Re: [Freesurfer] LGI data for each region?

2017-02-24 Thread Antonin Skoch
Dear Shane, use this command: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats Look at the info on FreeSurfer wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI Antonin Skoch Hi Freesurfer, How can I get the LGI

[Freesurfer] LGI data for each region?

2017-02-24 Thread Shane Schofield
Hi Freesurfer, How can I get the LGI measurements for each brain region in Desikan atlas? Instead of getting thickness with aparcstats2table, I want the gyrification instead. Thank you. Cheers, Shane --  Shane Schofield___ Freesurfer mailing list

Re: [Freesurfer] Mindboggle official software release and publication!

2017-02-24 Thread Ritobrato Datta
Hi Arno, This is fascinating stuff. In my research, I have come across instances when I felt that a hybrid of ANTS and freesurfer would be very useful. Is this pipeline possible for data processed with the earlier versions of freesurfer say 5.1 ? FS6 just got released in Jan 2017 and I am sure

Re: [Freesurfer] Mindboggle official software release and publication!

2017-02-24 Thread Shane Schofield
Hello, Thanks. Seems very interesting! Is there any way to run this on Mac? Cheers -- Shane Schofield ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] help error RB_ALL_2008-03-26

2017-02-24 Thread Bruce Fischl
Hi Flavia can you send us the reon-all.log and also what version you are trying to run? cheers Bruce On Wed, 22 Feb 2017, Flavia Arduini wrote: > Hi, > I try tu run this code: > recon-all -s CAROFILO -i > /home/matlab/Scrivania/SEGMENTAZIONE/CAROFILO/T2/Phase2/c2scCAROFILO.nii > -autorecon2-wm

Re: [Freesurfer] recon-all error (6.0)

2017-02-24 Thread Bruce Fischl
Hi Trisanna are you sure you aren't running out of disk space? If not, what happens when you run the mri_convert command directly on the command line? cheers Bruce On Thu, 23 Feb 2017, Trisanna Sprung-Much wrote: > Hi All > > I am trying to run a subject in 6.0 (it ran perfectly well in

Re: [Freesurfer] mri_binarize --gm

2017-02-24 Thread Douglas Greve
try making it executable, chmod a+x mri_binarize then run rehash and see if it work On 2/24/17 12:13 AM, Jinsong Tang wrote: Dear all, I am trying to run a mri_binarize command on FS 5.3 mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz I obtain this: ERROR: Option –gm unknown

Re: [Freesurfer] Virtualbox for FS v6.0 ?

2017-02-24 Thread Z K
Based on the subtle issues that arose with previous releases of VirtualBox FS images, it was decided that a better solution was to simply have users install a Linux VirtualBox image themselves (e.g. Ubuntu 16) and let them install the Linux release of FS in that image. This is a much more

Re: [Freesurfer] Mindboggle official software release and publication!

2017-02-24 Thread Olivier Coulon
Thanks to Docker, you can run it on a mac, it's all explained on the Mindboggle website. Olivier Shane Schofield a écrit : Hello, Thanks. Seems very interesting! Is there any way to run this on Mac? Cheers -- Shane Schofield ___ Freesurfer

Re: [Freesurfer] mri_segstats

2017-02-24 Thread Douglas N Greve
That is everything that has a segmentation number = 0. You can exclude it with, --excludeid 0 On 02/24/2017 10:08 AM, John Anderson wrote: > Dear Freesurfer experts, > I have used the following commandline to generate the final statistics > in my analysis: > mri_segstats --seg aseg.mgz

Re: [Freesurfer] Mindboggle official software release and publication!

