Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Error with write_annotation program !
by Martin Juneja 15 Jul '20

15 Jul '20

External Email - Use Caution Hi FreeSurfer experts, I am trying to run write_annonation program in MATLAB and getting following error: >> [v, L, ct] = read_annotation('lh.Yeo2011_7Networks_N1000.annot'); >> ct.table(1:6,1:3) = 1; >> write_annotation('lh_Yeo2011_DMN',v,L,ct); Error using fwrite Invalid file identifier. Use fopen to generate a valid file identifier. Error in write_annotation (line 55) count = fwrite(fp, int32(length(label)), 'int'); I would really appreciate any help in resolving this issue. Thanks !

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mri_aparc2aseg with flag --a2005s
by Anja Samardzija 15 Jul '20

15 Jul '20

External Email - Use Caution Hello, I am trying to run mri_aparc2aseg with the flag --a2005s on a subject that I previously ran recon-all --all on. When trying to run mri_aparc2aseg with --a2005s I get the following error: could not read annot file 010/label/lh.aparc.a2005s.annot No such file or directory ERROR: MRISreadAnnotation() failed 010/label/lh.aparc.a2005s.annot. How do I solve this issue (get the lh.aparc.a2005s.annot file)? Thank you, Anja

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Re: [Freesurfer] aparcstats2table error
by Devika K 15 Jul '20

15 Jul '20

External Email - Use Caution I tried doing cortical parcellation using Destrieux atlas. I ran the aparcstats2table command from the SUBJECTS_DIR directory containing all of the output from recon-all. But I got an error, PFA. Do I need to run any other commands before running aparcstats2table command, I would be grateful if anyone could help me to resolve this issue. Many thanks in advance. Regards Devika K Research Scholar, Dept of EEE e: k_devika(a)cb.students.amrita.edu Amrita Vishwa Vidyapeetham Coimbatore, India

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Segmentation with FreeSurfer 7.1
by Sara PONTICORVO 15 Jul '20

15 Jul '20

External Email - Use Caution Dear FreeSurfer experts, we are performing some morphometric analyses using the new FreeSurfer 7.1 and we have encountered some large segmentation problems, mostly in the occipital pole. You can find some example images attached to this email. As the raw data do not present any particular problem, we selected the subject with the worst errors and performed, on the same workstation, the recon-all procedure using the old FreeSurfer 6. We noticed that the segmentation obtained with FreeSurfer 6 is good and does not present any particular defects. Do you have any clue on why there are these discrepancies between the two versions? Thanks a lot, Sara -- Sara Ponticorvo PhD Student Departement of Medicine Surgery and Dentistry, University of Salerno

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 14 Jul '20

14 Jul '20

Hard to tell, Jenna! Please do upload a sample subject using the instructions in the wiki, and I’ll take a look. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus(a)uwm.edu> Reply to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 14 July 2020 at 13:15 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Eugenio, I might have fixed this particular issue. I ran AFNI's 3dUnifize on the T1 before submitting it to recon-all and this improved the segmentation (it now overlays on the hippocampus). However, I still have some other files that this solution did not work for (see attached picture). I have a few subjects where the segmentation is slightly superior to the hippocampus. Editing the aseg or running 3dUnifize did not fix this issue. Do you have any suggested solutions? Thank you for your help! Jenna

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Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
by Iglesias Gonzalez, Juan E. 13 Jul '20

13 Jul '20

Hi Jenna, Would it be posible for you to share the subject? This is very weird. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus(a)uwm.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, July 13, 2020 at 19:29 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment External Email - Use Caution Hi Eugenio, I reran the segmentations after editing the aseg.presurf.mgz files and copying the edited HC to the wmparc.mgz files but the segmentations did not improve. Is there anything else you would suggest to do? Here is an example of one of my subjects. As you can see the left segmentation is not aligned with the left hippocampus. Thanks, Jenna

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Re: [Freesurfer] QAtools with Freesurfer version 6.0
by Hoopes, Andrew 13 Jul '20

