Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

84 participants
123 discussions

FreeSurfer Password
by Mattia Pagano 20 Jun '22

20 Jun '22

External Email - Use Caution Good morning, I need the password to expand the archive for Freesurfer 7.2.0 release in Ubuntu. Thanks, Mattia

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mris_label2annot seed not set
by Benjamin Deck 19 Jun '22

19 Jun '22

External Email - Use Caution Hi Freesurfer experts, While trying to create a custom annotation file I get the following warning: mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi rh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label 7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi rh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317 subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 25700 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot The annotation file looks fine, however, I am worried that this warning may be pointing at a larger issue. Can you advise? Thanks! FS: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b OS: WSL2 Ubuntu -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1JUYvI6qR2KHny5pu-f9lEzMAikHDQnJEQzEy2bQcsPQ6R…> Virus-free. http://secure-web.cisco.com/1vXe16WpLwEeffCQQEIzrJynVkOZTnYNK4zHjcPCpq_MyoN… <https://secure-web.cisco.com/1VFMgx5tZC9GQwomPBkbGypdqGMLfiP59efwXDTUjsVj-S…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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SPM to FreeSurfer
by Rachel Wagner 19 Jun '22

19 Jun '22

External Email - Use Caution Hello, I am trying to take my SPM images and cortically project them with free surfer (SpmPainting - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1o3IHzvB09pwh3UU64pSKXFgTUAafyWmRKJ9lNBgTQW81z…>. As it might be quite obvious, I have very little experience using these softwares. I am typing in the suggested code as follows: developer@developer-VirtualBox:~$ mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img mri_convert /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz brain.img reading from /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz... error: mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, -1): could not open file developer@developer-VirtualBox:~$ ^C developer@developer-VirtualBox:~$ Is there something I am doing incorrectly? Thank you! Rachel

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Freeview GUI overlay and registration
by Kuo, Yi-Ling 19 Jun '22

19 Jun '22

Hi Freesurfer experts, I am trying to use the Freeview GUI to load fMRI BOLD activation data (analyzed in FSL) and project on the inflated surface. I used the feature “Overlay/Load generic” and was prompted to select overlay file and/or apply registration. The selected overlay file didn’t seem to project on the right spot on the inflated surface as would be seen in T1. If registration was the issue, what registration file should be selected in the Freeview GUI? My Freeview was updated. Thank you very much for helping. Irene

2 3

-hires flag sometimes breaks recon-all
by Schneider, Christoph 19 Jun '22

19 Jun '22

Hi, I have 7T MP2RAGE data of 25 individuals with an isotropic 0.7mm voxel resolution. I initially ran FS with the -hires flag to preserve the additional detail, but in 4 cases this crashed the process, while running the same image without the -hires flag works fine (surfaces visually inspected). I just wanted to know what could be the cause for this difference in behavior between the two options. Many thanks in advance, Chris Christoph Schneider, PhD Postdoctoral Research Fellow Harvard Medical School Massachusetts General Hospital Gordon Center for Medical Imaging

2 1

mri_label2vol misaligned for subcortical atlas
by Christopher Pirrung 19 Jun '22

19 Jun '22

External Email - Use Caution Hi Freesurfer Devs, I’m attempting to transform the Harvard-Oxford subcortical atlas (obtained from https://secure-web.cisco.com/1Tup0RI4qms0go1SEsu5ke-k7Cz5iL5tezC3TmgzZcvjKq…) to my subjects’ native anatomical space to create individualized versions of this atlas. To do so I used the line: mri_label2vol --seg H-O_subcortical_parcellation_thr50.nii --temp rawavg.mgz --o HO-subcort.mgz --regheader H-O_subcortical_parcellation_thr50.nii based on the recommendation from https://secure-web.cisco.com/1bcvHE7fWzSmfgBGxlww4NvvAmOJRlTofNlaCk_OCSbG9A… However, when I load the rawavg.mgz and individualized atlas in freeview, the atlas is ~30 mm away from being aligned. Do you have any idea why this might be the case or recommendations to get a better alignment? Thanks! Chris

2 1

Incorporating samseg segmentation into the recon-all pipeline
by Julian McGinnis 19 Jun '22

19 Jun '22

External Email - Use Caution /Hello everyone,/ /We have been utilizing freesurfer for our brain morphometry and processing pipelines, and have recently tested the samseg segmentation algorithm on a clinical cohort./ /With respect to some regions, we currently prefer its results to the ones generated by the standard freesurfer segmentation algorithm. / /As SAMSEG only provides volume calculation (please correct me if I am wrong) and does not feature cortical thickness measurements,/ /I was wondering if the recon-all pipeline can be modified to utilize the samseg segmentation instead, and if so, which script(s) or chain of commands would be a good starting point to implement this./ /Looking forward to your feedback,/ /Julian / Julian McGinnis PhD Candidate TUM-Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany Department of Computer Science, Technical University of Munich, Munich, Germany Email:julian.mcginnis@tum.de

2 1

(no subject)
by Bouchra Guelib 18 Jun '22

18 Jun '22

External Email - Use Caution Hi, I try to do something like that, Would anyone help me -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: Guelibbouchra(a)gmail.com

1 0

Setting Location?
by Rachel Wagner 17 Jun '22

17 Jun '22

External Email - Use Caution Hello, I am attempting to convert an image file and am getting the following error: developer@developer-VirtualBox:~$ mri_convert Combined_roi_meanRD.nii Combined_roi_meanRD.img mri_convert Combined_roi_meanRD.nii Combined_roi_meanRD.img reading from Combined_roi_meanRD.nii... error: niiRead(): error opening file /home/developer/Combined_roi_meanRD.nii I believe this is due to the location I have stored it (desktop); how do I set the location? Thank you, Rachel Wagner

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TRACULA Configuration Question
by Daliah Ross 17 Jun '22

17 Jun '22

External Email - Use Caution Hi FreeSurfer experts, I am planning to use TRACULA and have a question regarding the configuration file and whether we can start with already processed data. We have already run some steps involved in the TRACULA configuration script, which take several hours per subject to complete. Specifically, we already ran topup to handle B0 distortions and already processed eddy distortion corrections. Could this be bypassed when configuring TRACULA so we are not redoing these hours, or does it have to be run within TRACULA? Thank you, Daliah -- *Daliah Ross, M.A.* | dross3(a)mail.yu.edu Ph.D. Candidate, Clinical Psychology with Health Emphasis Neuropsychology Concentration Ferkauf Graduate School of Psychology, Yeshiva University Albert Einstein College of Medicine *pronouns: she/her/hers*

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Freesurfer June 2022