Freesurfer June 2019

freesurfer@nmr.mgh.harvard.edu

82 participants
138 discussions

picture edit
by Abby tang 18 Jun '19

18 Jun '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to get some pictures about my results , so QDEC was used. However I can't adjust those pictures which QDEC produced, such as picture1. When I read other's paper, they provided different pictures just like picture2. I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV. I want to get more beautiful pictures, but the ability of QDEC is limited. I have tried freeview, but I don't know what file should be loaded in freeview. After qdec processing, what file format should be selected to load freeview? Or if there are other method to use freeview direct to regressive age and thickness? Could you give me some advices? Thank you! Hope your reply. Thank you for your help. Best regards Abby

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DesikanKilliany ROI for mri_glmfit
by Tammi Kral 18 Jun '19

18 Jun '19

External Email - Use Caution Hello, I would like to use the insula label/ROI from the DesikanKilliany atlas with mri_glmfit. How do I reference this label, as I don't see a LUT for this atlas. I appreciate any suggestions. Thanks, Tammi R.A. Kral, M.S. -- Doctoral Candidate, Psychology University of Wisconsin-Madison Center for Healthy Minds Waisman Brain Imaging Laboratory

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Smoothing the pill surface
by Nillo, Ryan Michael R 17 Jun '19

17 Jun '19

Hello FreeSurfer users/developers, I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI) without having to run the entire recon-all process. Additionally, I want to map this surface to the white surface. Is there an easy way to do this? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

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running recon -all and trac -all from different FreeSurfer home
by Costanza Gianni' 17 Jun '19

17 Jun '19

External Email - Use Caution Hello, FreeSurfer Developers, I'm trying to run trac -all (I prepared the configuration file following the instructions from v. 5.3) on a set of subjects already processed with recon -all in another computer with a different FREESURFER HOME, and I'm getting this error: Too many ('s. INFO: SUBJECTS_DIR is /home/costanza/extra/PET/PET INFO: Diffusion root is /home/costanza/extra/PET/PET Actual FREESURFER_HOME /home/costanza/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 /home/costanza/freesurfer/bin/dmri_motion: Command not found. /home/costanza/freesurfer/bin/dmri_group: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory INFO: current FREESURFER_HOME does not match that of previous processing. Current: /home/costanza/freesurfer Previous: /autofs/cluster/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013 dcmlist: Subscript out of range. I've searched the list and I couldn't find any similar error. Do you think the main problem is running commands from different FREESURFER HOME? 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Ubuntu 14.04.5 LTS 3) umane -a Linux wks4 3.13.0-166-generic #216-Ubuntu SMP Thu Feb 7 14:07:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thanks a lot for your help, Costanza -- Costanza Giannì, MD Radiologist PhD student Sapienza University, Rome +39 348 711 8987 -- ___________________________________________ *Il tuo 5 diventa 1000* Fai crescere la tua università Dona il 5 per mille alla Sapienza Codice fiscale: *80209930587* https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cin… <https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cin…>

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Aligning structural and fMRI data
by Wenzhen Zhao 17 Jun '19

17 Jun '19

External Email - Use Caution Dear whom it may concern, I have a structural image (orig.mgz) that has 256 * 256 * 256 dimension, c_r: 0 c_a: 0 c_s:0, and a functional file that has 64*58 * 48* 200, c_r = -0, c_a = 11.9, c_s = 2.7. Two files have different start and end time, too. I have went through processing steps, but the output does not overlap with orig.mgz. tkregister-sess —bbr-sum value is 0.95. How can I overlap these two brain images with different dimensions, start/end times, geometry? I appreciate your help! Thanks, Wenzhen

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Re: [Freesurfer] hippocampal subfields error
by Iglesias Gonzalez, Eugenio 17 Jun '19

17 Jun '19

External Email - Use Caution Dear Angelika, Can you please send us a screenshot of the inaccurate T1 segmentation? Cheers, /Eugenio -- 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 "Mennecke, Angelika" <Angelika.Mennecke(a)uk-erlangen.de> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, 17 June 2019 at 06:36 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampal subfields error External Email - Use Caution Hi all, I’m doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high resolution T2 data from a 7T MRT. With at least one of my datasets Matlab throws an error during the hippocampal-subfields-T2 –pipeline: Making Unknown map to reduced label 14 Computing hyperparameters for estimation of Gaussians of T2 data Error using | Inputs must have the same size. Error in segmentSubjectT2_autoEstimateAlveusML (line 1064) With other patients, the pipeline on the T2 images is correctly working without errors. I’m wondering what is causing this error and whether there is something I can do to avoid it? As far as I can see, the only difference between the “error” dataset and the others is that hippocampal subfields-T1 is also not calculated correctly. It finishes without errors, but the final result does not cover the hippocampus correctly (probably due to a T1-hypointense cyst in the hippocampus of that patient). Best regards, Angelika

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ExploreDTI Workshop in December 9-11 2019@Costa Rica
by Szabolcs David 17 Jun '19

17 Jun '19

External Email - Use Caution More info: http://www.exploredti.com/workshop/ [image: EDTI_flyer.jpg]

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(no subject)
by Erik Lindberg 17 Jun '19

17 Jun '19

External Email - Use Caution Post-doc position for MRI-research on dementia and normal aging available at Karolinska institute. We are looking for a Post-doc researcher for a 1-year scholarship (with a possibility for an extension to 2-year) at our section at the NVS-department at Karolinska institute. For further information see: https://ki.mynetworkglobal.com/se/what:job/jobID:273493/type:job/where:4/ap…

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hippocampal subfields error
by Mennecke, Angelika 17 Jun '19

17 Jun '19

External Email - Use Caution Hi all, I'm doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high resolution T2 data from a 7T MRT. With at least one of my datasets Matlab throws an error during the hippocampal-subfields-T2 -pipeline: Making Unknown map to reduced label 14 Computing hyperparameters for estimation of Gaussians of T2 data Error using | Inputs must have the same size. Error in segmentSubjectT2_autoEstimateAlveusML (line 1064) With other patients, the pipeline on the T2 images is correctly working without errors. I'm wondering what is causing this error and whether there is something I can do to avoid it? As far as I can see, the only difference between the "error" dataset and the others is that hippocampal subfields-T1 is also not calculated correctly. It finishes without errors, but the final result does not cover the hippocampus correctly (probably due to a T1-hypointense cyst in the hippocampus of that patient). Best regards, Angelika

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Segmenting internal capsule
by Chinappen, Dhinakaran Maheswaran 16 Jun '19

16 Jun '19

Dear Freesurfer community experts, We're looking to segment the internal capsule using T1 data. We found documentation in the FreeSurfer white matter segmentation atlas that states that the right and left anterior and posterior portions of the internal capsule are segmented as regions 155-158, but they don't actually appear in any of the output parcellations. We've seen this question appear in previous email threads, <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-August/047133.h…>, but can't find the script "intcapseg" that Doug mentioned here: <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020985.…>. If anyone could send us this script it would be much appreciated. Thanks! Lauren and Dhinakaran.

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Freesurfer June 2019