Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Running Recon-all without the skullstrip & neck removal steps
by Toren Stearns 01 Nov '10

01 Nov '10

I'm trying to run recon-all on brains that have already been skullstripped and had their necks removed. I ran autorecon1 without the skullstrip steps. To generate brainmask.mgz I just created a renamed copy of T1.mgz. Is this okay? I'm currently stuck on autorecon2's segstats step. (For autorecon2 I opted out of the neck removal.) At the segstats step I get an error that says that I am missing transforms/talairach_with_skull.lta. talairach_with_skull.lta is created from autorecon1's skullstripping step, but I skipped that step because my brain is already skullstripped. How would I generate this file so that I may proceed with segstats?

1 0

Output dt_recon
by Ed Gronenschild 01 Nov '10

01 Nov '10

Hi, Is it possible to give the exact definition of the output of dt_recon, in particular: - adc - ra - radialdiff - ivc Ed

2 1

Re: [Freesurfer] 3 button mouse for macintosh
by Ed Gronenschild 01 Nov '10

01 Nov '10

Dear Isabelle, In the System Preferences -> Keyboard & Mouse you should select the buttons as follows: left one: primary button, right one: secondary button top on: Button 3 You will now have a 3-button mouse that works fine with FreeeSurfer. Ed > Hello, > > Just getting started with Freesurfer. > I'm hoping someone can recommend a 3-button mouse that works well > with Freesurfer, on a Macintosh. I purchased a Logitech wireless > mouse, but can't get it to work properly. Freesurfer does not seem > to recognize the 2nd and 3rd buttons as any different than the 1st/ > left button. So I cannot get edits to work, for example, when > trying to edit white matter. > > Any tips appreciated. > > -Isabelle > > > --------------------------------------------------------------------- > Isabelle M. Rosso, Ph.D. > Assistant Professor of Psychology > Licensed Psychologist -- Certified Health Service Provider > > McLean Hospital > Neuroimaging Center > 115 Mill Street > Belmont, MA 02478 > Phone: 617.855.2607 > Fax: 617.855.2770 > irosso(a)hms.harvard.edu

1 0

Re: [Freesurfer] subcortical structure coordinates
by Aya Ben Yakov 31 Oct '10

31 Oct '10

Hi I tried running the following process. Convert aseg.mgz back to native space using: mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg_nat.mgz --regheader aseg.mgz Then I loaded the aseg_nat (which, to my understanding, should be in native space) to matlab. Now mri.vol (using MRIread) has data 256X256X176, the same dimensions as the original data However, when I convert to nii, and then to brainvoyager format, there's a rotation (perhaps also distortion, but I couldn't see with the rotation), the dimensions don't match (sagittal appears in coronal etc.). When I try to flip the two 256 dimensions, it doesn't help, which means somehow the 176 dimension and the 256 dimension got flipped in the process. If anyone has an idea how to solve this it would be very helpful. Thanks, Aya __________________________________________________ >From Aya Ben Yakov <ayab(a)mail.weizmann.ac.il> Sent Wed 10/27/2010 3:04 PM To Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Cc freesurfer(a)nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates Hi I'm sorry for all these questions, but I'm very new to freesurfer, and I still don't really understand how things work. Is it necessary to convert to nifti? if I understand correctly, mri.vol should hold the needed information. In what space is this information (assuming some processing was done on the original data)? Can I convert it back to the original data space? or to talairach? The original data includes only 256X256X176, since there were only 176 slices, yet in mri.vol there are 256 slices. In short - how can I convert correctly to the original space and to talairach? Thanks for your help! Aya __________________________________________________ >From Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent Wed 10/27/2010 2:41 PM To Ørjan Bergmann <orjan.bergmann(a)medisin.uio.no> Cc freesurfer(a)nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates yes, and all the volumes have the same index structure, so you can load any of them. The aseg.mgz contains the labeled volume, with the label to structure name conversion in the FreeSurferColorLUT.txt cheers Bruce On Wed, 27 Oct 2010, [UTF-8] Ørjan Bergmann wrote: > I'm also interested in these segmentations for analysis in Matlab. > > In particular, which volumes should be loaded to get the coordinates of the > segmentations? > > I assume the segmentation volumes are just indices (all voxel belonging to > the same segment are assigned the same unique index), correct ? > > --- > Sincerly, > Dr. Ørjan Bergmann > > > > On Wed, Oct 27, 2010 at 14:25, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu (mailto:fischl@nmr.mgh.harvard.edu)>wrote: > >> Hi Aya, >> >> you should be able to convert our segmentations to Nifti, which I assume >> Brainvoyager can read. You can load any of our volumes into matlab with >> either MRIread.m or load_mgh.m and go from there. >> >> cheers >> Bruce >> >> >> On Wed, 27 Oct 2010, Aya Ben Yakov wrote: >> >>> Hi >>> >>> I used FreeSurfer to automatically segment subcortical structures, and I >> would now like to transfer the data to Matlab. I am looking for a way to >> load the coordinates of all structures (or, if it isn't possible, for each >> structure, by its number) to Matlab, in Talairach coordinates. Is this >> possible? If so - how can it be done? >>> >>> I use BrainVoyager, not FSL, for analysis, and I would like to somehow >> use the segmentation from FreeSurfer for analysis in Matlab, in combination >> with data I have from BrainVoyager (the functional data). I don't >> necessarily need talairach coordinates, but otherwise I'm not sure how it >> would be possible to convert between FreeSurfer and BrainVoyager. >>> >>> Any suggestions? >>> Thanks! >>> Aya >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > __________________________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 2