2017-02-24 Thread Arno Klein
Great question! You can certainly run Mindboggle on FreeSurfer output for earlier versions of FreeSurfer. In fact, we did this for part of the work described in the PLoS Computational Biology article: "For this study we used FreeSurfer v5.1-derived labels and meshes, but the recently released

Re: [Freesurfer] Intensity information of Hippocampal Subfields

2017-02-24 Thread Douglas N Greve
The basic command is mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz where seg is the hippo sub field seg and input is the input where you want to get the intensities from (probably norm.mgz). Note that you need to use the hipp sub field output that is 1mm (not the high

[Freesurfer] XL defect detected

2017-02-24 Thread Shane Schofield
Hi Freesurfer Team, I am running recon-all on Freesurfer version 6. A few of my subjects have “XL defect detected …” and their recon-all have been running for more than 20 hours. I hope this is not a silly question, but will this XL defect be corrected eventually…?  Another question, what are

[Freesurfer] TRACULA and priors problem

2017-02-24 Thread Juergen Haenggi
Dear TRACULA experts I run TRACULA FS 6.0 on a Mac and get the following error: #@# Priors Fri Feb 24 17:11:18 CET 2017 /tmp/subj33.interpreter_control_01/.15208.txt: No such file or directory. In the FS archive I found the following email

Re: [Freesurfer] recon-all error (6.0)

2017-02-24 Thread Trisanna Sprung-Much
Hi Bruce I tried and still get the same error. Would this mean a space issue? I'm not sure how this is possible as I'm working off a 2Tb drive trisanna@kaplan:~$ mri_convert ./tmp.mri_nu_correct.mni.1798/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin

[Freesurfer] make average subject

2017-02-24 Thread Limachia, Gaurang (NIH/NINDS) [F]
Hello Freesurfer Experts, I received this error while running the make_avg_subject script. I would greatly appreciate it if you can point me in the right direction. Also, I do not know how the aparc.annot file is supposed to be created. not aligning hemispheres before averaging. zeroing medial

[Freesurfer] Disastrous Soft Error

2017-02-24 Thread Rockers, Elijah D.
Hello all, I recon-all'd ~40 different subjects. I have been going through all the images to make sure they were processed correctly. Most required no no editing and recon-all did a very good job. But for one scan in particular, it looks like Freesurfer thinks the top of the spinal cord is the

[Freesurfer] Hippocampal Segmentation

2017-02-24 Thread Jessica Sevick
Hello FreeSurfer Team , I was wondering if you could explain to me what the “Left-Hippocampus” and “Right-Hippocampus” labels in the subfield segmentation are? Are they the tail of the hippocampi? Or everything that is not assigned to one of the other seven labels? Additionally I am wondering

Re: [Freesurfer] Disastrous Soft Error

2017-02-24 Thread Rockers, Elijah D.
As far as I can tell, everything looks OK up until brainmask.mgz. The skullstrip step seems to have cropped out the brain and left the neck... On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote: > Hello all, > > I recon-all'd ~40 different subjects. I have been going through all the >

Re: [Freesurfer] Disastrous Soft Error

2017-02-24 Thread Rockers, Elijah D.
OK, sorry for spamming the list. I fixed the the faulty skullstrip by using recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid Currently redoing the surface reconstructions, but it should be OK now. Thanks for the nice documentation. Eli On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers

Re: [Freesurfer] Segmentation question

2017-02-24 Thread Bruce Fischl
HI Yusif you can read our 1999 paper (Anders Dale first author) for the basics, although it has evolved considerably since then cheers Bruce On Thu, 23 Feb 2017, yusif Al-kheder wrote: > Hello, > I was wondering how does Freesurfer segment the white matter from the grey > matter. > > >

[Freesurfer] Intensity information of Hippocampal Subfields

2017-02-24 Thread ali reza mohammadi nejad
Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command? Thank you in advance for

[Freesurfer] mri_segstats

2017-02-24 Thread John Anderson
Dear Freesurfer experts, I have used the following commandline to generate the final statistics in my analysis: mri_segstats --seg aseg.mgz --ctab-default --i suvr.nii --mask mask.nii --sum stats.dat The final output of this command is (attached). Depedning on the anatomical location of the

Re: [Freesurfer] Hippocampal Segmentation

2017-02-24 Thread Iglesias Gonzalez, Eugenio
Hi Jessica, I believe that those are the old labels. What version of FreeSurfer are you using? 5.1 - 5.3? If so, you should upgrade to 6.0. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com