Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

getting vertex-wise correspondences across subjects
by John Griffiths 02 Feb '16

02 Feb '16

Dear surfers, Could you please help me with the following analysis workflow: I am doing an analysis where I identify patterns on the ?h.orig surfaces. What I want to do now is to resample these patterns over vertices, such that I have vertex-wise correspondence across subjects. I believe this essentially requires the construction of and projection to a group template (although I'm aware this could be done with e.g. fsaverage). Here is where I'm at: cd(freesurfer dir) 1. Read ?h.orig surfaces; compute patterns (...some in-house stuff...) 2. Write patterns out to .mgh file Matlab save_mgh(pat,outfile,eye(4)); Python nibabel.MGHImage(pat[:,numpy.newaxis,numpy.newaxis].astype(np.float32),numpy.eye(4)).to_filename(outfile) 3. Generate group template make_average_subject --out avgsub --sd <fs dir> -subjects subj1 subj2 subj3 .... 4. Register a single example subject to the new group template mris_register -curv subj1/surf/lh.sphere avgsub/lh.reg.template.tif subj1/surf/lh.sphere.reg.avgsub 5. Project the surface patterns identified above on to the new group template, so that the vertex values correspond across subjects, and can be averaged, statistically compared. etc. mri_surf2surf --srcsubject subj1 --srcsurfreg sphere.reg.avg_sub --trgsubject avg_sub --trgsurfreg sphere.reg --hemi lh --sval <pattern mgh file> --tval /tmp/test_avgsub.mgh However this breaks down at mri_surf2surf, and I'm not particularly confident that the earlier parts are exactly right either. Could you please show me what commands I should be using for the aims as described above? Many thanks, John -- Dr. John Griffiths Post-Doctoral Research Fellow Rotman Research Institute, Baycrest Toronto, Canada and Honorary Associate School of Physics University of Sydney

1 0

PostDoc at UC San Diego - Epilepsy and Brain Tumor Research {Disarmed}
by Leyden, Kelly 01 Feb '16

01 Feb '16

Hello FreeSurfers, I am writing on behalf of Dr. Carrie McDonald to advertise a Postdoctoral position with our lab at UC San Diego. Location: UCSD Multimodal Imaging Laboratory (MMIL) UCSD Center for Translational Imaging and Precision Medicine (CTIPM) Start date: As soon as possible Seeking a full-time postdoctoral scholar to work with a multidisciplinary team of scientists on projects related to the use of multimodal imaging for improving cognitive and health outcomes in patients with epilepsy and primary brain tumors. Our multimodal imaging team includes full-time faculty from Psychiatry, Radiology, Neurosciences, and Radiation Oncology. This group of researchers and clinical investigators are primarily focused on integrating research imaging tools into the clinical work flow to directly and immediately improve patient outcomes. The scholar will work closely with other postdoctoral fellows, medical residents, graduate students, research assistants, and faculty members to help develop methods, analyze structural, diffusion, and functional (fMRI) imaging data, prepare manuscripts and assist with grant applications. The fellow should have strong programming (i.e., MATLAB) and writing skills, experience in neuroimaging or a related field, and a strong interest in pursuing an academic career path. Applicants with a strong background in bioengineering, cognitive science, and/or experience working with neurological populations are encouraged to apply. For any addition questions or to apply for the position, please send CV and cover letter to Dr. Carrie McDonald (camcdonald(a)ucsd.edu) Thank you, Kelly Neuroimaging Research Associate Multimodal Imaging Laboratory University of California San Diego

1 0

Recon for Rhesus Macaque
by Casas, Rafael (NIH/CC/DRD) [F] 01 Feb '16

01 Feb '16

Hello, I'm wondering what is the first step in reconstruction when working with rhesus macaque. script 01.05 requires files to be in mgh format initially ? I understand that the recon-all scipt is not setp to work with monkey data [cid:image003.jpg@01D15CF6.FFDB5710] Thanks, Rafael

2 3

recon_checker error
by LIEWALD David 01 Feb '16

01 Feb '16

Opensuse 11.4 : Freesurfer 5.3 :QAtools_v1.1 I am trying to generate QC data from data generated using Freesurfer ver 5.3 and I'm getting the following error " Checking if all files exist...PASSED Checking actual file order...FAILED (read ../1006454_20216_2_0/scripts/recon_checker.log) ERROR: Actual file order disagrees with common file order for subject 1006454_20216_2_0" On checking the recon_checker.log it states This subject may have been processed with a different version of FreeSurfer other than the version used to create the common file order file (based on v5.1 by default if not specified by the user). Consider generating an output file order file for your specific dataset using the 'genoutputorderfile' flag. See the '-help' flag for details. I cannot find any details of this flag in any help file or any online help as to how to correct his problem Dave Liewald The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

1 0

Error on Linux
by Ankita Chatterjee 30 Jan '16

30 Jan '16

Hello, I am trying to run freesurfer on a machine I got access to that has Ubuntu (14.04) on it. When I run the tutorials and try to run qdec or freeview, I get this error - qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory I tried running sudo ln -s libjpeg.so.8 libjpeg.so.62, but it says libjpeg.so.62 already exists. Any ideas? I ran tkmedit and tksurfer and those run fine - only freeview and qdec are giving this error. Thanks! Ankita

