Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30091 discussions

Re: [Freesurfer] fs-fast processing questions
by Douglas N Greve 21 Mar '13

21 Mar '13

Oh, yes, I was thinking you were starting at 1 not 0. Sorry about that. doug On 03/21/2013 12:45 PM, preciado(a)nmr.mgh.harvard.edu wrote: > So, to clarify I got the number of the acquisitions that I want to exclude > from an fs-fast output file: fmcpr.dat in .../project/session/bold/008/ > > This file starts with scan number 0. So if > Scan 0 is seconds 0, 1, 2 > Scan 1 is seconds 3, 4, 5 > ..... > Shouldn't then; > Scan 134 be 402, 403, 404 > > > -Ronny > > >> Hi Ronny, >> >> On 03/20/2013 05:57 PM, preciado(a)nmr.mgh.harvard.edu wrote: >>> Hello all, >>> I am starting to run some analysis using fs-fast and I had a few basic >>> questions that I couldn't find answers on the wiki/tutorial. >>> >>> 1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat >>> What is the format of the input file for -tpexclude? Is it simply a >>> single >>> column of integers representing the seconds that need to be excluded? My >>> example, my TR is 3 and I know I want to remove acquisitions 134 and 140 >>> because of motion. Do I simply need to have a file that has the >>> following >>> content? >>> 402 >>> 403 >>> 404 >>> 420 >>> 421 >>> 422 >> This is correct, except that time starts at 0. So time point 1 = 0, tp2 >> = 3sec, etc. So tp134 = (134-1)*3 = 399, not 402 >>> >>> 2) bold data - Resampling to "common space" >>> In the preprocessing step, the bold data is resampled to 76x76x93. My >>> data >>> is 96x96x50. Does starting with data that is larger than the "common >>> space" cause a problem in the analysis? >> No >>> 3) Viewing analysis for individual bold data runs >>> When the First level analysis is completed, the resulting files are a >>> combination of all of the bold data runs of the session. Is there a way >>> to >>> make it so that I can also see the different activity for individual >>> runs >>> within the session or does the analysis only do it by combining data for >>> all runs within a session? >> By default it combines all the runs. If you want to see what it looks >> like in each run, there are two things you can do. First, you can run >> selxavg3-sess with the -run-wise option. This causes it analyze each run >> separately. This the easy way. Second, you could recode your stimulus >> numbers to be run specific. This means you have to create a new analysis >> and specify new contrasts. >> doug >>> Thanks in advance! >>> -Ronny >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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 >> 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 >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

mri_info crashing (bits stored vs bits allocated?)
by Ostuni, John (NIH/NINDS) [E] 21 Mar '13

21 Mar '13

We have a data set that mri_info cannot work with. We've tried multiple architectures and freesurfer versions, but mri_info either crashes with segmentation fault or generates errors such as *** glibc detected *** mri_info: free(): invalid pointer: 0x000000000000006b *** One feature of the data set is that the bits stored(12) is different than the bits allocated(16). Could this be the problem? I have an anonymized version of the data set I can upload if that helps. Thanks for any assistance, John

3 3

Talairach General Question
by obregon＠nmr.mgh.harvard.edu 21 Mar '13

21 Mar '13

Hi, I have a rather general, and perhaps even naive, concern regarding the Talairach transform. I've noticed that the coronal and/or horizontal views of the Talairach transform viewed under tkregister2, though generally correctly aligned with respect to the midline of the brain, they tend to have a scaling offset compared to the orig volume, i.e., smaller in size in the XZ and XY planes, respectively. A minor rotation around the x-axis is also generally present in the sagittal view. Considering that everything in both the volume and surface pipelines is affected by the Talairach transform, is it adviseable to manually stretch and rotate the moveable volume so it matches the orig volume as closely as possible, or will this have negligible effects on the surface reconstructions? Thanks, --G

