Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

FDR in FS-FAST
by stdp82＠virgilio.it 07 Dec '15

07 Dec '15

Hi list,I have two concerns, please:1) It is possible to apply FDR correction on rs-fMRI seed based analysis by FS-FAST? If yes, I can I do it?2) I have apply the FS guidelines and I have used Montecarlo correction with threshold at 1.3 but in the within group analysis the clusters are very large. In the guide I read examples with a threshold at 3. Is there a specific reason?Thanks Stefano

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Recon-all Bug: Applying Pial Edits with -FLAIRpial Option
by Tori Williams 07 Dec '15

07 Dec '15

Hello, I am running Freesurfer version 5.3.0 with the FLAIR surface refinement bbregister patch installed. I have recently encountered a problem with applying pial edits concurrently with the option of surface adjustment using T2 FLAIR scans during recon-all. After initially running recon-all with the FLAIR option flags: 'recon-all -subjid <subj> -all -FLAIR <flair_scan.mgz> -FLAIRpial' I had tried to apply pial edits without the -FLAIRpial flag on the 2nd recon assuming the adjustments would carry over.: 'recon-all -subjid <subj> -autorecon-pial' This did not work out and the surfaces were worse than before as T2 adjustments were not applied. I then reran the same command adding the -FLAIRpial option: 'recon-all -subjid <subj> -autorecon-pial -FLAIRpial' Although the surfaces were better due to the T2 adjustment and similar to the initial recon, recon-all did not apply any of the pial edits. This was odd because other scans that required control points (with '-autorecon2-cp -autorecon3') or white matter edits (with 'autorecon2-wm -autorecon3') did apply all manual edits, including adjusting the pial surfaces for deleted voxels and refining by the T2 scans. After some detective work looking into the log file and recon-all code, I think I may have found the problem. Turns out, just in the case of pial edits, the ?h.woFLAIR.pial files are not being re-written to reflect the new surfaces correcting for edited voxels following the "Make Pial Surf" step. This is noted in the date stamp of the ?h.woFLAIR.pial files being older than all other surface files following the last recon-all procedure. This is likely because the ?h.pial output files from the "Make Pial Surf" are being overwritten by the "Refine Pial Surfs w/ T2/FLAIR" procedure, instead of being copied over to the ?h.woFLAIR.pial files which are the input to the FLAIR adjustment, and would thus carry on the pial edits. Here is the recon-all code: set nv1=(`mris_info $sdir/${hemi}.pial |& grep nvertices`) set nv2=(`mris_info $sdir/${hemi}.wo${t2flair}.pial |& grep nvertices`) if ( (! -e $sdir/${hemi}.wo${t2flair}.pial) || \ ("$nv1" != "$nv2") ) then set cmd = (cp -v $sdir/${hemi}.pial $sdir/${hemi}.wo${t2flair}.pial) I have attached the log file for one of my subjids that had this issue (Note, the 10/20/15 recon-all is after installing the patch due to the bbregister issues, and the last recon-all on 12/2/15 I tried starting the stream earlier with the -autorecon2-wm flag just to see if that would help). I think it would help to just copy the ?h.pial to ?h.woFLAIR.pial regardless of nvertices being the same. Please let me know if I can provide any more information! Thank you for your time and support! Victoria J. Williams, PhD Postdoctoral Fellow VA Boston Healthcare System Jamaica Plain Neuroimaging Research for Veterans Center (NeRVe) Memory Disorders Research Center 150 South Huntington Ave D11-102 Boston, MA 02130

1 0

Error with mri_nu_correct.mni in recon-all
by 木村一皓 07 Dec '15

07 Dec '15

Hi, I've recently used freesurfer after installing MINC Tool Kit, and got some problem. Seeing the log file, the problem seems to be in mri_nu_correct.mni with the following command. mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz I've attached the log file and error.log when I've done this separately. Before installing MINC Toolkit, I've done the process without problem for sure, so I think MINC-toolkit caused some error.. I found some threads about the error in mri_nu_correct.mni, but I couldn't find the answer. Does somebody has any solution or suggestion for this? Best, Ikko

1 0

including missing gray matter voxels
by Kendrick Kay 04 Dec '15

04 Dec '15

I am trying to figure out how to manually expand the pial surface boundary (generated via automatic segmentation with recon-all) to include additional gray matter voxels which have been erroneously labeled as skull or CBF. i found extensive documentation on how to delete voxels (for example from white matter mask), but i can't seem to find relevant information advising how to manually include some missing gray matter voxels (on either ends of the cortex - i.e. white matter/gray matter boundary or gray matter/pial surface boundary). Any help would be appreciated. -- Kendrick Kay, PhD Assistant Professor Center for Magnetic Resonance Research University of Minnesota, Twin Cities Web: http://cvnlab.net <http://cvnlab.net/> E-mail: kay(a)umn.edu <mailto:kay@umn.edu> Cell: 510-206-1059 Skype: kendrickkay

