Freesurfer December 2019

freesurfer@nmr.mgh.harvard.edu

85 participants
117 discussions

(no subject)
by Boris Rauchmann 16 Jan '20

16 Jan '20

External Email - Use Caution Dear all, my intention is to use the Brainnetome Atlas parcellation/segmentation in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used: gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg Is this the right approach to obtain a high resolution segmentation to run PVC methods? Thanks, Boris

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Max threshold marked as '-inf' in cluster summary file
by Bronwyn Overs 14 Jan '20

14 Jan '20

External Email - Use Caution Dear Freesurfer Mailing List, I have completed an LME analysis in matlab and have generated a number of different cluster summary files for my various contrasts. In many of resulting cluster summary files the 'Max' value for the largest cluster which encompasses most of the brain surface is reported as infinity ('-inf'). Please find an example file attached. As I was hoping to use these values to generate effect size estimates, can you please tell me what alternate value I could substitute here for 'Max'? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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hardware upgrade affect Freesurfer?
by Dincer, Aylin 03 Jan '20

03 Jan '20

External Email - Use Caution Hi FreeSurfer Experts, Would upgrading computer hardware affect FreeSurfer output? We are using FreeSurfer version 5.3-HCP and we are considering upgrading our server. It will have the same operating system but different computer specs (memory, cpu, graphics, etc.). Thank you! Aylin -------------------- _____________________________ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging Core, Benzinger Lab 314-362-3629 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mis-registration question
by Nasiriavanaki, Zahra 03 Jan '20

03 Jan '20

Dear Freesurfers Hi I have a subject that the registration is not done correctly in two runs (run 12 and run 15) . The tkregister-sess values for this subject is shown below. Subject 1 10 0.2628 Subject 1 11 0.3038 Subject 1 12 0.7639 Subject 1 13 0.3364 Subject 1 14 0.3346 Subject 1 15 0.9361 Subject 1 16 0.2584 Subject 1 17 0.2488 I attached the screen shots from tkregister2 to this email. The functional data is only collected in a slab of parietal and occipital lobe. I appreciate if you let me know how to fix them. Thanks Mona [cid:6833a8d0-828b-4f31-9b61-2a4a1c3a670d][cid:7d39f7e2-609a-43a5-a964-dd95f8179c30] Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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tracula error gradient vectors too many ('s
by Renew Andrade 02 Jan '20

02 Jan '20

External Email - Use Caution Dear FreeSurfer experts: I am trying to run tracula in 4 subjects of a public dataset. I have encountered one error. I leave the output of terminal below. I also attach the configuration file. I hope you can follow from there. Sincerely, Andrade. root@andraderenew:/usr/local/freesurfer/subjects# trac-all -prep -c /usr/local/freesurfer/subjects/dmrirc.IXI Too many ('s. INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects INFO: Diffusion root is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer trac-preproc -c /usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/dmrirc.local -log /usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.log -cmd /usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections sáb dic 21 15:06:13 CET 2019 mri_convert --bvec-voxel /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998725, -0.0503472, 0.00377193) j_ras = (-0.0504772, 0.994141, -0.0955763) k_ras = (-0.00106217, 0.0956448, 0.995415) writing to /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz... ERROR: Must specify input table of gradient vectors Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at sáb dic 21 15:06:13 CET 2019

2 1

mkanalysis-sess.new not found
by Marco Ninghetto 02 Jan '20

02 Jan '20

External Email - Use Caution Dear experts, my name is Marco and I'm using freesurfer to perform retinotopy analysis and I am having a problem with command: `mkanalysis-sess.new` after calling that command I get the following bash error: `bash: mkanalysis-sess.new: command not found` All the previous steps worked well. Why is this command unrecognized? Thank you all, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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Unable to run recon all
by Sahil Bajaj 02 Jan '20

02 Jan '20

External Email - Use Caution Hello FS experts, I am trying to run recon all on about 100 subjects. But one out of 100 subjects finishes recon all with error, and doesn't complete the process. Here I am attaching recon all log for your reference. Also, before installing freesurfer on MAC Catalina, I ran sudo spctl - -master -disable I would really appreciate any help in resolving this. Thanks, Sahil 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) Platform: MACOS Catalina 3) recon-all.log: see attached

2 1

Fill holes in BOLD surface
by Marina Fernández 02 Jan '20

02 Jan '20

External Email - Use Caution Hi Freesurfer experts, I have projected 4D-preprocessed BOLD data to Freesurfer cortical surfaces. Resulting individual surfaces have many holes (see attached image) that I would like to fill with nearest neighbors values around each hole (avoiding the medial wall). Could you indicate me how to do this? Thank you in advance. Marina

2 1

mapping the reliability of separating GM/WM
by Liu Y 02 Jan '20

02 Jan '20

External Email - Use Caution Hi Freesurfers, The contrast between GM/WM may vary regions by regions. Some regions have high contrast, some regions have low contrast, is there a method can map the reliability of separating gray and subcortical white matter? Thanks in advance, Yawu

3 4

No Colortable Found
by Baptista, Paulo 02 Jan '20

02 Jan '20

External Email - Use Caution Hello FreeSurfer Developers, I'm helping researchers test Freesurfer 4.5 and Freesurfer 6. Running same code on Freesurfer4.5 environment produces no image with tksurfer. It says "No colortable found." See attached. 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 2) Platform: CentOS release 5.11 (Final) We're are running this in a Singularity container. It's getting close to working properly. It would be nice to have a way to run old code on newer Linux systems. Thanks, Paulo

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Freesurfer December 2019