What is FreeSurfer V5.0 doing after -wmparc in -autorecon3
by Guang Zeng 30 Oct '10

30 Oct '10

Hi, there, In FS Ver4.5.0, -wmparc is the last step of -autorecon3. Recently, I tested FS Ver5.0, it looks like -wmparc is not the last step of -autorecon3 now, right? I noticed that it still ran several steps after -wmparc, Anyone can give a brief introduction about the -autorecon3 step of FS Ver 5.0? The ReconAllDevTable (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) at FreeSurfer WIKI still is Ver 4.5. Thanks! Zeng

1 0

Source matrix with zero determinant
by Lisa F. Akiyama 29 Oct '10

29 Oct '10

Hello FreeSurfers, I am trying to run autorecon-1 on data (nifti) downloaded from the NIH MRI Study of Normal Brain Development (Pediatric MRI Study) Repository. However, the command exited with errors mentioning that the source matrix has a zero determinant. I've read past e-mail conversations on this issue, but I did not see any ways of solving this issue. My main goal at the moment is just to perform intensity normalization and skull strip on these data (thus that is why i did not run -notalairach.) When I ran the command listed below on other non-NIH Pediatric MRI data, it performed without any errors. Here is what I ran: > ubuntu:~> *recon-all -autorecon1 -notalairach -s 1433_v1 -i > $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii -force* > INFO: /usr/local/freesurfer/subjects/1433_v1 exists with -i, but -force > specified. > Deleting any previous source volumes > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > Actual FREESURFER_HOME /usr/local/freesurfer > -rw-rw-r-- 1 todd todd 17815 Oct 28 12:00 > /usr/local/freesurfer/subjects/1433_v1/scripts/recon-all.log > Linux neptune-ubuntu 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 > UTC 2010 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/1433_v1 > > mri_convert > /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii > /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz > > mri_convert > /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii > /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz > INFO: using NIfTI-1 qform > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from > /usr/local/freesurfer/subjects/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, -1, 0) > k_ras = (-0, -0, 1) > writing to /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz... > #-------------------------------------------- > #@# MotionCor Thu Oct 28 12:01:59 PDT 2010 > Found 1 runs > /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz > WARNING: only one run found. This is OK, but motion > correction cannot be performed on one run, so I'll > copy the run to rawavg and continue. > > cp /usr/local/freesurfer/subjects/1433_v1/mri/orig/001.mgz > /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz > > /usr/local/freesurfer/subjects/1433_v1 > > mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz > /usr/local/freesurfer/subjects/1433_v1/mri/orig.mgz --conform > > mri_convert /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz > /usr/local/freesurfer/subjects/1433_v1/mri/orig.mgz --conform > *MRIresample(): source matrix has zero determinant; matrix is:* > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from /usr/local/freesurfer/subjects/1433_v1/mri/rawavg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, -1, 0) > k_ras = (-0, -0, 1) > Original Data has (0.976562, 0.976562, 0) mm size and (256, 256, 1) voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > 0.977 0.000 -0.000 -136.512; > 0.000 -0.977 -0.000 133.512; > 0.000 0.000 0.000 -73.100; > 0.000 0.000 0.000 1.000; > Linux neptune-ubuntu 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 > UTC 2010 x86_64 GNU/Linux > > recon-all -s 1433_v1 exited with ERRORS at Thu Oct 28 12:02:02 PDT 2010 > When I tried to open 001.mgz in tkmedit, as imagined, an error appeared as well: > ubuntu:~> tkmedit 1433_v1 001.mgz > mghRead(/usr/local/freesurfer/subjects//1433_v1/mri/001.mgz, -1): could not > open file > > > Error: Loading volume 001.mgz > > Couldn't read the anatomical volume. > > Tkmedit couldn't read the volume you specified. > This could be because the image format wasn't recognized, > or it couldn't find the proper header, > or the file(s) were unreadable, > or it was the wrong size. > Any help would be greatly appreciated. Thank you in advance. Best, Lisa Akiyama ____________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington