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How to divide the lateral and medial vertex index of fsaverage4?
by Meiling Li 04 Dec '15

04 Dec '15

Dear Freesurfer Now I have two ROIs on the fsaverage4, one on the lateral and the other is the on the medial, how can i separate apart the two rois? Acutally, how can i divide the vertex index of the lateral and medial on fsaverage4 or fsaverage5? Thanks in advance! Meiling

2 1

bring volumes to fsaverage space
by Shani Ben Amitay 04 Dec '15

04 Dec '15

Dear freesurfers, I would like to know what will be the best way to bring volumes in the individual subject's space to the fsaverage space. Thanks, Shani

4 6

Path Problem
by LIEWALD David 04 Dec '15

04 Dec '15

Environment : Opensuse 13.2 Freesurver Version 6 (Beta) Hi I hope you can help with this problem I'm using the version 6 Beta due to problems with license authentication. Freesurfer runs but bails out with a file not found error : Iteration 1 Fri Dec 4 09:38:57 GMT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc ./tmp.mri_nu_correct.mni.24767/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist! Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 (ec183cc) x86_64 x86_64 x86_64 GNU/Linux on examination of the file structure a directory named "tmp.mri_nu_correct.mni.24767" has been created under the "mri"directory and nothing has been created under the "tmp" directory in the subject root. I am guessing that this is the cause of the error. any advice on correcting this would be extremely useful Dave Liewald The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 5

g-w.pct vs. g-w. ratio
by Andrews, Derek 04 Dec '15

04 Dec '15

>Dear FreeSurfer Support team, > >Thank you for your quick response. > >Is it fair to present both g-w.pct (100*(w-g)/((w+g)/2)) and g-w.ratio >(g/w) as GWR? I have seen the pct calculation presented as GWR in an >abstract that cited Salat (2009) in its introduction text. >Also, is it fair to say that decreases in in g-w.pct indicate less >definition between >the g/w matter boundary as a decrease in g-w.ratio would indicate? If I >want to make a statement about reduced definition between the g/w matter >boundary, what calculation would you suggest? > >Thank you very much for your clarifications on this. > >Best, Derek > > > > >________________________________________ >Derek Sayre Andrews, MSc >PhD Candidate > >The Sackler Institute for Translational Neurodevelopment >Department of Forensic and Neurodevelopmental Sciences >Institute of Psychiatry, Psychology & Neuroscience, King's College London > >Telephone: +44 (0)20 7848 5701 >Email: Derek.Andrews(a)kcl.ac.uk > > > > > >On 03/12/2015 17:26, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > >>g-w.pct is computed as >> >>pct = 100*(w-g)/((w+g)/2) >> >>in the pctsurfcon script >> >> >>On 12/03/2015 12:18 PM, Andrews, Derek wrote: >>> Dear FreeSurfer Support team and Community >>> >>> I am wondering if someone can give me an explanation of the difference >>> between g-w.pct and g:w ratio (as calculated by; fscalc lh.gm.mgh div >>> lh.wm.mgh -o lh.ratio.mgh) >>> Will both these measures essentially measure the relationship between >>> grey and white matter signal intensity but in a different way? >>> >>> >>> Best, Derek >>> >>> >>> >>>------------------------------------------------------------------------ >>> >>> *Derek Sayre Andrews, MSc* >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> >>> Department of Forensic and Neurodevelopmental Sciences >>> >>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: Derek.Andrews(a)kcl.ac.uk >>> >>> >>> >>> >>> _______________________________________________ >>> 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. >> >

1 0

brainstemSsLabels.v10.mgz sub-labels (e.g., brainstem, pons, etc.) not included in mri_convert
by Jonathan Plasencia 03 Dec '15

03 Dec '15

Hello Everyone, I've run the Freesurfer 6.0 and created the sub-brainstem structures (e.g., pons, midbrain, etc.). I would like to convert the brainstemSsLabels.v10.mgz results to a .nii file. However, unlike when I use mri_convert for aseg.mgz, I only get an image of the brainstem itself as a single intensity (or label) and not subparts (or labels for pons, midbrain, etc.). Is there a way to get the labels for all sub-brainstem parts included in the nii writeout, using mri_convert or another function in freesurfer? Best, Jon

1 0

segmentation labels
by Lim, Lena 03 Dec '15

03 Dec '15

Dear Experts, I tried to run the following to get the segmentation volumes but encountered the errors below... How can I get the volumes of the insula and thalamus and also the inferior prefrontal cortex please? [spjwker@nanlnx2 FSL]1% asegstats2table --subjects PAC01... PAC70 --segno 9 48 19 55 --tablefile aseg.vol.table SUBJECTS_DIR : /home/spjwker_PAC/Lena/CT_SA/FSL Parsing the .stats files Building the table.. ERROR: cannot find the corresponding segmentation for the id:19 you provided in any of the .stats files parsed Many thanks, Lena

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Freesurfer December 2015