Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

[Re] medial wall label in Freesurfer 6
by M del Mar Velasco 30 Nov '17

30 Nov '17

Hi, We are not using the make_average_subject 6.0.0-patch. Do you think it would be a possible solution? Where can I find that patch? On the other hand, we've noticed that recon-all, which is a final make_average_subject step, fails. I send you the recon-all.log. However, maybe it is not related with previous issue becuase label files are generated before. All the best, M del Mar

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Recon-all with masked face and ears
by Buimer, E.E.L. 30 Nov '17

30 Nov '17

Dear FreeSurfer experts, We want to implement a deface method to ensure anonymity of participants before making the data available to researchers. Because the raw data is stored on the imaging platform XNAT, we preferred the mask_face method implemented on the XNAT server rather than FreeSurfer’s defacing. However, we will be using FreeSurfer for processing and segmentations afterwards. I am currently investigating the effect of face and earmasks on brain measures. I used FreeSurfer v5.3 (freesurfer-x86_64-unknown-linux-gnu-stable5-20130513) and the mask_face function developed for XNAT (Milchienko & Marcus, 2013) with the default normalized filter. The masks were not invasive and did not overlap with brain tissue. I compared output of the recon-all between T1 scans with and without masked face for a small sample. I found high correlations between the output of the two scans (extracted values: cortical thickness, surface area, (sub)cortical volume, global values). Slight differences seem to occur from the start of the recon-all (talairach transform). Adding ear masks to the face-masked scans, made the differences smaller (i.e. higher correlations with raw scans). Also, the recon-all run time appears to be reduced. Could you explain how face and ear information is used in the recon-all and why adding ear masks to masked-face scans might reduce run-time and improve reliability? Could it be the case that skull stripping is easier without ears for example? Thank you in advance. Kind regards, Elizabeth -------------------------------------------------------- Elizabeth Buimer, Research Assistant Department of Psychiatry, UMC Utrecht Room: A.01.161 e.e.l.buimer(a)umcutrecht.nl ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Estimated ICV much lower than mask volume?
by Patrycja Naumczyk 30 Nov '17

30 Nov '17

Hi experts! We are doing some QA exams with one subject scanned on different 3T scanners (with comparable/nearly identical imaging parameters). Afterwards, we looked into aseg values to compare them with the standard recon-all procedure. And we came across a strange result. Between two scanners the raw volumes are roughly the same, but the eICV's differ a lot (almost 30%). We looked into the data and found that even the mask volumes are alike (they differ less than 5% between the machines). the only outlier value is the eICV of one of the scanners. As this value is estimated, can this be a marker of some difficulties in normalization to Talairach upon the data of the scanner? Should it be alarming when an eICV is 30% lower than the mask volume? Best regards, Patrycja <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Wolny od wirusów. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Re: [Freesurfer] error in segmentHA_T2.sh
by Cong 29 Nov '17

