Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

FW: seeking MR physicist (fwd)
by Bruce Fischl 18 Oct '17

18 Oct '17

FYI ---------- Forwarded message ---------- Date: Wed, 18 Oct 2017 16:11:10 +0000 From: Elfar Adalsteinsson <elfar(a)mit.edu> To: mrigroup <mrigroup(a)mit.edu>, ptx <ptx(a)mit.edu>, fetal <fetal(a)mit.edu> Cc: "fischl(a)nmr.mgh.harvard.edu" <fischl(a)nmr.mgh.harvard.edu> Subject: FW: seeking MR physicist Hi All, West coast colleagues and friends are looking to fill a postdoc slot …if you are interested you can talk to me for info or reach out to Natalie May Zahr [mailto:nzahr@stanford.edu] Research Scientist Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine Stanford, CA 94305

1 0

Re: [Freesurfer] TRACULA qc: forceps minor and major
by Yendiki, Anastasia 18 Oct '17

18 Oct '17

Hi Linnea Marie – You’re right in your assessment. Are you using 6.0? You can reinitialize those bad cases, by adding “set reinit = 1” in your config file and changing the path list and subject list to specify only the tract and subjects that you want. Then rerun trac-all --prior and trac-all —path for those cases. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Linnea Marie Dramdal Borg <lmborg(a)stud.ntnu.no<mailto:lmborg@stud.ntnu.no>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, October 6, 2017 at 6:13 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA qc: forceps minor and major Hi, We have run into some issues with our forceps major and forceps minor tractographies. I have attached examples: In "fminor_bro_139.png", there is a "bridge" in forceps minor in the space between the hemispheres. We've also come across other cases of bridging in forceps minor, with somewhat unusual voxel intensity distribution, such as in "fminor_onestripe_otherwOK.png" and" fminor_litenbro_OKornot_210.png". Also, "fmajor_132_toolateral.png", fmajor brances out in the left hemisphere (right in the picture). All of these cases seem pretty bad to us. Do you agree? In contrast, "fminor_allslicesOKbutone_158.png" looks fine, but there is one slice where it branches out to some extent. Are we correct in assuming this won't affect the results too much, or is there something we can/should do about this? Thank you, Linnea Marie

2 2

FLAIR pial segmentation imprecisions
by Patrícia Klobušiaková 18 Oct '17

18 Oct '17

Dear Freesurfer experts, we used recon-all -s <subid> -i <T1> -FLAIR <FLAIR> -FLAIRpial -all on cca 100 subjects. About 10 of them have this pial surface error (see below). Pial surface on temporal lobes is erroneous. White matter seems pretty much OK to me. Would for example changing of -ghi parameter in mri_segment expert option help? What would be the best way to handle this? Thanks! Patricia [image: Vnorený obrázok 1]

1 0

Re: [Freesurfer] TRACULA bedpostx step with gpu
by Mehta, Chintan 18 Oct '17

18 Oct '17

Thank you Anastasia!

1 0

Fwd: running cross sectional analysis on .long outputs only
by Garret O'Connell 18 Oct '17

18 Oct '17

Hello FreeSurfer experts, I am trying to do a cross-sectional baseline analysis from the outputs of the longitudinal processing stream, following the advice on a previous question's thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016- March/044681.html >From my reading of the issue, I need to run the following command, entering the cross-sectional title folder as the first input. recon-all -long "subj_crossfolder" "subj_base" -qcache For this step, i know it is necessary that recon-all knows where the cross folders are located, although from my understanding, it does not actually use data from these folders., instead using the data in the .long folders. My issue is that I do not have access to the cross folders anymore, and was wondering if there was a work around to do the cross sectional analysis without them? Thanks for any help! Garret

2 2

ERROR: no voxels found in mask selxavg3-sess
by 王剑葆 18 Oct '17

18 Oct '17

Dear FreeSurfers, I'm trying to perform First level analysis using "selxavg3-sess -sf sessid -analysis color.sm0.mni305". However, the analysis was interrupted by the following error. ... ... Smoothing ACF /usr/local/freesurfer/bin/mri_fwhm --mask /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/mask.nii.gz --i /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/rho1mn.nii.gz --o /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only voxelvolume 1 mm3 Loading mask /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/mask.nii.gz ERROR: no voxels found in mask ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/mask.nii.gz --i /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/rho1mn.nii.gz --o /media/bob/DATA/FreeSUBcolorv2v4/functional01/Sess01/bold/color.sm0.mni305/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only ans = 1 I also loaded the mask and found that all the values are 0. I finished mkanalysis-sess and mkcontrast-sess without error. Is there anything possible wrong in the previous steps when generating the mask? Best, Bob

