Re: [Freesurfer] Creating functional ROI

Thank you, Doug. This worked. Now I have two questions: 1- Is it possible for a given threshold in funcroi-config to have let say 15 voxels on the surface but zero voxels in the volume? When I load the .sig map, I can see activation for a given threshold on the volume but when I run the

Re: [Freesurfer] freesurfer version update issue in MacOS

Hi Joonyoung. I'll leave this for Eugenio, but I think the answer is yes cheers Bruce On Tue, 12 Dec 2017, 강준영 wrote: Hi Bruce! Thank you for your fast and kind answer. I have one more detailed question that I forgot to ask.. The main reason I want to update freesurfer is to use better

Re: [Freesurfer] freesurfer version update issue in MacOS

Hi Bruce! Thank you for your fast and kind answer. I have one more detailed question that I forgot to ask.. The main reason I want to update freesurfer is to use better hippocampal subfield and I want to make the subfield based on my previous data (in the older version freesurfer path) I

Re: [Freesurfer] freesurfer version update issue in MacOS

Hi Joonyoung you can just install the new version in a new location and point your path at it instead of the older version. cheers Bruce On Tue, 12 Dec 2017, 강준영 wrote: Hello! I'm Joonyoung Kang, a graduate student in neuroscience. I've been using freesurfer over an year and I realized

[Freesurfer] freesurfer version update issue in MacOS

Hello! I'm Joonyoung Kang, a graduate student in neuroscience. I've been using freesurfer over an year and I realized that I've used an old version of it. So I decided to update freesurfer and I couldn't find a way to do that. Do I just have to re-install the new version of freesurfer? If so,

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9 cheers Bruce On Mon, 11 Dec 2017, Loeffler, Martin wrote: Dear

[Freesurfer] CORRECTING DEFECT recon-all giant cyst

Dear FreeSurfer team, For a case report I'm running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message): CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849) XL defect detected... It is stuck here since a whole day

Re: [Freesurfer] Global Signal Scaling in FSFAST Pipeline

Never mind, found the answer online, sorry about that! On Mon, Dec 11, 2017 at 2:13 PM, Taylor, Johnmark < johnmarktay...@g.harvard.edu> wrote: > Hello, > > When using preproc-sess and selxavg3-sess, how is global mean scaling > handled? Is the session-wide (4D) mean subtracted, is each volume's

Re: [Freesurfer] power analysis

For the power analysis, you need 3 or 4 things: 1. effect size (mean/std) 2. false positive rate (usually .05) 3. Number of subjects (or design matrix and contrast) 4. true positive rate (usually .8) Given any 3, you can compute the 4th. For the FS output, #1 should be gamma.mgh/rstd.mgh

Re: [Freesurfer] Global Signal Scaling in FSFAST Pipeline

The entire 4D volume is rescaled by the 4D mean. On 12/11/17 2:13 PM, Taylor, Johnmark wrote: Hello, When using preproc-sess and selxavg3-sess, how is global mean scaling handled? Is the session-wide (4D) mean subtracted, is each volume's mean subtracted, or neither? Thank you very much,

Re: [Freesurfer] Reset view command in freeview

Hi Anna, -viewport option is only to set your main view. So in your case, you should always use '3d'. There is no direct command-line option to set 3D view to a specific orientation. But it can be achieved with -cam option. You can run freeview -h and take a look at the description on how to

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, Sorry for the delay, I’ve uploaded the fix to https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface. If you copy this new version of make_average_surface to $FREESURFER_HOME/bin, this should hopefully solve the problem. Let me know if these

[Freesurfer] Reset view command in freeview

Hi all, I’m wondering whether there's a command-line equivalent to the the Reset View tool found in the Freeview GUI when you right-click a volume in 3d view. I tried using the -viewport tag (e.g. freeview -v myvolume.nii.gz -viewport coronal), but the problems with this are: (1) Though the

[Freesurfer] Global Signal Scaling in FSFAST Pipeline

Hello, When using preproc-sess and selxavg3-sess, how is global mean scaling handled? Is the session-wide (4D) mean subtracted, is each volume's mean subtracted, or neither? Thank you very much, JohnMark ___ Freesurfer mailing list

[Freesurfer] power analysis

Dear Freesurfer exerts, I read sentences similar to this one in multiple publications (e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500581/) "Power analyses were carried out using vertex-wise variance estimates from the coregistered cortical thickness maps, systematically varying

[Freesurfer] Postdoc position available at Martinos Center

Hi, I am looking for talented postdoc fellows. Please see below for details: Applications are invited for a postdoctoral research fellow position at Hesheng Liu Lab (http://nmr.mgh.harvard.edu/bid/Home.html), Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard

[Freesurfer] ?h.pial_avg in make_average_subject in FS6.0

Dear Doug Greve, Where can I find the rh/lh.pial_avg file in fsaverage/surf/ created in freesurfer 6.0? Is this file named differently in FS 6.0 or do I need to process this step (where it makes rh or lh.pial_avg) separetely? Thanks, Tugce Duran ___

[Freesurfer] Job posting: NeuroImaging Research Associate Department of Child and Adolescent Psychiatry Hassenfeld Children’s Hospital at NYU Langone {Disarmed}

[cid:B8DEC9D7-21A7-46E6-9E54-E04F15EBF0CE] NeuroImaging Research Associate Department of Child and Adolescent Psychiatry Hassenfeld Children’s Hospital at NYU Langone Dr. Adriana Di Martino at the Department of Child and Adolescent Psychiatry, Hassenfeld Children’s Hospital at NYU Langone