Freesurfer

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issue with voxel-wise map after multiple comparisons
by miracle ozzoude 15 Jul '20

15 Jul '20

External Email - Use Caution Hello Experts, I ran a surface based pet analysis and I found 6 surviving clusters in the cluster-wise map. However, when I tried to view the voxel-wise map ( mc-z.abs.13.sig.voxel.mgh), it displayed as yellow meaning there was nothing (see attached). Shouldn't it be showing regions that survived at voxel-wise level? Any ideas why it isn't displaying the appropriate figure? Also, what does the content of this file (mc-z.abs.13.sig.voxel.max.dat) mean? Thank you. Best, Paul [image: image.png]

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Re: [Freesurfer] Label on fsaverage failure
by Eleni Nikalexi 15 Jul '20

15 Jul '20

External Email - Use Caution Dear Douglas and Bruce,on the same subject, I wanted to ask two questions:1. since the ROIs were obtained on 2mm voxels, is the command $ mri_vol2surf --mov ROI_set1/LeftAngG.img --regheader MNI_1mm --interp nearest --hemi lh --out Left_AngG_tmpfs.mgh --projdist-max 0 1 0.1 --noreshape --trgsubject fsaverage correct, or should I run it on the MNI152 2mm? 2. how can I create afterwards labels for reconned subjects of 1mm voxel size? I already tried the $ mri_vol2label --i Left_AngG_tmpfs.mgh --id 1 --l LeftAngG_tmp.label --surf fsaverage lh white but permission was denied, so then I tried to use tksurfer, but I got an error message:"surfer: Interpreting overlay volume /project/RDS-FHS-ppa2018-RW/eleni/localizers/Left_AngG_tmpfs.mgh as encoded scalar volume". What would you suggest? Thank you in advance!Eleni On Monday, July 6, 2020, 09:29:19 PM GMT+3, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote: It has to be loaded as an overlay to a surface, not a surface itself. On 7/3/2020 10:10 AM, Eleni Nikalexi wrote: External Email - Use Caution Dear Douglas, thank you very much for your help; I run the recon of MNI152_T1_1mm_brain.nii.gz (which I moved into a directory called MNI_1mm). Then I run the following command, as you suggested: $ mri_vol2surf --mov ROI_set1/LeftAngG.img --regheader MNI_1mm --interp nearest --hemi lh --out LeftAngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape But then, in freeview I get the following result: I also get an error when I try to load it as a surface: "LeftAngG_tmp.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!" What could be the mistake? Best regards, Eleni On Thursday, July 2, 2020, 04:25:54 PM GMT+3, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote: Try running recon-all on the MNI152. Load the ROI onto the reconned MNI152; load the surfaces as well and make sure that the ROI intersects with the surface, then use #3 below with --regheader MNI152 instead of --reg tmp.dat. You can also specify --trgsubject fsaverage and mri_vol2surf will map the ROI all the way onto the fsaverage surface On 7/1/2020 10:03 AM, Eleni Nikalexi wrote: External Email - Use Caution Dear Freesurfer developers, We have a series of MRI scans and we are trying to extract cortical thickness in certain regions of interest. The ROIs already exist - some are in .img and some in NIFTI format - and we want to tranform them into labels and then register them on fsaverage. The problem is that the ROIs are in MNI152 space (from SPM), with voxel size=2mm. We have tried various commands to register one of the .img ROIs on fsaverage, but they all failed: - $ fslregister --s fsaverage --mov ROI_set1/LeftAnGG.img --reg tmp.dat - $ tkmedit fsaverage T1.mgz -overlay ROI_set1/LeftAngG.img -overlay-reg tmp.dat - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz The result is that the ROI is either not in the right place, or the right size or we just end up with a weird 3D cross shape in freeview. Could you please suggest something that we could do to fix this? Thank you so much in advance! Best regards, Eleni _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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