Re: [Freesurfer] Registration file types confusion

you can use lta_convert with the --outreg option On 3/27/2020 3:20 PM, Xiaojiang Yang wrote: External Email - Use Caution Hi Douglas, The link you gave to me (https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) has some information about .dat file, but no information about

Re: [Freesurfer] Registration file types confusion

External Email - Use Caution Hi Douglas, The link you gave to me ( https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) has some information about .dat file, but no information about .lta file at all. I

Re: [Freesurfer] hippocampal-subfields-T1 error

Dear Aleks, Please try: chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/* Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Duvnjak, Aleksandar" Reply-To: Freesurfer support list

Re: [Freesurfer] hippocampal-subfields-T1 error

External Email - Use Caution To clarify, upon copying the entire FreeSurfer 6.0 package to our personal directory, we have then downloaded the matlab runtime MCRv80 folder to that directory and the issue does not appear to be the hippocampal-subfields-T1 pipeline accessing

Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm

External Email - Use Caution This is the actual command that fails: mri_surfcluster --in rh.50to50.glmdir//con_nonpos/sig.mgh --mask rh.50to50.glmdir//mask.mgh --cwsig rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.mgh --sum

Re: [Freesurfer] Volume-defined roi

not sure what  you are referring to. Can you provide more context? On 3/27/2020 11:06 AM, Erik Lindberg wrote: External Email - Use Caution Hi I am reading your tutorial about how to extract Cortical Thickness of a volume-defined ROI Wonder if there is a script that would run these

Re: [Freesurfer] mri_vol2vol

oK, this will not be that pretty, but you can mri_vol2vol --mov yourRoi.mgz --targ orig.mgz --interp nearest --regheader --o yourRoiOrig.mgz mri_convert yourRoiOrig.mgz yourRoiOrigAverageSpace.mgz --apply_transform subject/mri/transforms/talairach.xfm -rt nearest On 3/27/2020 11:03 AM,

Re: [Freesurfer] Fwd: recon-all-lh error : cannot allocate memory

This is probably a big defect (eg, cerebellum or skull still attached). Try correcting it manually by viewing the lh.orig.nofix and the wm.mgz (or the brainmask.mgz) On 3/23/2020 10:24 PM, Jong-eun Lee wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm trying

Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm

External Email - Use Caution Actually I was just sending an example command to demonstrate the same error. I'll see if I can get the actual command fspalm was running. -syam From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of

[Freesurfer] Volume-defined roi

External Email - Use Caution Hi I am reading your tutorial about how to extract Cortical Thickness of a volume-defined ROI Wonder if there is a script that would run these steps in a bach particularly the steps that needs to be done on each individual subjects: map subject

Re: [Freesurfer] mri_vol2vol

External Email - Use Caution The space i created from all subjects using make_average_subject. Douglas N. Greve schrieb am Fr. 27. März 2020 um 15:32: > What do you mean by "the average space of the subjects"? > > > On 3/24/2020 2:01 PM, Benjamin Ineichen wrote: > >

Re: [Freesurfer] selxavg3-sess not working

I don't understand what the problem is. There is no error in the log file. If you want to redo the  preprocessing, you should rerun preproc-sess with the -force flag On 3/20/2020 12:25 PM, Nasiriavanaki, Zahra wrote: Hi Doug Thanks for your reply. Unfortunately I am still having problem.

Re: [Freesurfer] Permutation with Non-Ortohgonal Matrices

Have you looked at our updated permutation wiki? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 3/26/2020 2:32 PM, Hua, Jessica wrote: External Email - Use Caution Hi FreeSurfer Experts, I am trying to correct for multiple comparisons by running

Re: [Freesurfer] Registration file types confusion

Part of you answer can be found here https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems tkregister2 and the .dat file format are obsolete, use tkregisterfv. This is just a front-end for FreeView; it always uses LTA. I'm not sure if there is documentation for the LTA format. The first

Re: [Freesurfer] Using mri_glmfit to regress out wm and ventricle signal

I don't know what you mean by " matter and csf signal in my nuisance regressor matrix". It looks like your matrix only has motion and trends. Also, look at this page http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough On 3/25/2020 12:16 PM, Mcnorgan, Christopher

Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm

Hi Syam, it looks like fspalm is not creating the correct command line for mri_surfcluster (the --in should be an output of palm, not the fsaverage surface). Can you send the full terminal output? doug On 3/25/2020 9:13 AM, Syam Gadde wrote: > External Email - Use Caution > > Hi, > >

Re: [Freesurfer] PetSurfer reference region

On 3/24/2020 6:11 PM, Dincer, Aylin wrote: External Email - Use Caution Hello PetSurfer experts, We found the SUVR values for the reference region (lh/rh cerebellum cortex) does not equal 1 in the gtm.stat.dat file. We tried a few things: 1) leaving the PET image as multi-frames

Re: [Freesurfer] mri_vol2vol

What do you mean by "the average space of the subjects"? On 3/24/2020 2:01 PM, Benjamin Ineichen wrote: External Email - Use Caution Dear Freesurfer experts, I am aware that these are busy times. Please still allow me to repost my FreeSurfer problem: I created manual masks on the

Re: [Freesurfer] Density of the skull

No, though Oula Puonti is working on ways to segment spongy bone from hard bone. I'm also CC'ing David Izquierdo who has worked on this kind of thing for PET applications. I'm not aware of a way to get the actual density from MRI, but I'd be curious if there is such a method. On 3/24/2020

Re: [Freesurfer] Run FreeSurfer recon-all on isoDWI

FS requires a T1-like contrast. I don't think that there is much you can do with DWI, and we would not support it if you were able to get it to run On 3/24/2020 11:50 AM, Yixin Ma wrote: External Email - Use Caution I was trying to use the average of DWI images (isoDWI) to run

Re: [Freesurfer] mri_deface download link not found

I don't know what you mean by ' getting a "Not Found" error when I try to download the tools for it.' Can you elaborate? On 3/24/2020 7:23 AM, D'Silva, Hailey wrote: External Email - Use Caution Hello Freesurfer Experts! I'm trying to anonymize a number of T1s by using mri_deface,

Re: [Freesurfer] Default GCA atlas FreeSurfer 6?

Hi Andrei, in the future, please post to the FS list. On 3/23/2020 5:21 PM, Andrei Mouraviev wrote: External Email - Use Caution Hello, I’m trying to find the default atlas that was used to segment T1W images(freesurfer v6.0.1). Is this the still the right file?