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30132 discussions

Re: [Freesurfer] Petsurfer mri_gtmpvc error
by Agrawal, Shubhi (NIH/NINDS) [E] 29 Mar '17

29 Mar '17

Thanks for the response. I ran the command again with FWHM 6, but am getting a 'MatrixAlloc(23680000,100): allocation failed' error. mri_gtmpvc --i OutBrick_run_008.nii --reg template.reg.lta --psf 6 --seg gtmseg.mgz --default-seg-merge --o gtmpvc.output This is the output log file- $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects cd /home/agrawals8/freesurfer/subjects/NIH047 mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta --psf 6 --seg mri/gtmseg.mgz --default-seg-merge --o gtmpvc.output sysname Linux hostname ndsw-eeg-dreifuss.ninds.nih.gov machine x86_64 user agrawals8 vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Loading seg for gtm mri/gtmseg.mgz Loading ctab mri/gtmseg.ctab Reading mri/gtmseg.lta Data load time 24.9 sec nmask = 23680000, nsegs = 100, excluding segid=0 FWHM: 6 6 6 Std: 2.54797 2.54797 2.54797 nPad 13, PadThresh 0.0001 Segmentations used for rescaling 174 Pons MEM: Size 479268 Peak: 956464 RSS: 339992 Data: 338176 Stk: 92 MEM: Size 10095992 Peak: 10095992 RSS: 969132 Data: 9954900 Stk: 92 MEM: Size 10189788 Peak: 10190808 RSS: 1062848 Data: 10048696 Stk: 92 System specs for this computer- CentOS 6.7, 7 Processors- Intel Xeon CPU @2.2GHZ, Memory 11GB, Available disk space 419 GB. Regards Shubhi ________________________________________ From: freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Thursday, March 23, 2017 10:08 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 157, Issue 61 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Petsurfer mri_gtmpvc error (Douglas Greve) 2. Re: contrast between two independent CTh maps? (Uquillas, Federico D'Oleire) 3. Re: A Bug in Monte-Carlo Simulation. (Douglas Greve) 4. Re: Qdec 1.5 (Douglas Greve) 5. Re: Fw: PETsurfer surface based analysis (miracooloz(a)gmail.com) 6. Re: LME mass univariate model (Bronwyn Overs) 7. Re: Qdec 1.5 (Duy Nguyen) 8. Correcting Skull-Strip Errors - Watershed Algorithm Question (Abhinav Kurada) 9. Petsc Error in Freesurfer v6.0 (Michael ONeill) 10. Re: Thickness asymmetry and LH/RH corresponding vertices in fsaverage (Dorian P.) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Mar 2017 17:11:49 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Petsurfer mri_gtmpvc error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <7422f5df-b0e5-587b-d71c-7dd2cc14aba3(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" FWHM should be the impulse response FWHM for your scanner. This is a number (eg, the HR+ is about 6), not the string 'FWHM' On 3/22/17 4:16 PM, Agrawal, Shubhi (NIH/NINDS) [E] wrote: > Hi, > I am trying to run SGTM partial volume correction in Petsurfer by > following the tutorial on the wiki. Every step preceding mri_gtmpvc > has been successful and the coregistration looks good. > the last step, mri_gtmpvc command gives an error- > Segmentation fault (core dumped) > > This is the information from the log file- > > $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ > setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects > cd /home/agrawals8/freesurfer/subjects/NIH047 > mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta > --psf 6 --seg mri/gtmseg.mgz --default-seg-merge --auto-mask FWHM .01 > --o gtmpvc.output > sysname Linux > hostname ndsw-eeg-dreifuss.ninds.nih.gov > machine x86_64 > user agrawals8 > vgthresh 0.001000 > nReplace 18 > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > Loading seg for gtm mri/gtmseg.mgz > Loading ctab mri/gtmseg.ctab > Reading mri/gtmseg.lta > MEM: Size 479268 Peak: 955936 RSS: 339984 Data: 338176 Stk: 92 > MEM: Size 570956 Peak: 955936 RSS: 431688 Data: 429864 Stk: 92 > Data load time 25.9 sec > nmask = 2680458, nsegs = 100, excluding segid=0 > FWHM: 6 6 6 > Std: 2.54797 2.54797 2.54797 > nPad 13, PadThresh 0.0001 > Segmentations used for rescaling > 174 Pons > MEM: Size 422356 Peak: 955936 RSS: 283024 Data: 281264 Stk: 92 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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seed to seed resting state?
by Corinna Bauer 29 Mar '17

29 Mar '17

Hi all, I was just wondering if it was possible to do seed to seed resting state analysis in freesurfer, rather than seed to voxel? I am wanting to examine connectivity within specific Yeo networks, using a spherical ROI as a seed. The spherical ROI will be generated from one of the peak areas of activation listed in the original 7 network Yeo paper. Thanks Corinna

