Re: [Freesurfer] freeview 3.0

External Email - Use Caution Hello Xiaomin, It might help for you to send along an example freeview command and file that demonstrates this issue in the WSL environment. - R. On Jul 8, 2020, at 12:08, Xiaomin Yue yu...@hotmail.com wrote:External Email - Use CautionDear all,The

[Freesurfer] label to surface

External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Question about 3T images and brain atlas compatibility

External Email - Use Caution Thank you for the response. Just to clarify, when you say as long as the surface reconstruction is correct do you mean that the surface should not have any gross defects and surfaces such as the pial surface show correct wm/gm boundaries? Best, Julia

[Freesurfer] The thalamic atlas in MNI space

External Email - Use Caution Dear experts I am performing a fMRI analysis about the thalamus. I would like to see the overlap of my thalamic ROI with the atlas derived in 'A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology' (Iglesias,

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

Just the subfields ;-) Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Jenna Katherine Blujus Reply-To: Freesurfer support list Date: Wednesday, July 8, 2020 at 18:11 To: "freesurfer@nmr.mgh.harvard.edu"

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

External Email - Use Caution Hi Eugenio, Great, thank you! One last question - after I edit the aseg and wmparc files would you recommend that I only rerun the recon-all hippocampal-subfields-T2 step or should I rerun certain autorecon steps of recon-all? Thank you! Jenna

Re: [Freesurfer] Freesurfer and singularity container (bash script)

External Email - Use Caution Hello Ahmed, There is one error message indicating you are running out of disk space to write to. Not clear to me if that is inside or outside the container, but either files need to be deleted and/or your disk partition needs to be larger. I would

[Freesurfer] Freesurfer and singularity container (bash script)

External Email - Use Caution Hello, I have a question related to the singularity container to run a bash script that includes freesurfer commends. The issue is I have built a singularity container and included the freesurfer license in the container. Recalling and

Re: [Freesurfer] (no subject)

External Email - Use Caution Yes. On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve wrote: > Does that file exist? > > On 7/7/2020 8:59 AM, Peka Savayan wrote: > > External Email - Use Caution > Dear experts, > > I try to run recon-all using FS 7.1.0 on a cluster with OS

[Freesurfer] white vs pial target surface

External Email - Use Caution Hello, mri_vol2surf has the option to add a target surface (--surf) which can be the white (default) or pial surface. I get slightly different results depending on whether I use the white or pial surface as the target surface, so I was wondering in

Re: [Freesurfer] output of mri_surf2vol looks fragmented

External Email - Use Caution Thanks Doug. I added --ribbon ribbon.gz to the mri_vol2surf command but the output was exactly the same as omitting it. I think mri_vol2surf automatically loads ribbon.mgz when I include the --subject sub01. Just for my understanding, why shouldn't

[Freesurfer] Alternative Cerebellum parcellations

External Email - Use Caution Hello people! I was wondering how can I run a parcellation of the cerebellum with a different strategy than the one provided by the default subcortical segmentation (which only differentiates lh and rh white and grey matter). I'm currently analyzing

Re: [Freesurfer] Updating submillimeter data from 5.3 to 7.1 with -hires?

External Email - Use Caution Hi Douglas, It looks like the previous processing used 'recon-all -all -norm2-b 20 -norm2-n 5 -no-isrunning', this was from 2012 so I referenced the recon-all.log for this info. According to the log the original data was 0.9 mm size and then

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

Hi! I meant that if the hippocampus was oversegmented (e.g., over the amygdala), you’d still have to paint new labels in those regions (as amygdala, in our example). You could use the Matlab functions under $FREESURFER_HOME/matlab (in particular MRIread and MRIwrite) to programmatically move

[Freesurfer] freeview 3.0

External Email - Use Caution Dear all, The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, pial, white) in a solid color. The Freeview is currently running under WSL and was running without a problem until I updated libXm4. Is there a particular

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

External Email - Use Caution Hi Eugenio, Thank you for the tips! This has happened to a number of my subjects but I have finished editing the HC label in their aseg files. How would I copy the HC from aseg.mgz to wmparc.mgz? Can you clarify what you mean by "you still need to

Re: [Freesurfer] Updating submillimeter data from 5.3 to 7.1 with -hires?

How did you do the 5.3 analysis? in 1mm/conformed space? And what are you hoping to accomplish by running it in v7.1 with -hires? On 7/8/2020 10:46 AM, Daniel Westfall wrote: External Email - Use Caution Hi Everyone, I have access to two large datasets (~600 scans) that were

Re: [Freesurfer] Question about 3T images and brain atlas compatibility

This is a surface-based atlas, so it is not sensitive to field strength as long as the surface reconstruction is correct because surfaces align with curvature and not intensity On 7/8/2020 12:39 AM, Hye Min Shin wrote: External Email - Use Caution Hello, I wanted to extract brain

Re: [Freesurfer] Mapping labels from left hemisphere to right hemisphere in fsaverage space

Use instruction 1.4 from this page ("Map a label") where the subject is fsaverage https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 7/7/2020 11:40 PM, Yash Patel wrote: External Email - Use Caution Hi all, I have manually drawn roi onto fsaverage space on the left hemisphere. Is

Re: [Freesurfer] mri_aparc2aseg with flag --a2005s

That file is  no longer created by recon-all. But you can recreate it. cd $SUBJECTS_DIR/subject/label mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject lh $FREESURFER_HOME/average/lh.atlas2005_simple.gcs ../label/lh.aparc.a2005s.annot And the same for

Re: [Freesurfer] Atlas question

Not that I know of, sorry On 7/7/2020 4:17 PM, Sara Lyn wrote: External Email - Use Caution Hi FS developers I'm doing an ROI analysis with data data and was wondering if there exists a merged Freesurfer white matter parcellation and Johns Hopkins University white matter label

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

Is the T2 aligned with the T1? On 7/7/2020 4:53 PM, Iglesias Gonzalez, Juan E. wrote: Dear Jenna, 1.Manually editing aseg.mgz fixes the initialization (super important). 2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important) If it’s only 1 subject

Re: [Freesurfer] (no subject)

Does that file exist? On 7/7/2020 8:59 AM, Peka Savayan wrote: External Email - Use Caution Dear experts, I try to run recon-all using FS 7.1.0 on a cluster with OS CentOS6. I got the recon-all.log error message: ERROR: cannot find

Re: [Freesurfer] bbregister using freesurfer v7

On 7/7/2020 3:14 AM, Ellen Ji wrote: External Email - Use Caution Dear experts, I am running bbregister and have a couple questions: 1) I am using freesurfer version 7. My understanding is that I do not need any --init argument anymore, and without it, by default it uses

Re: [Freesurfer] output of mri_surf2vol looks fragmented

They will not look exactly the same. Try adding --ribbon ribbon.mgz On 7/6/2020 10:47 PM, Sam W wrote: External Email - Use Caution Hi, I'm trying to understand mri_surf2vol and mri_vol2surf but I'm not able to get the expected output when converting a surface back to volume. These

[Freesurfer] Updating submillimeter data from 5.3 to 7.1 with -hires?

External Email - Use Caution Hi Everyone, I have access to two large datasets (~600 scans) that were previously collected, processed, QC'd, and manually edited where necessary in Freesurfer 5.3 with recon-all. However, the data is 0.9 mm isotropic collected in a 3T scanner. I

Re: [Freesurfer] Error in Trac-All Pre-Processing step

External Email - Use Caution Hi Anastasia! Thank you for taking the time to help me with this! I will send along the trac-all.log file for my run directly to you via email, since my previous attempts to post it were rejected by the Freesurfer mailing list moderators. Thank you