3 3

Re: [Freesurfer] fast_selxavg3 error when Octave is used
by Douglas N Greve 30 Jan '16

30 Jan '16

Does octave now have a version of textread? I looked over my notes and saw that it did not support it at one point, which I apparently forgot and put it into the code. Can't do much about your space issue On 01/29/2016 11:37 AM, m.abouelyazid(a)gmail.com wrote: > > Okaii, so I fixed that last issue by changing the version of octave > installed then I found I needed to install FSL also. Problem is… now > the virtual machine drive has run out of space… > > Sent from Mail <http://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > *From: *m.abouelyazid(a)gmail.com <mailto:m.abouelyazid@gmail.com> > *Sent: *Friday, January 29, 2016 12:01 PM > *To: *Douglas Greve <mailto:greve@nmr.mgh.harvard.edu> > *Subject: *RE: [Freesurfer] fast_selxavg3 error when Octave is used > > Are there any other paths that I need to add? because now I get > another error > > Extension format = nii.gz > > error: `textread' undefined near line 210 column 17 > > error: evaluating argument list element number 1 > > error: evaluating argument list element number 1 > > error: called from: > > error: /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m at line > 210, column 10 > > error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line > 53, column 9 > > > *From: *Douglas Greve <mailto:greve@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 11:41 AM > *To: *m.abouelyazid(a)gmail.com <mailto:m.abouelyazid@gmail.com>; free > surfer <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used > > yes > > On 1/28/16 9:31 PM, m.abouelyazid(a)gmail.com > <mailto:m.abouelyazid@gmail.com> wrote: > > I am running on the virtual machine where I don’t have MATLAB so I > installed Octave… > > Maybe I should include the folder into the Octave path? > > > *From: *Douglas Greve <mailto:greve@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 11:27 AM > *To: *m.abouelyazid(a)gmail.com <mailto:m.abouelyazid@gmail.com>; > freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used > > Is that directory in your matlab path? does it run properly in matlab? > > On 1/28/16 8:36 PM, m.abouelyazid(a)gmail.com > <mailto:m.abouelyazid@gmail.com> wrote: > > Yes, it exists in the location you mentioned… > > > *From: *Douglas N Greve <mailto:greve@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 2:27 AM > *To: *freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is > used > > Does fast_fileexists.m exist in $FREESURFER_HOME/fsfast/toolbox ? > > On 01/28/2016 07:16 AM, m.abouelyazid(a)gmail.com > <mailto:m.abouelyazid@gmail.com> wrote: > > > > > > Since I am a windows user I got the Virtualbox version of > FreeSurfer > > > and to use fs fast, I installed Octave on the virtual > machine, I set > > > the environment variables and then when I run the command > > > > > > selxavg3-sess -analysis rtopy.lh -sf sessid > > > > > > which runs a retinotopy analysis, I get the following error: > > > > > > sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx > > > > > > sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess > -analysis > > > rtopy.lh -sf sessid > > > > > > error: `fast_fileexists' undefined near line 5 column 4 > > > > > > ------------------------------------------ > > > > > > ERROR: fast_selxavg3() failed\n > > > > > > Any idea of the cause of this error and how to run around? > > > > > > Thank you, > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > > 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 > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > 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 . 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 2

Re: [Freesurfer] tracula quality assessment dwi_motion.txt units
by Ruth Carper 29 Jan '16

29 Jan '16

Anastasia, Thanks for the quick reply.And millimeters for the translation? Ruth

2 1

Wm correction
by maryam koochaki 29 Jan '16

29 Jan '16

Hi Bruce, I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral Ventricle. As you can see in the image attached, the big part is excluded in both hemisphere. I tried to fill it by editing wm volume but the problem still exists.Do you have any suggestion?Thanks,Maryam

2 7

HSF in 5.3
by Alan Francis 29 Jan '16

29 Jan '16

Hi Eugenio: I am trying to run the HSF method on 42 subjects. The FS version on our cluster is 5.3. However when I use the following command I get an error message. [alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields ERROR: Flag -hippocampal-subfields unrecognized. -s Smoke_d004 -hippocampal-subfields Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I tried adding the -hippocampal-subfields-T1 but that did not work too. thanks, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

3 8

mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh
by Erik Lindberg 29 Jan '16

29 Jan '16

Dear Bruce and Freesurfer, Yes, that is what I am saying! This what appears in the commandprompt when running the command: input cache.th13.abs.sig.cluster.mgh frame 0 nErode3d 0 nErode2d 0 output thresholded.mgh Binarizing based on threshold min 1.3 max +infinity binval 1 binvalnot 0 Found 12485 values in range Counting number of voxels Found 12485 voxels in final mask mri_binarize done Yet nothing is visible when I open the thresholded surface in tksurfer. previous: what was the command line and screen output of the binarization? And are you saying that pre-binarization you have locations that are above threshold, but they are set to 0 anyway?

2 1

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