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TRACULA - subjects with different number of directions
by Rizvi, Batool 29 Mar '17

29 Mar '17

Hi, We were wondering if it would be an issue if we used a dataset in which we included 5 subjects that have a different number of directions (49 directions) than the rest of the subjects with a standard number (16 directions). Even if the preprocessing steps work, will it be an issue comparing the subjects statistically? If so, how can we treat the 5 subjects differently, but still include them in our study? Thank you! Batool

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correlation between cortical thickness and cognitive measure
by Liu Y 29 Mar '17

29 Mar '17

Dear Experts, Is there any instruction to analyze correlation between cortical thickness and cognitive measure? Thanks, Yawu

2 2

pial problem and g-cut
by 巍魏 28 Mar '17

28 Mar '17

dear freesurfer experts： I ran my subjects and i found there were lots of pial leave in the brainmask and affects the cortical surface, by following the troubleshooting tutorial i use the g-cut flag, the pial was cut while some brain matters were cut, too, and i found in my data fix the cutted brain matter in brainmask.gcut.mgz file is easier than manul correct the pial in brainmask.mgz, so i wanna if there is a way to use the manul corrected brainmask.gcut.mgz file to do the skullstrip progress, is this can be done, please help me. cheers ________________________________ weiqi77777(a)live.com

1 0

Re: [Freesurfer] mri_vol2surf error in FS6
by Fred Lado 28 Mar '17

28 Mar '17

yes, I have the /Applications/freesurfer/lib/gcc directory.(actually, ‘had’ as I reinstalled 5.3) I installed 6.0 on top of 5.3 without uninstalling 5.3 first, so it was not a clean install. I will try a clean re-install with the tar file with the steps you suggest. Thanks. Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST) From: zkaufman(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf error in FS6 To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <62233.174.63.82.222.1488770521.squirrel(a)mail.nmr.mgh.harvard.edu> Content-Type: text/plain;charset=iso-8859-1 Hello Fred, Do you have the /Applications/freesurfer/lib/gcc directory? Also, out of curiosity, did freesurfer 5.3 exist on your system before installed 6.0? That error shouldnt happen if FS6 is cleanly installed and definitely shouldnt happen of SIPS is disabled. I suppose as a last resort could you just completely remove FS from your machine and just install it directly from the tar file (save the license.txt file): ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwi… $> cp /Applications/freesurfer/license.txt ~ $> sudo rm -rf /Applications/freesurfer $> sudo tar -C /Applications -xzvf freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz $> sudo mv ~/license.txt /Applications/freesurfer/ > Dear FreeSurfer Experts, > I just installed FS6 and encountered the following error, which I can > replicate by just entering ???mri_vol2surf??? on the command line: > > /Users/fred 3> mri_vol2surf > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > I am running Mac OS X El Capital 10.11.6, after searching the archives I > also tried turning off SIP, which did not help. Any other advice? > > Thanks, > Fred > > > Fred Lado, MD PhD > Director, Epilepsy - Central and Eastern Regions > Northwell Health > 917-608-1881 (mobile) > 516-325-7000 (practice) > 516-325-7001 (fax) > flado(a)northwell.edu > > > > > > Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527 > PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information. Any unauthorized review, > use, disclosure or distribution is prohibited and may be unlawful. If you > are not the intended recipient, please delete this e-mail immediately. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 7

How can I get cerebral WM and cortex volume
by shi yao wang 28 Mar '17

28 Mar '17

Dear FS experts: How can I get the whole cerebral WM and cortex volume. I am using following command: asegstats2table --subjects 10001 --segno 2 3 41 42 24 --tablefile 10001_WB_table It shows that no 2,3, 41,42 segment NO, however, they can be found in the FreeSurferColorLUT.txt file. thanks Lawrence

2 1

Left hemisphere
by yusif Al-kheder 28 Mar '17

28 Mar '17

Hello is it possible to just create the left hemisphere with white and grey matter intact? Youssif AlKheder Youssif Alkheder

3 6

measuring basal ganglia volume
by shi yao wang 27 Mar '17

27 Mar '17

Dear FS experts: We are measuring population based basal ganglia volume. Except the absolute volume of BS, any other parameters could be a reliable marker to reflect BS volume? such as ratio of total subcortical GM volume. Thanks! Lawrence

1 0

white matter disease
by Rockers, Elijah D. 27 Mar '17

27 Mar '17

Hello, We have a large number of subjects processed with the default settings of recon-all. Unfortunately the presence of white matter creates problems when creating the white matter surface. There are large hypo-intensities in the white matter which badly distort the surfaces in multiple areas of the brain. It is unfortunate because these areas seem to have about the same signal intensity as true cortex, leading to a confused algorithm, and very pronounced segmentation errors. I have been manually editing and reconstructing these surfaces, but the process is tedious and error prone. Are there any flags that might help recon-all perform better on brains with white matter pathology? Or otherwise things that I can do to make fixing the segmentation less painful? Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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