Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

Question
by Aya Kabbara 03 Nov '16

03 Nov '16

Dear FreeSurfer team, First, I would like to thank you for your interesting and very helpful tool. Actually, I'm beginner in using Freesurfer. I have an individual anatomy (.nii) for each subject . After reconstructing the surface using free surfer, I would like to link the surface to the brainnetome atlas. http://atlas.brainnetome.org<http://atlas.brainnetome.org/> [http://www2.clustrmaps.com/stats/maps-no_clusters/atlas.brainnetome.org--th…]<http://atlas.brainnetome.org/> Brainnetome Atlas | Home<http://atlas.brainnetome.org/> atlas.brainnetome.org Brainnetome atlas Brainnetome atlas will be an in vivo map, with more fine-grained functional brain subregions and detailed anatomical and functional connection ... I wonder how can we link automatically the two surfaces using Freesurfer. Thank you for your help. Aya

2 1

Error on rawavg
by Noah Markowitz 03 Nov '16

03 Nov '16

Hi all, As I’m doing manual edits, one of my subjects stops running due to the following error: ERROR: could not read subj1/mri/rawavg.mgz as type 3 Any ideas how to correct this? Please let me know. Noah

2 1

mri_binarize --gm option unknown
by HOSSU Gabriela 02 Nov '16

02 Nov '16

Hello everyone, I am trying to run a mri_binarize command on FS v 5.2, Linux 64bit, but when I use the option -gm (also for -subcort-gm). I am getting an error that says the -gm option is not recognized. Here is the command line and the following error (from the mri folder of a subject): mri_binarize -i aparc+aseg.mgz -gm -o gmmask.mgz I obtain this: ERROR: Option -gm unknown Thanks very much, Gabriela HOSSU

2 1

morphometric stats and global measure of volume
by Muhammad Naveed Iqbal Qureshi 02 Nov '16

02 Nov '16

I want to know which atlas is used by Freesurfer to calculate morphometric stats and global measure of volume. Specifically for the sub-cortical regions. Thank you. Best, Naveed

2 1

Is there any way to measure the volume of substantia nigra and red nucleus via FS?
by nellie 02 Nov '16

02 Nov '16

Hi, FreeSurfer experts, I would like to know is there any command to measure the volume of substantia nigra, red nucleus, and anyother nucleis in brainstem by using FS ? Thanks in advance, Nellie

2 1

Re: [Freesurfer] Segmentation depends on image file format
by LaMontagne, Pamela 01 Nov '16

01 Nov '16

We are preparing a large dataset for sharing. It has already been processed and edited through freesurfer with the dicom files. We would like to share the MR scans in Nifti format instead of dicom, however we are encountering this difference in results. We are using dcm2niix to convert. We would like to stick with this program for conversion and the BIDS package. Any suggestions on how we can use this nifti output and get similar freesurfer results? Thanks Pamela Douglas N Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Thu, 28 Jan 2016 09:35:38 -0800<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> I suspect that it has to do with the image geometry information. In nifit, this is stored in quaterion format. In FS, this is converted to direction cosines. This conversion is not reversible. So when you mri_convert the DICOMS to nii, mri_convert will get the direction cosines from the dicom file and convert them to quaternions. When you run recon-all using the nii file, the quaternions are converted back to direction cosines. But this does not yield exactly the same as what was in the dicom file. This conversion does not happen when you start out with mgz files. In version 6 I changed the code to try to reduce this effect, but I think it will always be there. On 01/28/2016 10:49 AM, Bruce Fischl wrote: > can you run mri_diff on the orig.mgz in the two runs and send us the > output? > On Thu, 28 Jan 2016, Parzer, Peter wrote: > >> mri_convert >> ________________________________________ >> Von: freesurfer-boun...(a)nmr.mgh.harvard.edu >> <freesurfer-boun...(a)nmr.mgh.harvard.edu> im Auftrag von dgw >> <dgwake...(a)gmail.com> >> Gesendet: Donnerstag, 28. Januar 2016 15:55 >> An: Freesurfer support list >> Betreff: Re: [Freesurfer] Segmentation depends on image file format >> >> What software did you use to generate the NIFTI files? Many of the >> converters do different things to the axes of the data, and this does >> affect results. >> >> hth >> d >> >> On Thu, Jan 28, 2016 at 8:49 AM, Parzer, Peter >> <peter.par...(a)med.uni-heidelberg.de> wrote: >>> Hi, >>> >>> we have brain images stored as DICOM and as NIFTI files. For some time we >>> used to import the NIFTI files to freesurfer for segmentation. I was >>> curious if it makes a difference if we would import the DICOM files >>> directly, and was surprised that it actually did. Here are the commands we >>> used: >>> Pamela LaMontagne, PhD Clinical Research Coordinator Washington University School of Medicine Department of Radiology Phone: (314) 362-3487 Voice: (314) 669-4551 ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