13 Jul '20

Hi Kamy, The QA tools are actually developed outside of our lab. It might be helpful to contact the Reuter lab directly - https://github.com/Deep-MI/qatools-python best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Wakim, Kathryn-Mary" <KathrynMary_Wakim(a)urmc.rochester.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, July 9, 2020 at 7:51 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] QAtools with Freesurfer version 6.0 External Email - Use Caution Hi all, I’m relatively new to Freesurfer, and I am just beginning to check the output of my recon-alls using QAtools. However, I’m running into a number of difficulties and errors with QAtools, and I’m wondering if this tool is not yet optimized for the current version of Freesurfer. I have attached the recon_checker.All.summary.log output from QA tools. Below, I’ve also highlighted some of the errors and issues I see in the recon_chcker log file. Please note thatt, per the subject’s recon-all log file, recon-all ran to completion with no errors. Overview of recon_checker errors: 1) ERROR: Subject 10201003 missing output file ../mri/nu_noneck.mgz * Note: this is repeated for a number of different output files 2) ERROR: Recon-all steps missing in subject 10201003 status file 3) View your snapshots by opening this file in an internet browser: * Note: I have attached a screenshot of the output .html file in-browser. Note that I have installed and verified installation of ImageMagick. Thank you very much for your help, Kamy Wakim

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Dockerized version of Freesurfer 7.1
by Morgan Botdorf 13 Jul '20

13 Jul '20

External Email - Use Caution Hi Freesurfer Team, I am working on running recon-all on a large dataset using AWS. I saw that there is a dockerized version of Freesurfer 6.0. However, I would like to use Freesurfer 7.1. I was wondering if you could give me any information on whether there is (or will be) a dockerized version of Freesurfer 7.1? I appreciate any information you can provide! Thank you, Morgan Morgan Botdorf, M.S. Doctoral Candidate Neurocognitive Development Lab University of Maryland, College Park mbotdorf(a)terpmail.umd.edu Office: 301.405.5922

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Negative Longitudinal Hippocampal Subfield Values
by Ashwati Vipin (NNI) 13 Jul '20

13 Jul '20

External Email - Use Caution Dear FreeSurfer Developers, I think my earlier email may have gotten lost. I've run the longitudinal hippocampal subfield pipeline using the following command on freesurfer version 6.0: longHippoSubfieldsT1.sh PAWS001_base_FS I received no errors and everything seems to have run fine. But on computing the subfields using the following command: quantifyHippocampalSubfields.sh T1.long PAWS_longitudinalhipsubfields.txt I noticed that all of subfields have negative volume values. I checked the individual text files within each subject's timepoint and indeed the output is showing negative volumes. I have also tested the same subject and run the cross-sectional hippocampal subfield pipeline using the following command: recon-all -s PAWS001_TP1_FS -hippocampal-subfields-T1 I'm really not sure why the longitudinal pipeline is showing negative values. Could it be a Freesurfer version issue? Am I doing something wrong? It is especially mind-boggling since I receive no error and the command is running smoothly! Please help. I have attached the text files of the same subject run cross-sectionally and longitudinally. 1. A single subject processed cross sectionally - lh.hippoSfVolumes-T1.v10.txt 2. The same subject process longitudinally - lh.hippoSfVolumes-T1.long.v10.txt Thank you so much!! Best regards, Ashwati [cid:image9b8575.PNG@bec4f33e.43bdc947] nnitagl1

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Re: [Freesurfer] discontiguous regions assigned to same label by mris_divide_parcellation
by Mcnorgan, Christopher 11 Jul '20

11 Jul '20

External Email - Use Caution Thanks Bruce, The effect can be replicated on the attached .annot in fsaverage space. Step 1: MacBook-Pro:label chris$ mris_divide_parcellation fsaverage lh ABCD_task_p001.annot 1600 ABCD1600 Step 2: MacBook-Pro:label chris$ mris_divide_parcellation fsaverage lh ABCD1600.annot 400 ABCD400 You should find that the large ventral temporal cluster in lh.ABCD400.annot has three of pairs of discontiguous clusters with the same label name. Thanks for your help!

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