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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

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

29 Nov '17

Dear experts, I recently finished processing a subject for whom I had performed a skull-strip on the brainmask.mgz volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following command as the troubleshooting tutorial suggested to regenerate the surfaces based on the new brainmask.mgz volume: recon-all -autorecon-pial -subjid <subject name> However, after the subject finished processing the surfaces were generated/outlined on the dura as well. I tried performing a g-cut command but it did not get rid of the dura. I also had issues with the subcortical segmentation as the ventricles were not completely segmented. I've attached screenshots for you to see as well. Would it be necessary to manually erase the extra dura and then re-process the subject? Please let me know. Thank you for your help. Best, Arsenije

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mri_convert partial support of nrrd file format for diffusion MRI data
by Michael Dayan 29 Nov '17

29 Nov '17

Hi, I was pleasantly surprised when I discovered that mri_convert could convert the nrrd file format (to NIFTI in my case). However for diffusion MRI data, while it displays the diffusion gradients information on the terminal, it does not create the associated bval and bvec files. After looking at the mri_convert command-line usage I could not find any option to do so. Would anyone know how to create the bval and bvec files? Best, Michael

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Error with mri_vol2surf
by Elena Theißen 29 Nov '17

29 Nov '17

Hello, I am new to freesurfer and have a problem following the step ,mri_vol2surf‘ as described in your tutorial ,cortical thickness of a Volume-defined ROI‘. During step 3 I always received the error: Could not read (path to) as type 24 The file is a .nii I checked my FS version (6) and redid all the previous steps. Also converting did not help. I tried to convert the nii. in mgz but then error 3 appeared. I would be glad if you could give me a hint how to fix it. Kind regards, Elena Von meinem iPhone gesendet

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