1 0

recon-all errors
by Marcos Martins da Silva 21 Mar '13

21 Mar '13

Hi, freesurfers I am trying to execute the post installation tests as recommended at freesurfers website. Using a CentOS6 Virtual Machine (kernel 2.6.32-358.2.1.el6.x86_64) over Fedora 18 using VirtualBox 4.2.8. Tkmedit, Tksurfer, qdec and freeview all work great. But recon-all tests return errors. Thanks in advance for your help. _______________________________________ recon-all -s bert -autorecon1 running loop to estimate saturation parameter: A or b constain NAN or infinity values!! _______________________________________ recon-all -s bert -all talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log _______________________________________ The log indicated above shows: imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

1 0

Re: [Freesurfer] Tracula bbr errors
by Douglas N Greve 21 Mar '13

21 Mar '13

Hi Salil, I'm posting this to the list since others (i,e Zeke and/or Nick) can better diagnose installation problems. doug On 03/20/2013 05:21 PM, Salil Soman wrote: > Hi Doug, > > Following up on our previous emails, I have been able to get the > entire tracula process to work on our sun grid engine using FLT and > disabling bbr. > > However, if I enable bbr I still get a number of errors, the first of > which appears to be > > mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory > > The log file and a text file with the lines with the word error are > attached. > > Any suggestions on how to address this issue would be greatly appreciated. > > Best wishes, > > Salil > > > On Wed, Mar 13, 2013 at 9:55 PM, Salil Soman <salsoman(a)stanford.edu > <mailto:salsoman@stanford.edu>> wrote: > > Dear Doug, > > Thank you for your email. I apologize for the delay in responding. > At present the file > /mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregister.30396/template.nii > does not exist. > > These are the files in the directory > /mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregister.30396: > > fslregister reg.init.dat.fslregister.log > reg.init.dat.fslregister.log.old > > the 2 files are attached. > > Best wishes, > > Salil > > > > > On Sun, Mar 10, 2013 at 10:17 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hmmm, I think that these failures are happening because it is > looking for an input that does not exist. Does > /mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregister.30396/template.nii > exist? This was in a temporary directory, and it is likely > that it was deleted when the script was run. > > doug > > > > > On 3/8/13 8:43 PM, Salil Soman wrote: >> Dear Doug, >> >> Thank you for your email. >> >> Please find the output attached. >> >> Best wishes, >> >> Salil >> >> >> On Fri, Mar 8, 2013 at 8:47 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> Salil, can you run fslregister with --debug as the first >> option, capture the terminal output, and send it to me? >> thanks >> doug >> >> >> >> On 03/07/2013 09:02 PM, Anastasia Yendiki wrote: >> >> >> Hi Salil - I'm cc-ing Doug who may be able to help. >> The error happens when bbregister invokes >> fslregister, in this particular line of fslregister: >> set refvol = `stem2fname >> $SUBJECTS_DIR/$subjid/mri/$fsvol` >> >> When run on brainmask.mgz, it returns "ERROR: could >> not determine file". >> >> a.y >> >> On Wed, 6 Mar 2013, Salil Soman wrote: >> >> >> Thank you for your email. Changing the mask >> option got me past the error I >> was having initially, but now I get these new errors: >> >> mri_convert ERROR: could not determine file for >> /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis >> >> ter.30396/fslregister/refvol.fslregister.nii >> mri_convert ERROR: could not determine file for >> /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis >> >> ter.30396/fslregister/refvol.fslregister.nii >> >> Thank you for your consideration. >> >> Best wishes, >> >> -S >> >> On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu >> <mailto:ayendiki@nmr.mgh.harvard.edu>> wrote: >> >> Hi Salil - The problem is that you've set dob0 = >> 1 but you haven't set >> b0mlist and b0plist, so it doesn't know where to >> find your field maps to do >> the B0 unwarping. >> >> a.y >> >> >> >> >> >> >> -- >> 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 <tel:617-724-2358> >> Fax: 617-726-7422 <tel: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> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> >> >> 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. >> >> >> ---------- Forwarded message ---------- >> From: *Salil Soman* <salsoman(a)stanford.edu >> <mailto:salsoman@stanford.edu>> >> Date: Fri, Mar 8, 2013 at 11:41 AM >> Subject: fslregister output >> To: salsoman(a)gmail.com <mailto:salsoman@gmail.com> >> >> >> > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