29 Nov '17

Dear Eugenio, Using full path solved the problem, thank you very much! Best Regards Cong > From: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> > Subject: Re: [Freesurfer] error in segmentHA_T2.sh > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <2706B24C-1442-46B9-8A8B-15492520BEBA(a)ucl.ac.uk> > Content-Type: text/plain; charset="utf-8" > > Hi Cong, > This totally looks like a problem with absolute/relative paths. Can you please try again, but using the full path to the T2? Something like: > segmentHA_T2.sh control004 /Users/cong/data/subjects/control004/mri/T2.nii T2 1 > If this works, let me know and I?ll fix the code. > Cheers, > /E > > > -- > Juan Eugenio Iglesias > ERC Senior Research Fellow > Translational Imaging Group > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Cong <3110103623(a)zju.edu.cn> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Date: Wednesday, 29 November 2017 at 09:55 > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] error in segmentHA_T2.sh > > Dear freesurfer experts > I am trying segment hippocampal and amygdala subregions in dev version(freesurfer-i386-apple-darwin11.4.2-dev-20171024), the segmentHA_T1.sh works well. However, when I try to add a T2 propeller sequence it doesn?t work. I am sure the T2.nii file is in mri folder, and this T2.nii file works well in 6.0.0 version for segmenting hippocampal subregion. I pasted the wrong scripts, could you tell me what?s wrong? Thanks! > > Best Regards > Cong > > > BrainwaverdeMacBook-Pro:subjects Brainwaver$ segmentHA_T2.sh control004 control004/mri/T2.nii T2 1 > #-------------------------------------------- > #@# Hippocampal Subfields processing (T1+T2) left 2017?11?29? ??? 17?27?20? CST > ------------------------------------------ > Setting up environment variables > --- > DYLD_LIBRARY_PATH is .:/Users/Brainwaver/Documents/freesurfer/MCRv80//runtime/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//bin/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//sys/os/maci64: > Warning: application is running on a locale different from the original platform locale. > Registering norm.mgz to additional volume > znzreadInt: znzread failed > znzreadInt: znzread failed > niiRead(): error opening file control004/mri/T2.nii > mri_robust_register.bin: could not open MRI target control004/mri/T2.nii. > > /Users/Brainwaver/Documents/freesurfer/bin//mri_robust_register --mov /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/norm.mgz --maskmov /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_left//wholeBrainMask.mgz --dst control004/mri/T2.nii --lta /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 > ERROR: cannot find transform file /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta > gunzip: can't stat: /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_left//T2resampledLikeT1.mgz (/Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_left//T2resampledLikeT1.mgz.gz): No such file or directory > ERROR: problem reading fname > SWITCH expression must be a scalar or string constant. > > Error in myMRIread>load_mgh (line 550) > > > > Error in myMRIread>myMRIread_aux (line 92) > > > > Error in myMRIread (line 63) > > > > Error in segmentSubjectT1T2_autoEstimateAlveusML (line 198) > > > > MATLAB:badSwitchExpression > #-------------------------------------------- > #@# Hippocampal Subfields processing (T1+T2) right 2017?11?29? ??? 17?27?31? CST > ------------------------------------------ > Setting up environment variables > --- > DYLD_LIBRARY_PATH is .:/Users/Brainwaver/Documents/freesurfer/MCRv80//runtime/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//bin/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//sys/os/maci64: > Warning: application is running on a locale different from the original platform locale. > Registering norm.mgz to additional volume > znzreadInt: znzread failed > znzreadInt: znzread failed > niiRead(): error opening file control004/mri/T2.nii > mri_robust_register.bin: could not open MRI target control004/mri/T2.nii. > > /Users/Brainwaver/Documents/freesurfer/bin//mri_robust_register --mov /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/norm.mgz --maskmov /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_right//wholeBrainMask.mgz --dst control004/mri/T2.nii --lta /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 > ERROR: cannot find transform file /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta > gunzip: can't stat: /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_right//T2resampledLikeT1.mgz (/Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_right//T2resampledLikeT1.mgz.gz): No such file or directory > ERROR: problem reading fname > SWITCH expression must be a scalar or string constant. > > Error in myMRIread>load_mgh (line 550) > > > > Error in myMRIread>myMRIread_aux (line 92) > > > > Error in myMRIread (line 63) > > > > Error in segmentSubjectT1T2_autoEstimateAlveusML (line 198) > > > > MATLAB:badSwitchExpression > > All done! >

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Editing brainmask and white matter volumes when erasing dura
by Arsenije Subotic 29 Nov '17

29 Nov '17

Dear experts, After I erasing dura from my brain mask volume, I noticed that the white matter volume still had dura when I clicked on it. Is it usually fine to only edit the brain mask when we’re trying to erase the dura and regenerate the surfaces? The dura on the white matter volume has both the pial and white surfaces outlined and areas that have wm intensity of ~250. I know that the pial surfaces grow from the white matter so I figured that the -autorecon-pial command in the tutorial won’t solve my issue. Thanks for your help. Arsenije

