Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

requesting password for FS_7_2_0_ubuntu_18_04_06.ova.7z
by Ranjini Garani Ramesh 05 Jul '23

05 Jul '23

External Email - Use Caution Hi, I am requesting the password to extract "FS_7_2_0_ubuntu_18_04_06.ova.7z". Regards Ranjini

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Longitudinal Pipeline Issue
by Atwater, Emanuel R 05 Jul '23

05 Jul '23

External Email - Use Caution Hello Freesurfer Team I'm attempting to create the base for the longitudinal scan process, as described in the Longitudinal Tutorial (https://secure-web.cisco.com/1nkZqRPPwsOtKx4RoeA_xG1zIjqnnyVHLQdZ7CBucl4swE…) but for some reason I am unable successfully complete the base. FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Recon-all.log: see attached V/r, Emanuel Atwater

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Variation in volume when recon-all is run 1416 times on the same subject
by 神保岳大 05 Jul '23

05 Jul '23

External Email - Use Caution Dear FreeSurfer team, We were interested in the reproducibility of multiple runs of recon-all and repeated recon-all 1416 times on the same subject. We then checked the left and right brain results for the volume obtained from the Aseg process. The right brain showed exactly the same volume, while the left brain showed a small variation. We thought that the variation in volume between the left and right brains would be the same. But why is this not the case in reality? The volume_attemps1416.csv is attached. For example, the Left-Lateral-Ventricle in this file has variation, but the Right-Lateral-Ventricle has no variation, as shown below. *Left-Lateral-Ventricle*12377.8 12375.9 12375.9 12380 12376.4 ... *Right-Lateral-Ventricle*7514.7 7514.7 7514.7 7514.7 7514.7 ... 1) FreeSufer vesion: 7.2.0 2) Platform: Red Hat Enterprise Linux 8.6 3) uname -a: Linux fn01sv01 4.18.0-372.36.1.el8_6.x86_64 #1 SMP Thu Nov 17 16:37:07 EST 2022 x86_64 x86_64 x86_64 GNU/Linux 4) volume_attemps1416.csv: Summarized results of 1416 aseg.stats.

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dcmunpack: Issues with the -run argument
by Sara Teso Cuesta 03 Jul '23

03 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, I am trying to use dcmunpack to transform dicom images to a nifti format inside a FSFAST formatted directory ( https://secure-web.cisco.com/1JV-FemocV4fiLoKofgFHZ2hQTt_nlpR8LAqJEXvFr3d88…) however I am having issues understanding how to use properly the -run argument. This is the command I am trying to use: dcmunpack -src fMRI_dir -targ sessionid -fsfast -run 2 rest nii.gz f.nii.gz I assume I am making some mistakes with the command, specially with the run arguments since this is the error that I got in the terminal: ERROR: could not find run 2 in data My directory contains fMRIs downloaded directly from the ADNI database and grouped in folders following this structure: /fMRI_dir/subject_id/Axial_rsfMRI/date/image_uid/dicom images I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to solve this? 1) FreeSurfer version: freesurfer_ubuntu20-7.4.0_amd64.deb 2) Platform: Ubuntu 20.04 in WSL Thanks for your help.

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unsubscribing from mailing list
by Rana Ghamari 03 Jul '23

03 Jul '23

External Email - Use Caution Hi Freesurfer Team Please unsubscribe my email from the list Email: ghamarirana(a)gmail.com Thanks

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Error Help
by Misque Boswell 03 Jul '23

03 Jul '23

External Email - Use Caution Hi, I am new to FS and recently downloaded the package per instructions on your site. I set up the path and everything seems to be fine until I attempt to use any functions. I have searched for answers on this error, but I cannot seem to find anything so I am hoping you can direct me in fixing this. I am attaching the error log. I also tried to preprocess “bert” and got the same message. Thank you! Misque

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Hippo subfields long
by Andrei Bieger 03 Jul '23

03 Jul '23

External Email - Use Caution Hello everyone, Quick question. After running the longitudinal recon-all pipeline, is it required to run all subjects/tps through the segmentHA before running the segmentHA_long? If no, since I already ran the segment_HA in a few subjects, if I stop and start running the segmentHA_long, will I have any trouble in overlaying output files? Thank you in advance! Andrei -- Andrei Bieger

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trac-all with or without sub-thalamic nuclei segmentation
by Woo-Suk Tae 02 Jul '23

02 Jul '23

External Email - Use Caution Dear FreeSurfer developer. I successfully completed the tracula trac-all analysis using freesurfer 7.4.1. ThalamicNuclei.v13.T1.FSvoxelSpace.mgz images were obtained using segmentThalamicNuclei.sh, and trac-all analyses results were obtained using both set usethalnuc = 0 and 1 in the tracula config option. The tracts obtained from the two analyzes were similar in general, but slightly different in detail. Can you elaborate a bit more on what the usethalnuc option does to the results? Sincerely yours. Woo-Suk, Tae Seoul, Korea ---------------------------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: wstae(a)korea.ac.kr, woosuk.tae(a)gmail.com, wo <woostae(a)naver.com>ostae(a)gmail.com ----------------------------------------------------------------------------------------

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Cluster summary table
by Maria Czarnecka 02 Jul '23

02 Jul '23

External Email - Use Caution Dear Experts, I calculated a conjunction using "mri_concat". I have a beautiful map but I need a cluster summary table for it. How can I get that? Best, Maria Czarnecka

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Re: [Freesurfer] mris_label2annot
by Maria Czarnecka 02 Jul '23

02 Jul '23

External Email - Use Caution Dear Yujing, Thank you so much for your answer. My ctab looks like this: 11100 Unknown 0 0 0 0 11102 G_and_S_occipital_inf 0 0 0 0 11111 G_cuneus 0 0 0 0 11119 G_occipital_middle 221 60 60 0 11120 G_occipital_sup 0 0 0 0 11121 G_oc-temp_lat-fusifor 0 0 0 0 11122 G_oc-temp_med-Lingual 0 0 0 0 11130 G_precuneus 0 0 0 0 11143 Pole_occipital 221 60 60 0 11145 S_calcarine 221 60 60 0 11158 S_oc_middle_and_Lunatus 0 0 0 0 11160 S_occipital_ant 0 0 0 0 11161 S_oc-temp_lat 20 180 140 0 11162 S_oc-temp_med_and_Lingual 0 0 0 0 11166 S_parieto_occipital 221 60 60 0 a sample of one of my label files: #!ascii label , from subject fsaverage vox2ras=TkReg 1630 139 -4.532 -75.888 20.953 0.0000000000 300 -15.423 -72.840 16.348 0.0000000000 301 -15.452 -76.689 23.049 0.0000000000 571 -15.631 -67.683 9.887 0.0000000000 573 -4.258 -84.880 12.147 0.0000000000 version of FreeSurfer: freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275

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Freesurfer July 2023