(no subject)
by martina.andellini＠fastwebnet.it 21 Mar '13

21 Mar '13

Hi FreeSurfer experts, I would need to use the registration tools in freesurfer because the fsl ones ga ve me some problem. Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav e three questions: 1) mri_ca_registration generates a talairach tansform file in .m3z format and I would need to apply it to my high res image. Any hint? 2) Converting RB_all_2008-03-26.gca to nii and opening it to mricron it seems to superimposable to the mni atlas. does it mean that what it comes out from mri_c a_registration coincides to an mni atlas image? 3) Running mri_cvs_registration (on bert data...just to try) I do not know where to find the registered volume file (I have tried few volume .mgz but with no su ccess...). Should i look for a transform file too? Thanks so much! Martina

3 2

fs-fast processing questions
by preciado＠nmr.mgh.harvard.edu 21 Mar '13

21 Mar '13

Hello all, I am starting to run some analysis using fs-fast and I had a few basic questions that I couldn't find answers on the wiki/tutorial. 1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat What is the format of the input file for -tpexclude? Is it simply a single column of integers representing the seconds that need to be excluded? My example, my TR is 3 and I know I want to remove acquisitions 134 and 140 because of motion. Do I simply need to have a file that has the following content? 402 403 404 420 421 422 2) bold data - Resampling to "common space" In the preprocessing step, the bold data is resampled to 76x76x93. My data is 96x96x50. Does starting with data that is larger than the "common space" cause a problem in the analysis? 3) Viewing analysis for individual bold data runs When the First level analysis is completed, the resulting files are a combination of all of the bold data runs of the session. Is there a way to make it so that I can also see the different activity for individual runs within the session or does the analysis only do it by combining data for all runs within a session? Thanks in advance! -Ronny

2 1

Job: Research Associate in Cognitive Neuroscience
by Peter J. Molfese 21 Mar '13

21 Mar '13

Job Announcement – March 2013 Research Associate Haskins Laboratories, 300 George Street, Suite 900, New Haven CT 06511 Project Directors: Dr. Kenneth Pugh, Dr. Jay Rueckl Haskins Laboratories is seeking a Research Associate for projects related to Cognitive Neuroscience and Language/Reading Development as part of several recently funded NIH R01 and P01 grants. Responsibilities will include: - Assisting with MRI data acquisition, analysis, and data management - Assisting with recruitment of both child and adult participants - Performing data analysis for ongoing and completed projects - Administering behavioral assessments and assisting with MRI scans Requirements: - BA in Psychology, Cognitive Science, Computer Science or related field - Previous research experience with human populations Additional Desired Skills: - Previous research experience with neuroimaging techniques and data analysis (EEG/ERP, structural and functional MRI, DTI) - Experience with AFNI, FSL, or SPM - Experience with E-PRIME, Presentation, and/or PsychoPy - Strong analytical skills and basic undergraduate statistics - Strong computer skills using Mac OS X and UNIX/Linux - Programming skills (e.g. Python, R, MATLAB, C/C++, JAVA) are highly desirable Interested applicants should contact Dr. Steve Frost (frosts(a)haskins.yale.edu) with cover letter, resume, and three letters of recommendation. This position will remain open until filled; desired start date is on or before June 1, 2013. Compensation is commensurate with skills and experience. Haskins provides a vibrant research and learning environment, and actively supports skill development for all employees. Haskins Laboratories is a private, non-profit research institute with a primary focus on speech, language, reading, and their biological basis. Haskins has long-standing, formal affiliations with the University of Connecticut and Yale University. Haskins Laboratories is an Equal Opportunity Employer.

1 0

3T MPRage flags
by Joshua Lee 21 Mar '13

21 Mar '13

The new Freesurfer has an optional flag to adjust NU intensity correction parameters for images acquired on 3T scanners. There exists also a flag for MPRage sequences. I use 3T MPRages. What is the recommended use in this case? Thanks Josh

4 3

Brainsuite --> FreeSurfer
by Valtina Pouegue 21 Mar '13

21 Mar '13

Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz.That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way. VP

2 6

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