Re: [Freesurfer] [External] The thalamic atlas in MNI space

You may be interested in https://www.oxcns.org/aal3.html? AAL3, which has the estimations of the thalamus nucleis from fs6 Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ??? Sent:

Re: [Freesurfer] [External] The thalamic atlas in MNI space

I had no idea they had added the FreeSurfer thalamic nuclei; thanks a lot for the pointer! Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" Reply-To: Freesurfer

Re: [Freesurfer] The thalamic atlas in MNI space

You can run the mni152 through recon-all, then run the thalamic seg on it. I'm sure that it will give you something that looks reasonable, but it is probably a bogus way to analyze your data because the mni is so blurry and the structures are so small that a small misregistration would cause

Re: [Freesurfer] The thalamic atlas in MNI space

Dear GZ, The atlas lives in its own space, and it is hard to register to MNI because it only describes probabilities, and not image intensities. But you could try registering your subjects to MNI, propagating the thalamic segmentations, and analyzing the data in that coordinate frame. Cheers,

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

Yes On 7/8/2020 9:01 PM, Hye Min Shin wrote: 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

Re: [Freesurfer] (no subject)

Do you have read permission to it? On 7/8/2020 2:25 PM, Peka Savayan wrote: External Email - Use Caution Yes. On Wed, Jul 8, 2020 at 10:01 AM Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: Does that file exist? On 7/7/2020 8:59 AM, Peka Savayan wrote:   

Re: [Freesurfer] Lesioned hemisphere

Use -lh instead of -hemi lh On 7/9/2020 12:16 PM, Alina Rojas wrote: External Email - Use Caution Hello Bruce, I let it run with recon-all -sd ${TARGET_FOLDER}-subjid $SUBJECTID-i $T1-T2 $T2-qcache-all -3T -T2pial -hemi lh died it died unexpected and searching for the surf

Re: [Freesurfer] (no subject)

External Email - Use Caution The file that I sent you is the recon-all.log file. If copying file 'RB_all_2008-03-26.gca' from another FS version to directory /freesurfer-7.1.0/average will solve my problem? On Thu, Jul 9, 2020 at 12:30 PM Douglas N. Greve wrote: > Can

Re: [Freesurfer] (no subject)

Can you send the recon-all.log file? On 7/9/2020 1:25 PM, Peka Savayan wrote: External Email - Use Caution I can open it. Can you? No permission required to my knowledge. On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: Do you have read

Re: [Freesurfer] label to surface

Use mri_label2label with the --outmask option On 7/8/2020 10:14 PM, Sam W wrote: 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

Re: [Freesurfer] mri_aparc2aseg with flag --a2005s

External Email - Use Caution Hi, Thanks for the help! When I run the suggested commands I get redirected to the help output of the mris_ca_label. The command does not execute and looking at the mris_ca_label help page it seems as though the flags that you have suggested do not

Re: [Freesurfer] Visualising atlas ROIs on inflated surface

You can use mri_annotation2label to split the annotation into individual labels On 7/9/2020 12:58 PM, Leah Kelly wrote: External Email - Use Caution Hello. Previously I have been able to visualise Desikan and Destrieux ROIs separately on a participant's inflated surface, as

Re: [Freesurfer] (no subject)

Can you run recon-all again with -debug as the first argument? Send me the command line and all the terminal output On 7/9/2020 2:10 PM, Peka Savayan wrote: External Email - Use Caution The file that I sent you is the recon-all.log file. If copying file 'RB_all_2008-03-26.gca' from

Re: [Freesurfer] mri_aparc2aseg with flag --a2005s

External Email - Use Caution Hi, Thank you! That worked. I was also wondering if you can help me in getting the 9001 and 9002 masks. I tried to replicate the work from an archived post but had no luck. Thanks, Anja On Thu, Jul 9, 2020 at 2:51 PM Douglas N. Greve wrote: >

Re: [Freesurfer] (no subject)

External Email - Use Caution I can open it. Can you? No permission required to my knowledge. On Thu, Jul 9, 2020 at 11:53 AM Douglas N. Greve wrote: > Do you have read permission to it? > > On 7/8/2020 2:25 PM, Peka Savayan wrote: > > External Email - Use Caution > Yes.

Re: [Freesurfer] mri_aparc2aseg with flag --a2005s

Sorry, gave you the wrong command line, try this mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject lh ../surf/lh.sphere.reg $FREESURFER_HOME/average/lh.atlas2005_simple.gcs ../label/lh.aparc.a2005s.annot On 7/9/2020 2:12 PM, Anja Samardzija wrote:  

[Freesurfer] Help with LGI

External Email - Use Caution Dear Freesurfer experts, I'm needing some simple help running LGI. After downloading MATLAB + Image processing toolbox and double checking if the ?h.pial file is located in the SUBJECT_DIR, the recon-all -s (subject_ID) -localGI command still doesn't

[Freesurfer] Visualising atlas ROIs on inflated surface

External Email - Use Caution Hello. Previously I have been able to visualise Desikan and Destrieux ROIs separately on a participant's inflated surface, as demonstrated below. I would like to be able to see more ROIs in this way but cannot remember how to do this. Would you be able

Re: [Freesurfer] label to surface

External Email - Use Caution It works great Doug, thanks a lot! Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

External Email - Use Caution Hi Eugenio, Sorry! Can you specify how to copy the edits from aseg to wmparc within Matlab? aseg=MRIread('aseg.presurf.mgz') wmparc=MRIread('wmparc.mgz') asegHC=find(aseg.vol == 17 | aseg.vol=53) How would I then replace the data corresponding to

[Freesurfer] Freesurfer Digest, Vol 197, Issue 7 {Disarmed}

External Email - Use Caution Hi Eugenio! Thank so much for your reply. Please find attached the following files you requested: 1. A single subject processed cross sectionally - lh.hippoSfVolumes-T1.v10.txt 2. The same subject process longitudinally -

Re: [Freesurfer] freeview 3.0

External Email - Use Caution Thanks for your response. Why does freeview 2 work? Thanks, Xiaomin From: fsbuild Sent: Thursday, July 9, 2020 10:20 PM To: freesurfer@nmr.mgh.harvard.edu Cc: