Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30093 discussions

tksurfer vertex location
by Nabin Koirala 24 Jan '17

24 Jan '17

Dear freesurfer team, I was trying to obtain the values at a vertex in tksurfer and this is what is written in tksurfer manual. ....*At first, an empty plot will be displayed in a separate window. To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex and the plot window will be updated accordingly.* But is it possible to enter the desired vertex and get the plot rather than trying to point the mouse to exact vertex and update the plot because it looks like I am not good at pointing mouse to exact vertex I want. Thank you and excuse me for the naive query. Best, Nabin

3 4

mri_vol2surf
by Zhivago 24 Jan '17

24 Jan '17

Hi, I do not have a good understanding of the mri_vol2surf command. 1) Can this only project the part of the volume that lies between the white & pial matter? 2) What is the default projection parameter that it uses? 3) Does projection always start from the white matter, i.e. is 0 the white matter surface? 4) What is the nature of the mgh file that is created by: mri_vol2surf --src mri/spmT_0002.img --regheader s04 --interp nearest --hemi lh --o lh.sig.mgh Thanks, Zhivago...

3 10

FreeSurfer Version 6
by Douglas N Greve 23 Jan '17

23 Jan '17

Dear Freesurfers, At long last, the new version of Freesurfer v6.0 is available for download! For a list of what it contains, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes To download it, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall We are working to set up some mirrors, so it may be slow to download if lots of people try to download at once. And remember our home page is here: http://surfer.nmr.mgh.harvard.edu Our advice concerning your data and different freesurfer versions is the same: do not mix versions when processing a set of subjects in your project. Thank you to everyone who downloaded and tested the beta release of v6.0 and thank you for your patience in regards to this release. The Freesurfer Team -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 1

longitudinal stream v 5.3 - transfer edits of the wm.mgz from cross to base?
by Antonin Skoch 23 Jan '17

23 Jan '17

Dear experts, I am currently starting longitudinal analysis of data I previously corrected in cross-sectional stream (FreeSurfer v5.3). The analysis comprises quite large number of subjects - approx 150 subjects, each scanned twice. All subjects are already inspected and errors corrected in cross-sectional analysis. Some of them needed quite large edits, mainly to the wm.mgz and the whole process took large time. As I read the documentation, the wm.mgz edits in cross are not currently transferred to base. However, wm.mgz has to be correct in base in order to estimate surfaces correctly. From this it implies to me that I would need to edit all wm.mgz errors in base again. Do you think that it could be possible/reasonable to transfer some wm.mgz edits from cross to base, for example to make intersection of edits of all cross timepoints and to transfer it to the base? This could significantly reduce time spent on edits. Does it make sense? Regards, Antonin Skoch

2 1

Stable version of freesurfer 6.0
by miracooloz＠gmail.com 23 Jan '17

23 Jan '17

1 0

?h.pial_lgi does not look right
by Mihaela Stefan 23 Jan '17

23 Jan '17

Hello FreeSurfers, I successfully ran the command recon-all -s <subj> -localGI for one of my subjects. However, the resulted ?h.pial_lgi files don't look right to me. I am attaching a pic for the right hemi (I made sure the overlay is rh.pial_lgi). Can someone help me figure out what went wrong? Thank you! Mihaela

1 0

qdec on LGI data
by André Schmidt 23 Jan '17

23 Jan '17

Dear FS experts I want to perform a 2-sample test on my LGI data using qdec (whole brain analysis with potential covariates). I already ran the recon-all -s my_subject_id -qcache -measure pail_lgi command for each of the subjects and included pial_lgi as measure in the QDEC Design tab. However, it is not clear to me how I need to create the qdec.table.dat file with the output from recon-all -s my_subject_id -qcache -measure pail_lgi. Do I need the lh/rh.pial_lgi.fsaverage.mgh files, and if yes, how can I extract the information from these files? Many thanks for your help! Best wishes André

2 1

Edits to aseg [repost]
by Tamara Tavares 23 Jan '17

23 Jan '17

Hello, After I make edits to my aseg output in the longitudinal stream, do I just run the following command to recreate the final volumes: recon-long -autorecon2-noaseg -subjid <Subj_ID> I assume the -subjid is the name of the edited time point and <Subj_ID> is the name of the recreated volumes? Thank you, Tamara

1 0

Generating intermediate surfaces?
by Souheil Inati 22 Jan '17

22 Jan '17

Hi All, I would like to generate some surfaces a bit below the white surface (in the white matter) and at several locations between the white and pial surfaces. Having trouble finding enough on the wiki - I’m guessing it’s some combination of mris_make_surfaces and mris_inflate? Any help would be greatly appreciated. Thanks, Souheil

2 2

Regarding: Habenula ROI
by Dr Sampada Sinha 22 Jan '17

22 Jan '17

Dear freesurfer experts, Is it possible to create Habenula as region of interest from fsaverage (orig.mgz images) using tkmedit? I will be using following links to guide me for creating Habenular region of interest https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurfe… Thanks for your help. Kind regards, Sampada -- Sampada Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India

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