[Freesurfer] Freesurfer hippocampal segmentation in patient with temporal lesion

External Email - Use Caution Dear all, I have a subject for whom I need to segment the right hippocampal and amygdalar subfields. However, they have a significant white matter lesion and large ventricles in the right temporal lobe, such that skull-stripping consistently cuts away

[Freesurfer] freesurfer subcortical segmentation

External Email - Use Caution Hi teams, Does freesurfer supports calculate subcortical volumes like globus pallidus internus, globus pallidus externa, subthalamic nucleus , ventral intermedius nucleus, like these areas? Thanks___ Free

Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask

Yes, that is correct. Sorry for leaving it out On 5/19/2020 12:55 AM, Elena Pozzi wrote: External Email - Use Caution Hi Douglas, Thank you very much for your answer. I tried the command you suggested and it did not seem to transfer the edits, so I added the flag -keep_mask_deletion

Re: [Freesurfer] freesurfer subcortical segmentation

No, not yet On 5/19/2020 10:17 AM, ZhangBo wrote: External Email - Use Caution Hi teams, Does freesurfer supports calculate subcortical volumes like globus pallidus internus, globus pallidus externa, subthalamic nucleus , ventral intermedius nucleus, like these areas? Thanks ___

Re: [Freesurfer] FREESURFER-7.1: recon-all exited with error "ERROR: cannot find or read transforms/talairach.m3z"

It looks like mri_ca_register failed to create the m3z. If this is failing on 13 subjects, then there is something systematically wrong. What kind of input do you have? Eg, MPRAGE? What is the resolution? Is it whole brain? On 5/19/2020 11:17 AM, Safi Ullah . wrote: External Email -

[Freesurfer] question on partial volume correction

Dear Freesurfers, We need to analyze PET data after correcting for partial volume effect in the cortex, white matter and subarachnoid space. Is Freesurfer's partial volume correction working on all these areas or only the grey matter volume and surface? Is there a way to use gtmseg on the white

[Freesurfer] Freeview on debian

External Email - Use Caution Hi everyone, I have a problem with freeview. My university created for me a virtual machine in a small analysis cluster. Unfortunately, they installed Debian 4.19.98. I read that freeview has some problems with Debian, and in fact I am not able to open

[Freesurfer] Uploading fs7.1 to hms o2 cluster

?Hi, Can someone from the martinos center who has access to /n/app/martinos/freesurfer in the Harvard O2 cluster upload freesurfer 7.1? Right now it just has freesufer 6.0. Thanks in advance, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

Re: [Freesurfer] Volume timeseries to native and fsaverage

External Email - Use Caution Hi Doug, I think I might have some gaps in my knowledge regarding the type of surface spaces Freesurfer uses and can produce, so I wanted to make sure that I got everything right. So my belief is that Freesurfer has the conformed surfaces which repr

[Freesurfer] circular/cyclic color map for polar data in freeview

External Email - Use Caution Hello freesurfer community, I am trying to setup a retinotopy pipeline. I have analysed pRF data generating polar angle and eccentricity maps which I project onto an inflated surface / flattened surface in freeview. Is there a way to display a circula

Re: [Freesurfer] FREESURFER-7.1: recon-all exited with error "ERROR: cannot find or read transforms/talairach.m3z"

External Email - Use Caution Thank you Sir, I downloaded the volumes from PPMI, it is .nii, it is whole brain. Can I send you one sample volume? On Wed, May 20, 2020, 12:33 AM Douglas N. Greve wrote: > It looks like mri_ca_register failed to create the m3z. If this is failing >

Re: [Freesurfer] Freeview on debian

External Email - Use Caution Hello Gian, Maybe you can report back with the version of Debian linux you are using so we could look into it. You could try downloading and running the Ubuntu VM image we have with freesurfer 6 and 7 beta release installed on it.  If you are going to

Re: [Freesurfer] FREESURFER-7.1: recon-all exited with error "ERROR: cannot find or read transforms/talairach.m3z"

Have you looked at the images? Are they T1-weighted? What is their resolution? On 5/19/2020 5:20 PM, Safi Ullah . wrote: External Email - Use Caution Thank you Sir, I downloaded the volumes from PPMI, it is .nii,  it is whole brain. Can I send you one sample volume? On Wed, May 20,

Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask

External Email - Use Caution Thanks so much! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FREESURFER-7.1: recon-all exited with error "ERROR: cannot find or read transforms/talairach.m3z"

Sure, send us a .nii volume that fails and we will take a look Bruce > On May 19, 2020, at 11:38 PM, Safi Ullah . wrote: > >  > External Email - Use Caution > > Thank You Sir, > > Below is the header info of the volume, I read in Matlab. > " srcbext: '' > analyzehd

[Freesurfer] Freesurfer version 7.0.0 and hippocampal segmentation

External Email - Use Caution Hello Freesurfer team, I have just become aware of the release notes concerning v7.0.0 being recalled and not to be used, with the recommendation to use v7.1.0 instead: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes I have a couple of questio