Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Grey matter， white matter and CSF volumes
by Jinsong Tang 03 Dec '15

03 Dec '15

Hello, I want to calculate the Grey matter, white matter and CSF volumes. The total gray matter volume is already in the ASEG file. Then I add up following volumes for ventricular CSF: Left Lateral Ventricle + Left Inferior Lateral Ventricle + Right lateral Ventricle + Right Inf Lateral Ventricle + 3rd Ventricle + 4th Ventricle + 5th Ventricle + Right choroids plexus + left choroids plexus. also, I add up following volumes for white matter volume: CorticalWhiteMatterVol +Left-Cerebellum-White-Matter + Right-Cerebellum-White-Matter. Are these right? Thanks, Jinsong

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converting labels to MNI space
by Francesca Strappini 03 Dec '15

03 Dec '15

Dear FreeSurfer experts, I'm trying to convert some retinotopic labels I created on the surface of each individual subject to MNI305 space for FSL. I run the following commands, but the output is not registered correctly. It seems to be shifted downward. mni152reg --s LG mri_label2label --srclabel lh.V1dorsalLG.label --s LG --regmethod surface --trglabel lh.V1dorsalLG_new.label --hemi lh mri_label2vol --label lh.V1dorsalLG_new.label --reg /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_new_MNI.nii.gz Thanks for your help, Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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g-w.pct vs. g-w. ratio
by Andrews, Derek 03 Dec '15

03 Dec '15

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

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obtain volumetric data with qdec
by Clara Kühn 03 Dec '15

03 Dec '15

Dear FreeSurfer Experts, I'm trying to follow the steps described in the univeriate LME for longitudinal data (https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) Could you explain how you did this step: "The qdec.table.dat file was then used to collect volumetric data for all subjects within the Freesurfer's Qdec interface. This resulted in a new Qdec table which had the previous columns plus three new columns." I followed the instructions with mri_preproc and mri_surf2surf but when I then open qdec to obtain the volumetric data for (in my case) BA45 it always gives out the error "Error in Analyze: Coudln't open /path_to_subject_base/lh.thickness.fwhm0.templatename.mgz or .mgh file" I understand that it can't find that file because it isn't there. Which steps do I additionally need to perfom to be able to be able to obtain said volumetric data. Is there an extra turorial or walkthrough for that? Cheers, Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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nu_correct error (FS 6 beta)
by COX Simon 03 Dec '15

03 Dec '15

Dear all, I'd be very grateful for a bit of help with the following problem. I'm running FreeSurfer 6.0 (I read a suggestion that there had been some compatibility issues running the current stable FS release with newer versions of openSUSE) on a cluster. However, nu_correct seems to be hitting an issue: ncopen: filename "./tmp.mri_nu_correct.mni.9548/0/nu1_est.mnc.temp": No such file or directory miopen: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct The directory exists, and there are several other files written here ("nu0.mnc", "nu1_corr.mnc", "nu1_mask.mnc", "nu1_residue.mnc" and "nu1_temp.mnc") so it doesn't appear to be having an issue with write access to this location. Many thanks in advance for your help, Simon ____ Simon R. Cox Centre for Cognitive Ageing and Cognitive Epidemiology University of Edinburgh 7 George Square Edinburgh EH8 9JZ The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image
by Ajay Kurani 03 Dec '15

03 Dec '15

Hello Freesurfer experts, I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the -hires flag to process an MNI template image which is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error during pocessing: Command run: recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts I supplied a skull stripped brain which was nu corrected and so I used the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage. I then ran autorecon2 and it was working well until I was at the -fix stage and ran into the following error: Error: mris_euler_number ./surf/lh.orig mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list I am not sure if this is due to the fact that we have a very high resolution image (template) and if there are any modifications needed aside from the hires flag. Are there any suggestions you have? Thanks, Ajay

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Freesurfer Version mismatch between Subject and Control Stamp in autorecon2 and autorecon3
by Amy L 03 Dec '15

03 Dec '15

Hi all, I'm sorry if this is a silly question, but what might cause the version of Freesurfer to be different in the Subject and Current Stamps of the output following autorecon2 and autorecon3? And is this a problem? The relevant lines of output are as follows: INFO: FreeSurfer build stamps do not matchSubject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Thanks very much for any insight!

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Re: [Freesurfer] Error - extracting percent signal
by Danielle Miller 02 Dec '15

02 Dec '15

Sure -- should be all here now! The last email contained the following text: "Hi Doug, > > Thanks for the response. I used the mri_label2label command: > mri_label2label --srclabel <labelfile> --s fsaverage --regmethod vol > --paint dmax --trglabel <output> --hemi lh > > When I input the output from this into mri_segstats as the --seg > volume, I get the error: > mri_read(): couldn't determine type of file > fsaverage/label/lh_ACC_label_test.label > ERROR loading fsaverage/label/lh_ACC_label_test.label > > Is there another step I am missing?" Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130 Hi Danielle, can you resubmit this email with the previous correspondence? On 12/02/2015 01:14 PM, Danielle Miller wrote: > Hi Doug, > > Thanks for the response. I used the mri_label2label command: > mri_label2label --srclabel <labelfile> --s fsaverage --regmethod vol > --paint dmax --trglabel <output> --hemi lh > > When I input the output from this into mri_segstats as the --seg > volume, I get the error: > mri_read(): couldn't determine type of file > fsaverage/label/lh_ACC_label_test.label > ERROR loading fsaverage/label/lh_ACC_label_test.label > > Is there another step I am missing? > > -- > Ph.D. Program in Behavioral Neuroscience > Boston University School of Medicine L-815 > 72 E. Concord St > Boston, MA 02118 > > > VA Boston Healthcare System Jamaica Plain > Memory Disorders Research Center > 150 South Huntington Ave D11-103 > Boston, MA 02130 > OFFICE:(857) 364-2130 It looks like the ces input is from a surface-based analysis. If you're label is already on the surface, then no need to do the label2vol step. If it is in the volume, then you'll need to transfer it to the surface with mri_label2label with the --paint option doug On 11/24/15 12:14 PM, Danielle Miller wrote: Hello freesurfer experts, I am trying to extract an average percent signal change from a functional roi label I created in tkmedit using fsaverage. I followed previously discussed methods: 1) mri_label2vol --label <name of label> --temp fsaverage/mri.2mm/orig.mgz --regheader fsaverage/mri/orig.mgz --o <name of label mask> 2) I checked (tkmedit fsaverage orig.mgz -overlay <label mask> -fminmax .5 1) and the label looked fine 3) I ran mri_segstats --i ces.nii.gz --seg <label mask from above> --id 1 --avgwf ces.label.dat ces.nii.gz is the file from my group analysis (isxconcat-sess) using the correct contrast It returns with this error: ERROR: dimension mismatch between input volume and seg input 163842 1 1 seg 76 76 93 Is there something I am doing wrong here? Also of note I tried using the following commands: 1) funcroi-config -label <label mask created from above mri_label2vol> -analysis <analysis directory> -roi <name of roicfg file> 2) funcroi-sess -sf sessid - roi <roicfg file from above> But this returns with this error: ERROR: cannot find /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_001_recon/label/label_lh_ACC_correct_mask.mgz Any suggestions would be extremely helpful. Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

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Re: [Freesurfer] Error - extracting percent signal
by Danielle Miller 02 Dec '15

02 Dec '15

Hi Doug, Thanks for the response. I used the mri_label2label command: mri_label2label --srclabel <labelfile> --s fsaverage --regmethod vol --paint dmax --trglabel <output> --hemi lh When I input the output from this into mri_segstats as the --seg volume, I get the error: mri_read(): couldn't determine type of file fsaverage/label/lh_ACC_label_test.label ERROR loading fsaverage/label/lh_ACC_label_test.label Is there another step I am missing? -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

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White matter and cp edits don't produce new results after reconall
by Annelinde Vandenbroucke 02 Dec '15

02 Dec '15

Dear all, I have a faulty wm map (brainmask.mgz) where some regions are not labeled as white matter where they should. I tried to correct both the wm.mgz map and add control points (and saved these), afterwards running either -autorecon2-wm or autorecon2-cp, but neither of these work. I can see the control points and wm edits in my maps, but the wm segmentation is still the same. I have not found a solution on the mailing list yet and was wondering whether anybody had a similar problem or could help. Thank you in advance, Annelinde -- Annelinde R. E. Vandenbroucke, PhD University of California, Berkeley || Helen Wills Neuroscience Institute 10 Giannini Hall Berkeley, CA 94720

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Freesurfer December 2015