[Freesurfer] (no subject)

Dear all, I am carefully starting up with the basics for analysis of 3T mri images. After having done the recon all I am about to begin the review and editting process where needed. However, I am now a bit overwhelmed. Is there any logical or recommended order to proceed with the several potential

[Freesurfer] Recon-all after edits

appropriate flag? Thank you -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] Qcache

Dear list, When processing the data for longitudinal analysis (or even for cross sectional) the -qcache has to be run before editing or after all the edits have been done? Thank you -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute

Re: [Freesurfer] Recon-all after edits

-wm does so it is redundant. If you run autorecon2-cp and autorecon3 you will get everything (unless you edit the aseg) cheers Bruce On Thu, 30 Mar 2017, Manuel Delgado wrote: Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found

Re: [Freesurfer] T1 error

e window levels in > freeview when you view it? And in general when you report errors please > include the full screen output of what you ran, and in cases like this, and > image to illustrate the issue. > > cheers > Bruce > > > On Fri, 17 Mar 2017, Manuel Delgado wrote: >

Re: [Freesurfer] T1 error

;gr...@nmr.mgh.harvard.edu> wrote: > what is the error exactly? Please provide the recon-all.log file and a > description of the problem > > > On 03/16/2017 06:28 AM, Manuel Delgado wrote: > > Dear list, > > After recon-all the T1 seems to have an error. Has anybody had this > &g

[Freesurfer] T1 error

Dear list, After recon-all the T1 seems to have an error. Has anybody had this problem before? Please find attached the image. I guess I have to recon-all again. I am using v 6.0 with Ubuntu 16.04. Thank you. -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla

[Freesurfer] wm topological defects

ace before correcting them? And, what is the purpose of the smoothwm.nofix, is it used for other issues? Thank you -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santan

[Freesurfer] Fwd: wm topological defects

To illustrate the previous case here there is an image in which there is a discrepancy between the wm surface and the smoothwm.nofix. Is it necessary to fix it or not? Thanks -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n

[Freesurfer] sulcus in the orbitofrontal wm

. Thanks in advance -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santander, Spain* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Longitudinal hippocampal subfields analysis

-- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Outputs from 5.3 to 6.0

, control points, wm and pial edits) or is it necessary to proceed with ordered steps (i.e -autorecon-pial, then -autorecon2-cp autorecon3, and so on)? Thanks in advance, Manuel -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL

Re: [Freesurfer] Outputs from 5.3 to 6.0

nin Skoch > > all the edits will be taken into account regardless of what command line args > you use > > On 6/9/17 3:08 AM, Manuel Delgado wrote: > > Dear all, > > > Regarding this issue: http://www.mail-archive.com/ > freesurfer@nmr.mgh.harvard.edu/msg51931.html we hav