[Freesurfer] WG: Save segmentation results as nifi files

Von: Fellhauer, Iven Gesendet: Donnerstag, 15. März 2012 10:29 Bis: Douglas N Greve Betreff: AW: [Freesurfer] WG: Save segmentation results as nifi files Dear all, in which space are the output files stored? If they are not stored in MNI space, which st

Re: [Freesurfer] WG: Save segmentation results as nifi files

they are stored in the native "conformed" anatomical space On Thu, 15 Mar 2012, Fellhauer, Iven wrote: Von: Fellhauer, Iven Gesendet: Donnerstag, 15. März 2012 10:29 Bis: Douglas N Greve Betreff: AW: [Freesurfer] WG: Save segmentation results as nifi

[Freesurfer] License Installation problem

Hi, I tried installing the free surfer license,but was not able to do so,if anyone could help me with a detailed approach to this,I would be most grateful.I am saying detailed cause i am not familiar with some computing procedures. Thanks, Kunal __

[Freesurfer] HELP needed to improving quality while processing CHILDREN'S DATA

Hello Freesurfers, I am new using freesurfer and I would like to know if any of you have some ideas (tools, tips, ...) on how to improve the quality of my results while processing structural T1 data from children aged 5 to 7 years old. Syncerly, Karla -- Karla Monzalvo Inserm U.992 - Neuroimag

[Freesurfer] export hippocampal subfields using mri_binarize

Hi all, I am trying to export the hippocampal subfields generated in Freesurfer 5.1. To do that I use mri_binarize with a minimum voxel threshold of 150 and a maximum of 255. However, some of these regions appear overlapped. Why does this happen if a minimum threshold of 150 correponds to a

Re: [Freesurfer] export hippocampal subfields using mri_binarize

Hi Caterina, This previous post to the mailing list may be helpful: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21491.html Allison On Thu, 15 Mar 2012, Catarina Duarte wrote: Hi all, I am trying to export the hippocampal subfields generated in Freesurfer 5.1. To do that I us

[Freesurfer] Crippled fiber tracts in healthy subjects (TRACULA)

Hi, We are using the ADNI Acc 3D FSPGR for structurals and 30 directional (5 B0s) repeat sequence for DTI which so far rendered really nice results. However, recently I encountered data from several healthy young subjects where the TRACULA fiber tract estimations would suggest severely crippled tra

Re: [Freesurfer] Crippled fiber tracts in healthy subjects (TRACULA)

Hi Ansgar, Can you send us an example screenshot of the one of the fiber tracts that look crippled? If you can send us an overlay of path.pd.nii.gz of that specific tract on the FA map, it will give us an idea of what is going on. Best, Priti > Hi, > We are using the ADNI Acc 3D FSPGR for struct

[Freesurfer] Crippled fiber tracts in healthy subjects (TRACULA)

Dear All, Please ignore my earlier incomplete message with the same title! We are using the ADNI Acc 3D FSPGR for structurals and a 30 directional (5 B0s) dual-spin repeat sequence for DTI (on a 3T GE 750 discovery) which so far rendered really nice results. However, recently I encountered data fro

[Freesurfer] volume mapping

Hi This is Johnson, I am researcher at univ. of IL at chicago, I have a question regarding freesurfer: What is the transformation matrix that relates the freesurfer aparc+aseg space to the aparc+aseg-in-rawavg space, I am asking this question for the following reason: I have white matter fiber tr

Re: [Freesurfer] HELP needed to improving quality while processing CHILDREN'S DATA

Hi Karla, what coil/scanner/sequence etc... are you using? And what quality are you finding is not sufficient? Bruce On Thu, 15 Mar 2012, Karla Zúñiga wrote: Hello Freesurfers, I am new using freesurfer and I would like to know if any of you have some ideas (tools, tips, ...) on how to im

Re: [Freesurfer] Q: Tkmedit

Those lines are just an artifact of the viewer. There's nothing wrong with your data. doug On 3/15/12 12:17 PM, Yiyu Chou wrote: Dear FS users, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

Re: [Freesurfer] strangely low lhCorticalWhiteMatterVol estimate

Hi Doug, As a post-mortem to this thread, in the process of going to "tweak" the wm.mgz as you suggested, I noticed that there were actually some substantial errors in the surfaces in the calcarine, presumably due to topology correction gone astray. So, whether or not that precipitated the probl

Re: [Freesurfer] License Installation problem

what happened when it failed? On Thu, 15 Mar 2012, Talvadkar, Kunal Girish wrote: > Hi, > I tried installing the free surfer license,but was not able to do so,if > anyone could help me with a detailed approach to this,I would be most > grateful.I am saying detailed cause i am not familiar with