2 6

3 button mouse for macintosh
by Rosso, Isabelle M. 29 Oct '10

29 Oct '10

Hello, Just getting started with Freesurfer. I'm hoping someone can recommend a 3-button mouse that works well with Freesurfer, on a Macintosh. I purchased a Logitech wireless mouse, but can't get it to work properly. Freesurfer does not seem to recognize the 2nd and 3rd buttons as any different than the 1st/left button. So I cannot get edits to work, for example, when trying to edit white matter. Any tips appreciated. -Isabelle --------------------------------------------------------------------- Isabelle M. Rosso, Ph.D. Assistant Professor of Psychology Licensed Psychologist -- Certified Health Service Provider McLean Hospital Neuroimaging Center 115 Mill Street Belmont, MA 02478 Phone: 617.855.2607 Fax: 617.855.2770 irosso(a)hms.harvard.edu ---------------------------------------------------------------------

2 1

How to save a new label after cutting an existing label?
by 李瑾 28 Oct '10

28 Oct '10

Hi freesurfers, I'm trying to generate a new label, from cutting an existed label. The process was shown as attached, First I load a label on fsaverage, lh.inflated, then cut the label along the yellow line and keep the needed part by "cut plane". Now I hope to save the remained label shown in blue in the right pic, into a new label, and use it as my ROI. I tried many methods but they didn't work. Any help would be greatly appreciated. Thank you in advance.

2 1

[Fwd: scientific programmer position with us]
by Douglas N Greve 28 Oct '10

28 Oct '10

Anyone interested should send email to Richard Baumgartner at richard_baumgartner(a)merck.com -------- Original Message -------- Hi Doug, we are urgently looking for a contractor position with us. The person should have good programming skills and some understanding of statistics. He/she will work with imaging, so some imaging experience would be welcome. If you know of someone who might be interested please let me know. Thanks, Richard. Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

Re: [Freesurfer] Make functional ROI's from clusters
by Douglas N Greve 28 Oct '10

28 Oct '10

If the labels and data are surface, you can use the --slabel feature. doug Alice Albrecht wrote: > Thanks Doug, > > I have successfully made the labels, but now I want to use those > labels on other data as ROIs and that is where I am having trouble > using the mri_segstats function. I don't see where I can load in my > labels. > > -Alice > > On Thu, Oct 28, 2010 at 2:20 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > As Allison says, you can use the tools listed below. > Alternatively, there is an easier way to do it in tksurfer. > > 1. Click on cluster you want to convert into a label. > 2. Click on the "Custom Fill" button (little paint bucket pouring > into a blue blob). This will popup a window > 3. Click on the "Up to functional values below threshold" box, > then "Fill". The cluster will temporarily turn white, then it will > have a yellow border. You have just created a "label". > 4. Save this label using the File menu. > > doug > > > Allison Stevens wrote: > > Alice, > You might find this tutorial helpful: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividu… > > and mri_volcluster or mri_surfcluster > > Allison > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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