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extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation
by Jessica Huang 29 Nov '17

29 Nov '17

Hi Freesurfer Experts, I've been looking to extract the timecourses of a couple regions of interest from fMRI data that's be registered against anatomical data. I've used commands such as recon-all and preproc-sess on all subjects. I've already used command fcseed-sess to extract timecourses from many regions in the default parcellations/ segmentations transferred through previous commands. I've also used fcseed-sess for regions that were labelled in each subject's anatomical labels folder. I'm still curious how to extract the timecourses for other ROIs not in the default parcellations/ segmentations. For example, with reference to the lookup table FreeSurferColorLUT.txt, how do I access the timecourse of: #9 Left-Thalamus 0 118 14 0 Thank you for any insight. Is there some folder I could look in or specific subject files that might help? Thank you again! Jessica p.s. for more examples of timecourses I have/ don't have access to already: In the default segmentation, I know how to extract these: - 1007 ctx-lh-fusiform In the labels folder of each subject, I know how to extract these: - 400 V1 Unsure how to extract these because they're not found in each of my subjects: - 406 BA6 -- Harvard College Class of 2020 A.B. Candidate in Computer Science jessicalihuang.com 1 (516) 343-4850

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error: dyld: lazy symbol binding failed
by steph 29 Nov '17

29 Nov '17

Hello freesurfer experts, when trying to run the local gyrification index I run into an error: >> recon-all -s S01 -localGI ... reading surface from lh.pial... 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 Abort ERROR: mris_fill -c -r 1 lh.pial /data/mri/freesurfer_subjects/S01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! Darwin mac.n.rr.com 17.2.0 Darwin Kernel Version 17.2.0: Fri Sep 29 18:27:05 PDT 2017; root:xnu-4570.20.62~3/RELEASE_X86_64 x86_64 recon-all -s S01 exited with ERRORS at Wed Nov 29 13:25:48 EST 2017 I’m running this on a macBook, macOS High Sierra 10.13.1, with freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c I tried different subjects, which caused similar errors. Any ideas would be greatly appreciated, thank you! Stephan

2 1

the ordering in ascii txt file
by Yi Li 29 Nov '17

29 Nov '17

Dear Freesurfer experts, I used the following mri_convert command to extract the skull stripped image and save it to a txt file. The file contains only one column, and has 256*256*256=16,777,216 rows. Does anybody know the ordering in which 256*256*256 array is transformed to the vector (eg, which of R-L, A-P, S-I changes fastest and slowest). Thanks! mri_convert $datadir/$subj/mri/brainmask.mgz $target/$subj.txt --ascii Best Regards, Yi Li (PhD) Senior Computational Scientist Computational Sciences The Jackson Laboratory Farmington, CT 06032 Tel: 860-837-2156 --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Re: [Freesurfer] Erroneous output after recon-all: Bad segmentation and surfaces
by Arsenije Subotic 29 Nov '17

29 Nov '17

Hi Bruce and Emma, I am running the latest version of Freesurfer, version 6.0. I will try manually erasing the voxels then and try re-processing the subject. Thank you so much for your help. Best, Arsenije

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Postdoctoral position in Machine Learning for 3D Histology
by Iglesias Gonzalez, Eugenio 29 Nov '17

29 Nov '17

Dear all, We are looking for a postdoc to work on my ERC Starting Grant project "Building Next-Generation Computational Tools for High Resolution Neuroimaging Studies", at the Translational Imaging Group<http://cmictig.cs.ucl.ac.uk/> (TIG) at University College London<http://ucl.ac.uk/> (UCL). Experience in neuroimaging is definitely a big plus. Details can be found here: https://atsv7.wcn.co.uk/search_engine/jobs.cgi?amNvZGU9MTcwMDA1NiZ2dF90ZW1w… and also here: https://sites.google.com/site/jeiglesias/news/postdocpositionavailable-3 Kind regards, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

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