Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

mri_coreg !
by Elijah Mak 16 May '16

16 May '16

Hi Doug, I just want to say that mri_coreg worked tremendously well for the registration of some very blurry PET-PK data. I was not getting any success with bbregister and init-fsl or mri_robust_register options. How does this technique differ from the boundary-based registration? Thanks a lot. Best Wishes, Elijah

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Longitudinal analysis: creat cluster ROI and extract baseline and followup values
by Liu Y 16 May '16

16 May '16

Hi Freesurfers, I am using the degree of cortical atrophy between two groups. The atrophy rate had no significant difference between two groups, but the average thickness of the baseline and followup showed significant clusters in two regions between the two groups. My question is how to create the ROIs covering the clusters, and then extract the thicknesses on baseline and followup MRIs? Thanks, Yawu

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ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 16 May '16

16 May '16

Hi freesurfer experts, I have recently begun to use freesurfer to do structural MRI analyses. I have been able to successfully process about 40 structural scans with recon-all thus far, but starting a few days ago, I started getting this error whenever I run recon-all: WARNING: file /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 CDT 2016 Here are a few of the troubleshooting steps I’ve tried to track down the cause of the error: - - Re-run recon-all with a couple of scans from my dataset that I have already successfully processed - - Re-run recon-all the same datasets but on a different computer - - Re-convert the scans from .ima files to dicoms in osirix, then run recon-all For all of these steps, I have gotten the exact same error message. The files should be anonymized, since I used osirix’s “anonymize and convert” function to generate the dicom files (the scans were given to me as .ima files). Any suggestions on what to try next? Thank you! Joseph Aloi The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Freesurfer program for 7 Tesla
by konasale prasad 16 May '16

16 May '16

Dear FSL experts, We are trying to run freesurfer volume measurements, primarily subcortical regions along with cortical surface area and thickness. We are also interested in hippocampal subfields and shape analysis. I was wondering whether the program would be reliable compared to 3T (that we have done quite a few). Are there any known problems? If there are, please let me know the work arounds. Thanks,

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reference for using T2 to improve pial surface
by Ritobrato Datta 16 May '16

16 May '16

Hi All, Can someone point to a reference which shows the advantage of using T2 alongside T1 to improve the gray - pial boundary ? Thank you, Ri

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V1 Atlas ( brodman maps)
by John Anderson 14 May '16

14 May '16

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visualization tk surfer
by maaike rive 14 May '16

14 May '16

Dear Freesurfer experts, I have a question regarding tk surfer. If I load the cache.h13.abs.sig.cluster.mgh file, I'll only see the clusters surviving the statistical threshold I set, don't I? (e.g. I set the cluster finding threshold at 0.05 (Monte carlo simulation), keeping all clusters with p<0.001, which gives me for example one cluster; it's only this cluster that will be visualized, right?) I ask this because sometimes only a few clusters are kept, but I see a lot of the brain coloured in tk surfer, presumably because the clusters are very large. Thanks, Maaike

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R: Re: mri_surf2vol
by stdp82＠virgilio.it 14 May '16

14 May '16

Thanks. I'm reading the surf2surf help but I do not understand the --trgsurfreg options. I'using mri_surf2surf --hemi rh --srcsubject fsaverage --srcsurfval thickness -- src_type curv --trgsubject Control21 --trgsurfval file?? Which is the file? Thanks Stefano >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 14-mag-2016 0.06 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] mri_surf2vol > >The overlay Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz is >in fsaverage space, so either change the subject to fsaverage, or use >mri_surf2surf to map the overlay into Control21's space, then run >mri_surf2vol > > >On 05/13/2016 06:03 PM, stdp82(a)virgilio.it wrote: >> Hi list, >> >> I'm using FS-FAST for seed based functional connectivity. >> For a subject, I would like to report the sig.nii.gz from the inflate >> to volume space. >> >> I'm using >> >> mri_surf2vol --surfval >> Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz --hemi rh >> --fillribbon --subject Control21 --identity Control21 --template >> Control21/orig.mgz --o ramg2rh_sig_volspace.nii.gz >> >> but this error reported below was obtained. >> >> ERROR: dimension inconsistency in source data >> >> Number of surface vertices = 123044 >> >> Number of value vertices = 163842 >> >> >> Thanks >> >> >> >> Stefano >> >> >> >> _______________________________________________ >> 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: 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/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)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. > >

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postdoc at UCSF
by Bruce Fischl 13 May '16

13 May '16

The Neuroradiology Section and Memory and Aging Center (MAC) at the University of California, San Francisco (UCSF) are seeking an exceptional postdoctoral candidate in imaging genetics of neurodegenerative disorders. Using a variety of techniques, ranging from human structural and functional MRI to whole genome sequencing, our research involves elucidating the genetic, neuroanatomic, and molecular characteristics of Alzheimer's disease, frontotemporal lobar degeneration, Parkinson's disease and neuroinflammation. We seek a postdoctoral candidate with a strong background in genetics (and preferably, human imaging) and a desire to use a multi-disciplinary approach to pursue neurodegenerative research. The candidate should have considerable experience with Matlab, R, PLINK and potentially, MRI image analysis tools such as Freesurfer, FSL and SPM. Applicants should have a Ph.D. or M.D. degree with less than five years of postdoctoral experience. Highly motivated individuals with a record of productive research are encouraged to apply. The position is available starting July 1, 2016. Salary is commensurate with qualifications and experience. Interested applicants should send curriculum vitae/NIH biosketch, and three references to: Drs. Rahul Desikan (rahuldesikan(a)gmail.com) and Jennifer Yokoyama (jennifer.yokoyama(a)ucsf.edu)

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WmParc
by Caroline Beelen 13 May '16

13 May '16

Dear FS team, We want to create a ROI based on the wm parcellation in the 2009s atlas. We ran the following command: mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz (<subjid> was replaced by our subject) We get the following error: option --ribbon unknown. The ribbon.mgz folders exist and are located in the right directory. We also tried to re-create them and this worked fine, but again after running the command above we got the same error. If we changed the command --ribbon to -- no ribbon, the script ran, but when we looked at the stats-file, only cortical grey matter labels were segmented (no wm). The same applies to other subjects we tried. Could you please help us out? Many thanks. Jolijn & Caroline

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