Re: [Freesurfer] Brainstem Substructures in Freesurfer 6.0 - how to calculate left/right volumes

Hi Chris, at this point, the software does not split the SCP into its left and right parts. But, you definitely gave me something to think about. When I have the time, I'll try to work on this and release a patch. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeig

[Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

Dear FS experts, 1) First Is it possible to use the partial volume correction provided in the v6 beta version of FreeSurfer despite the fact that recon-all have been done for all subjects with the v5.3 ? 2) Does this method supply an intensity normalisation for PET images ? Best regards, Matthie

[Freesurfer] Qdec question

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks_

Re: [Freesurfer] FreeSurfer 6 recon-all exiting with errors at -cortparc step

Hi Bruce, I re-ran the -cortparc step with the current dev version freesurfer-Linux-centos6_x86_64-dev-20151209 It took ~6 hours and the error is still the same. It seems to run through the left hemisphere, but crashes on the right one. Cheers! Natalia On 09 Dec 2015, at 14:37, Bruce Fischl m

[Freesurfer] summary files and figures from Monte Carlo simulation

Dear Experts, After running Monte Carlo simulation from the command line, I noticed two cluster summary files are produced for each contrast: cache.th20.neg.sig.cluster.summary and mc-z.neg.th20.sig.cluster.summary. They are quite similar, with different number of surviving clusters in some ca

Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011

Hi Professor Yeo, Thanks for providing a link to your split region MNI space files. Could you please advise on how to get these labels into subject native space? If using the standard version of the network labels that comes packaged with Freesurfer 5.3.0, I can get the annotation file into nat

Re: [Freesurfer] Recon-all get stucked without error during processing

Hi Bruce, Do you have an idea of how to solve this problem of skull stripping (below) ? Best regards, Matthieu 2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte : > Hi Bruce, > > In fact T1.mgz is ok, but the skull stripping failed and seemed to have > taken only the jawbone and the neck. > > Best

[Freesurfer] Shifted surface after gyrification index is calculated

Hey Freesurfer folks - I'm looking into using Freesurfer for doing electrode reconstruction / co-registration in electrocorticography. We're making good progress on figuring out recon-all for surfaces and doing co-registration to CTs. However, I think I've encountered a strange bug. I'm trying to

[Freesurfer] Errors when testing freesurfer installation

Dear freesurfer experts, I am new to freesurfer and I met this problem when I was testing freesurfer installation following the instructions on the 'Testing Freesurfer' website. I got the problems as follows when I tested command, 'tkmedit bert orig.mgz' on heavy data from tutorial web. Couldn't

Re: [Freesurfer] Shifted surface after gyrification index is calculated

Hi Chris how do you smooth the surface? Are you sure that you retain the surface header information? Try looking at the header with mris_info before and after smoothing cheers Bruce On Thu, 10 Dec 2015, Chris Holdgraf wrote: > Hey Freesurfer folks - I'm looking into using Freesurfer for doing

[Freesurfer] Freesurfer 6 exits with errors after recon edits on skullstrip

Dear Freesurfer experts, I ran recon-all on launchpad using /usr/local/freesurfer/stable6/bin/recon-all. This command worked nicely, but part of the occipital cortex was missing and I therefore ran the following command ( both in freesurfer6 ): recon-all -skullstrip -wsthresh 35 -clean-bm -no

Re: [Freesurfer] Shifted surface after gyrification index is calculated

Hey Bruce - thus far I have used pretty default parameters. I first ran recon-all on each subject, then simply ran `recon-all -s s_name -localGI`. Here are the transforms for the original vs. inflated surface On lh.pial: talairch.xfm: 1.103 0.015 -0.002 4.202; -0.032 1.064 0.063 -19.65

[Freesurfer] mri_label2vol --fill-ribbon argument

Dear Freesurfer's expert, I want to create a 3d volume using an annot file and I'm using mri_label2vol command. When running this command line: mri_label2vol --annot sub1/label/lh.Yeo2011_7Networks_N1000.annot --identity --subject sub1 --hemi lh --o sub1/mri/lh.Yeo.nii.gz --temp sub1/mri/T1.mgz

[Freesurfer] ABCD postdoctoral position at Florida International University

Dear Colleagues, Please find below an advertisement for our Postdoctoral position at Florida International University, Miami, FL. Details are also provided in the attached pdf. Thank you! Anthony >>> The Cognitive Neuroscience and Imaging Center at Florida International University (FIU) in

Re: [Freesurfer] Freesurfer 6 exits with errors after recon edits on skullstrip

Hi Lauri I think you forgot to attach the logs Bruce On Thu, 10 Dec 2015, Tuominen, Lauri Johannes wrote: Dear Freesurfer experts, I ran recon-all on launchpad using /usr/local/freesurfer/stable6/bin/recon-all. This command worked nicely, but part of the occipital cortex was missing and I t

Re: [Freesurfer] Shifted surface after gyrification index is calculated

and how do you determine they are shifted? In freeview? The surface geometry/position should be preserved in the smoothing but appears to not to be. Perhaps Marie can comment? Or you can try mris_copy_header to see if that does the trick cheers Bruce On Thu, 10 Dec 2015, Chris Holdgraf wrot

Re: [Freesurfer] Shifted surface after gyrification index is calculated

Yep - sorry, here's a pic: https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9e89-11e5-8485-dc97c8ca2ca7.png You can see the smoothed version is shifted lower. I couldn't find mris_copy_header on my path. Is it only included in the beta version? I'm running 5.3. Could try beta

[Freesurfer] reg-feat2anat error ("mri_convert ERROR: could not determine file")

Hello, I am having a similar problem to that posted several times previously. I get an error when running reg-feat2anat to register FSL feat files to the freesurfer reconstruction, see: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038437.html because the subjectsfeatfolder

Re: [Freesurfer] Shifted surface after gyrification index is calculated

what hardware are you running on? We can send you a version of mris_copy_header. Or you can can send me the two surfaces (before and after smoothing) and I can see if it fixes the problem cheers Bruce On Thu, 10 Dec 2015, Chris Holdgraf wrote: Yep - sorry, here's apic:  https://cloud.github

Re: [Freesurfer] Shifted surface after gyrification index is calculated

It's a cluster running Linux CentOS 64-bit. If it's as simple as getting the file and adding it to my path I'm happy to give it a try... Chris On Thu, Dec 10, 2015 at 1:47 PM, Bruce Fischl wrote: > what hardware are you running on? We can send you a version of > mris_copy_header. Or you can can

[Freesurfer] Gray matter intensity

Hello, I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. And have successfully gotten the wm-gm signal intensity contrast, but

[Freesurfer] Freeview PETSC Error

Hi, I downloaded and installed Freesurfer stable release 5.3 distribution linux_centos4_x86_64 on an Ubuntu 12.04 system. However freeview crashes with a PETSC error. I read the freesurfer archives and followed the instructions found on https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/201

[Freesurfer] Question about running recon-all with deface

Hello, We are currently in the process of analyzing some data that was defaced using mri_deface command of freesurfer. This defaced data was then used as an input to recon-all and the volume and thickness was computed. These results were then compared against the same subject's recon-all with t