White Matter Edits
by Kirkish, Gina 01 Nov '16

01 Nov '16

Hello, I am a staff research associate for a group that specializes in MRI of Multiple Sclerosis. We use freesurfer's reconstruction approach, however the white matter masks are not very good for the MS disease population. We have combined the FreeSurfer algorithm with ANTS in order to get more precise white matter masks – which in theory should improve the surface volumes and aparc+aseg masks. When we have tried putting the ANTS white matter mask into freesurfer and re-running recon-all (recon-all -autorecon2–wm –autorecon3 –w <subID>), the wm_surface and aparc+aseg mask do not seem to follow the white matter surface volume (see attached pictures for an example). How do we insure that the white matter mask is taken into consideration? I know that edits to the white matter mask are done with a value of 255 but the actual white matter volume is 110 – could this be the problem? Let me know if I need to explain anything further. [cid:F06B2C58-32ED-45A4-9FB4-27D90ECFA496][cid:CC736D56-1123-458E-8ADF-D6372F0ACCD9] Thank you, Gina

1 0

Re: [Freesurfer] BBR not recommended for PETSurfer?
by Elijah Mak 01 Nov '16

01 Nov '16

Hi Christopher, We have very positive experiences with mri_coreg too. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47135.html Quite a bit of manual tweaking had to be done along with BBR for our AV and PK BPnd data. It works just fine on the PIB SUVRs though. Then, we switched to mri_coreg and manual tweaking was hardly necessary after that. It truly works wonders :) Best Wishes, Elijah

2 1

tkregister2 + mri_vol2vol do not transform
by Chiara Giacosa 01 Nov '16

01 Nov '16

Dear experts, I am new to freesurfer and I am struggling making transformation of images from one subject to another as well as to a template. I have tried different ways, but I always end up with the original image as if the transformation was never applied. I used tkregister2 from command line and mri_vol2vol. I noticed that the transformation matrices are always the identity matrix in the first 3 columns/rows, no matter what transformation I tell the program to do. I don't think that this makes sense so I wonder if I am doing something wrong or if there might be an issue with the version of tkregister I have. My *commands *are: tkregister2 --mov $subj/mri/orig.mgz --targ my_template/mri/orig.mgz --regheader --reg $subj/reg/orig2templ_tkreg.dat --noedit mri_vol2vol --mov $subj/mri/rh.hand_manual.nii.gz --targ my_template/mri/orig.mgz --o $subj/mri/rh.hand_subj_in_mytempl.mgz --reg $subj/reg/orig2templ_tkreg.dat *Output Matrix *$subj/reg/orig2templ_tkreg.da: subject-unknown 1.000000 1.000000 0.150000 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -1.370635986328125e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 -4.750839233398438e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -1.000000000000000e+00 0 0 0 1 round Contents of my $FREESURFER_HOME/build-stamp.txt file: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Any suggestion will be much appreciated! -- Chiara Giacosa Ph.D. candidate Concordia University

3 6

Re: [Freesurfer] Questions about outputs in Longitudinal Stream
by Tamara Tavares 01 Nov '16

01 Nov '16

Thank you for the clarification Martin I have a follow-up question. When I load the base to make sure it doesn't look blurry, should I check the norm.mgz or brainmask.mgz? Online says norm.mgz but I just want to make sure. Similarly, when I open the base and the longitudinal runs to see whether they align, again should I load the brainmask.mgz for these as well? Thank you in advance for your help, Tamara

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer November 2016