brain render

External Email - Use Caution Hi Douglas, I would like to plot some values (z-scores) of ROI (grey matter) that are from freesurfer atlas and would like render them on the brain (freesurfer atlas) using surf ice. Is there .mz3 for the Desikan-Killarny atlas? Thanks k On Fri, Jun

Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

Yes 😊 the amydala labels are in the 7000 range and the hippocampal in the 200s. Feel free to use eg 4129 next time! Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Zeng, Qi" Reply-To: Freesurfer support list

Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

External Email - Use Caution Thanks, it works. Does the code mean that it only allows labels under 300 to pass through? Best, Qi On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Qi, > > You can try: > > mri_threshold -

Re: [Freesurfer] mz3 for freesurfer brain render

External Email - Use Caution I think she wants to render a brain surface mesh in an external 3D modeling software (like Blender), with the vertex colors of the mesh corresponding to a brain parcellation like Desikan. Tim > On June 5, 2020 at 8:09 PM "Douglas N. Greve" wrote: >

Re: [Freesurfer] mz3 for freesurfer brain render

I don't know what you are asking for. Can you elaboraet? On 6/5/2020 10:41 AM, Kate Marvel wrote: External Email - Use Caution Hi Freesurfer team, I would like to do a brain render using freesurfer ROIs. Is there .mz3 file for freesurfer brain atlas? Thanks, -- kate ___

Re: [Freesurfer] Permutation simulation cluster include vertices below cluster-forming threshold

The reason is that you specified a sign (pos). By default, all the FreeSurfer p-values are unsigned. When you specify a sign to mri_glmfit-sim, the unsigned p-value will be converted to a (more significant) signed p-value before applying the CFT. When you look at the unsigned sig map, try setti

Re: [Freesurfer] mri_watershed

External Email - Use Caution Is there a way to pass an already corrected brainmask file or force the function to do that so all the subsequent surf are created accordingly without using after mri_binarize? On Fri, 5 Jun 2020, 7:52 p.m. Douglas N. Greve, wrote: > mri_watershe

Re: [Freesurfer] dura edits .mgz~ file?

That would probably contain the brinmask.mgz before edits. Try changing the name to something like whatsthis.mgz, then see if you wan load that file On 6/4/2020 1:18 PM, KennethSPrice wrote: External Email - Use Caution Hello Freesurfers, I edited the brainmask.mgz file after running

Re: [Freesurfer] mri_glmfit masking strategy

On 6/4/2020 12:38 PM, Barletta, Valeria wrote: Hello Freesurfers, I need to perform a GLM in 25 patients versus 19 controls but I need the comparison to be done only on normal appearing cortex (in patients), thus excluding cortical lesions. * Is it possible to concatenate binary masks pro

Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

Hmmm, not sure what is going on here. I'm guessing that the back of the head was cut off (or wrapped around). Is that right? I'm not sure why this would create an error. If you upload one of your subjects, I'll take a look. See instructions below From the linux command line, Create the file yo

Re: [Freesurfer] Thalamic nuclei segmentation

It will ignore the projmap option, so you can just leave it as X (it can be any string, but there does have to be something there). For the reg, use regheader On 6/4/2020 6:00 AM, Quentin Devignes wrote: External Email - Use Caution Dear Doctor Greve, Thank you for your reply. I am

Re: [Freesurfer] mri_watershed

mri_watershed creates brainmask.mgz, and the inner_skull should fit around that. On 6/3/2020 9:36 AM, Edoardo Pinzuti wrote: External Email - Use Caution Dear Freesurfer community, I have a question regarding the mri_watershed. Is the inner_skull extracted from the brain.mgz  which 

Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

Dear Qi, You can try: mri_threshold -U [lr]h.hippoAmygLabels-T1.v21.mgz 300 [lr]h.hippoLabelsNoAmyg-T1.v21.mgz Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Zeng, Qi" Reply-To: Freesurfer support list Da

[Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

External Email - Use Caution Hi, I conducted longitudinal segmentation of both hippocampus and amygdala from running segmentHA_T1_long.sh. But is it possible for me to segment only the hippocampus region "mgz" from the stored [lr]h.hippoAmygLabels-T1.long.v21.mgz ? Best, Qi --

Re: [Freesurfer] mz3 for freesurfer brain render

External Email - Use Caution You can use the ones Anderson Winkler provides here on his blog: https://brainder.org/research/brain-for-blender/ Best, Tim > On June 5, 2020 at 4:41 PM Kate Marvel wrote: > > > External Email - Use Caution > > Hi Freesurfer team,

[Freesurfer] mz3 for freesurfer brain render

External Email - Use Caution Hi Freesurfer team, I would like to do a brain render using freesurfer ROIs. Is there .mz3 file for freesurfer brain atlas? Thanks, -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:/