[Freesurfer] patch for ribbon mgz failure

Hi freesurfer team, I got the same error described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats but I cannot

[Freesurfer] upsampling ?h.curv

Dear Freesurfers, I want to project a map on up-sampled inflated brain. Up-sampled inflated brain has been generated using mris_mesh_subdivide command (without any problem). But when I apply the same command to ?h.cuv I get an error message that: ERROR: MRISread: file 'surf/rh.curv' has many

Re: [Freesurfer] upsampling ?h.curv

try running mris_curvature -w ... On Wed, 30 Aug 2017, sha...@nmr.mgh.harvard.edu wrote: > Dear Freesurfers, >I want to project a map on up-sampled inflated brain. Up-sampled > inflated brain has been generated using mris_mesh_subdivide command > (without any problem). But when I apply th

[Freesurfer] Map of covariance

Hi list,by applying a design e.g. 4GV1 in fsgd I could assess the dependence of group differences taking in account the effect of covariate.Anyway, where I should look if I want assess the the map showing the clusters in which the dependent variable is associated to covariate, tacking in account

[Freesurfer] R: mris_anatomical_stats output

I have more that 5 clusters (from over 100 subjects, 12 different conditions). Manual extraction is impossible!Any suggestions?ThanksStefano Messaggio originale Da: std...@virgilio.it Data: 19-ago-2017 2.38 A: Ogg: [Freesurfer] mris_anatomical_stats output Hi list,how can I

Re: [Freesurfer] upsampling ?h.curv

Hi Bruce, Would you be more specific. The command that you suggested generates ?h.white.K and ?h.white.H. I am trying to generate ?h.curv. > try running > > mris_curvature -w ... > On Wed, 30 Aug 2017, > sha...@nmr.mgh.harvard.edu wrote: > >> Dear Freesurfers, >>I want to project a map o

Re: [Freesurfer] upsampling ?h.curv

?h.curv is just the spatially smoothed ?h.white.H. If you specify -a 10 (average 10 times) it should be pretty close th ?h.curv On Wed, 30 Aug 2017, sha...@nmr.mgh.harvard.edu wrote: > Hi Bruce, >Would you be more specific. The command that you suggested generates > ?h.white.K and ?h.white

[Freesurfer] Freesurfer Preliminary Questions

To whom it may concern, I am to attend the upcoming Freesurfer course session in Boston, and I would like to ask a few preliminary questions. I am currently attempting to run Freesurfer 5.3 on a windows unit via the Oracle VM VirtualBox Manager. I have tried to follow the instructions of the

Re: [Freesurfer] Freesurfer Preliminary Questions

Hi Jason can you elaborate about what you mean by you "cannot interact with the data"? In general, please send us the full command you ran and all its screen output including whatever errros you encountered cheers Bruce On Wed, 30 Aug 2017, Ledesma, Jason wrote: To whom it may concern,

[Freesurfer] Occipital Cortex Segmentation

Hello, I need to get the segmentation of the occipital cortex. I am attempting to generate the corresponding ROI, using the mri_annotation2label command and then running mris_anatomical_stats to merge the labels and get the actual volume. I am calling mri_annotation2label as follows: mri_annota

Re: [Freesurfer] Freesurfer Preliminary Questions

Hi Jason in general it is much easier for us if you can cut and paste text into the email. Pictures are useful for showing things in the data and such cheers Bruce On Wed, 30 Aug 2017, Ledesma, Jason wrote: Hi Bruce, Thank you for your quick response. Attached are photos in number order

Re: [Freesurfer] Freesurfer Preliminary Questions

Hi Bruce, Here is the command that I tried and the resulting output/error message: fsuser@xubuntu-VirtualBox:~$ export TUTORIAL_DATA=C:\tutorial data fsuser@xubuntu-VirtualBox:~$ export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs fsuser@xubuntu-VirtualBox:~$ cd $SUBJECTS_DIR bash:

Re: [Freesurfer] Freesurfer Preliminary Questions

thanks Jason does that directory exist? What happens if you try to ls it? Bruce On Wed, 30 Aug 2017, Ledesma, Jason wrote: Hi Bruce, Here is the command that I tried and the resulting output/error message: fsuser@xubuntu-VirtualBox:~$ export TUTORIAL_DATA=C:\tutorial data fsuser@xubuntu

Re: [Freesurfer] Freesurfer Preliminary Questions

Bruce, It appears that the directory does not exist. See the following: fsuser@xubuntu-VirtualBox:~$ ls C:\tutorial data ls: cannot access C:tutorial: No such file or directory ls: cannot access data: No such file or directory fsuser@xubuntu-VirtualBox:~$ ls tutorial data ls: cannot access tut

[Freesurfer] Software carpentry at the annual meeting of the Society for Neuroscience

Software Carpentry is a non-profit volunteer organization whose members teach researchers computing skills. On November 9th-10th INCF will hold a two-day Software Carpentry workshop at the George Washington University Marvin Center in Washing

[Freesurfer] aparc.DKTatlas+aseg.mgz

Dear experts, looking into the output of Freesurfer in this page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Do I need FLAIR images to get this file. I ran the command recon-all --s subj --all and I can';t find

[Freesurfer] How to estimate the Intracranial area?

Dear FS experts: I'am writting to ask for help about intracranial area. I can find the information of intracranial volume in aseg.stats file. But i did not find the information of intracranial area or is there any way to estimate the intracranial area ? Looking forward to any sugges

Re: [Freesurfer] R: mris_anatomical_stats output

Hi Stefano, never have done this myself, however, have you tried using the -f flag? The helps says this should output the stats to a tablefile. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von std...@virgilio.it Gesendet: Mi