1 0

Creation of V1 mask in volume
by Florence Campana 17 Oct '17

17 Oct '17

Dear freesurfer experts, I am trying to create a V1 mask in volume, based on the V1 label, in fsaverage space. I use the following command: mri_label2vol --label /Applications/freesurfer/subjects/fsaverage/label/rh.V1.label --temp /Applications/freesurfer/subjects/fsaverage/mri/orig.mgz --hemi rh --identity --o v1volume.nii When I check out the output (in freeview, I load orig,mgz and v1volume.nii as a mask), V1 as defined in v1volume.nii seems to be mislocated. I am surprised since I would think that I use the proper inputs ; or is my command line somehow wrong? Thank you very much, Florence

1 0

Advice on covariates in qdec or mri_glmfit
by Jeff Crawford 17 Oct '17

17 Oct '17

Hello everyone. I am having trouble understanding the statistical effects of a covariate versus a nuisance factor in freesurfer and I would appreciate some advice. I want to run a correlation between cortical volume and the measurement of an enzyme while covarying for ETICV. In qdec, I select volume as the measure, set the enzyme as a covariate, and select ETICV as a nuisance factor. This works fine, however, I want to also control for the difference in using two separate scanners. This would be a categorical variable and I understand that Freesurfer does not allow categorical variables to be nuisance variables. The solution I found to this problem from two separate emails is that you either use the Manuel stream of mri_glmfit or use set scanner as a fixed factor, which produces a description of: "Does the correlation between volume and enzyme, accounting for scanner, differ from zero? Nuisance factors: ETicV" This sounds right to me, but I am confused as to the difference between "accounting for scanner" and "Nuisance factors: ETicV", when I thought they were the same thing. Am I approaching this right? Do I need to use mri_glmfit to properly control for scanner? If so, then how would I specify a nuisance variable in a contrast?

1 0

Skull-stripped data submitted on FreeSurfer version 6.0.0
by Duran, Tugce 17 Oct '17

17 Oct '17

Dear FreeSurfer Team, I have recently submitted my skull-stripped data into FreeSurfer v6. Since this is a separate process than the default recon-all –all, I followed the recommended steps that are posted on the FSwiki website, here is the link for it: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealre… By doing so, I accidentally submitted my data both with recon-all -autorecon1 -noskullstrip -s <subjid> and –all flag at the beginning. Using PBS script, here is an example of this: list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 E008_V1 E010_V1 E011_V1 E013_V1 E014_V1 E015_V1" echo $list OUTDIR="/pathtodirectory/logs_KT" PREFIX="recon-all" for index in $list; do recon-all –autorecon1 –noskullstrip -i /pathtodirectory/$index/"$index".nii -subject $index -sd /pathtodirectory -all 1>$OUTDIR/$PREFIX.$index.out 2>$OUTDIR/$PREFIX.$index.err & done wait I forgot to remove the flag –all at the end of this command. Therefore, freesurfer v6 processed my data all the way till the end and Viola it worked! And I am wondering If I could trust this data since it looks OKAY when I look at the segmentation, parcellation. Can I trust this skull-stripped processes data with –autorecon1 –noskullstrip and –all options? I hope my explanation and question makes sense. Thanks, Tugce Duran durant(a)iupui.edu

2 8

recon-all error message
by lanbo Wang 17 Oct '17

17 Oct '17

recon-all.log <https://drive.google.com/file/d/0B8gDmAZ-2iJ6VzRyZ01UbXRMdFlId2pZR2cyZHJLNH…> Dear All, When I run recon-all -long, the error happend. This is the error message that I get at the end of the recon-all log file: /HD4/Subjects/subj_23_1.long.s23_base/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness WARNING: # of slices=-59 in header - assuming 124... read_signa(/HD4/Subjects/subj_23_1.long.s23_base/surf/I.001): could not open file No such file or directory mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any help is greatly appreciated. All best, Lanbo Wang

1 0

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