Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Re: [Freesurfer] Problem accessing Buckner40 dataset
by fsbuild 06 Jul '23

06 Jul '23

External Email - Use Caution It looks like Mr. Buckner has moved on from where the link points to on that web site, i.e., that link is no longer valid.  His current lab posts this link for tools and data,cnl.rc.fas.harvard.edu/data-tools - but it’s not clear to me the same subjects are available there.   I don’t believe we can  re-distribute our pre-existing in-house copy.- R. On Jul 6, 2023, at 12:39, vinuyan sivakolunthu <vinuyansivakolunthu(a)gmail.com> wrote:        External Email - Use Caution        Hello Freesurfers,I was trying to access the Buckner40 dataset. There is a fswiki page (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1z4yAeqKJPyvFsObHdvqaJln_dwai7U-KJwGI2DQuNZcPN…) that points to MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1HJMRA3U3EHGopGkvJohIBU6zqAVrXsd6MgZX2fBDDJmOia…, but the site is no longer up. Is there somewhere else where I could obtain the data?Thanks,Vin_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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free surfer gets stuck infinitely during recon-all
by Rona Haker 06 Jul '23

06 Jul '23

External Email - Use Caution I'm attempting to do a full brain segmentation for a subject in my study using recon-all but after hours of running it did not reach the final step of creating aparc+aseg (the file I need), even though no error was printed. The last file that was created was 14 hours ago (till I stopped the run manually just now). my command is: recon-all -s ./00_FSseg -i ./8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all Attached is the log report of the run. By the way, this is a subject I have tried 3 times already to segment with no success, although most subjects in my study succeeded on the first try. recon-all -version command outputs this: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thank you, Rona Haker

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Regarding the paper on SYNTHSR... accuracy of parcellations?
by KennethSPrice 05 Jul '23

05 Jul '23

External Email - Use Caution Hello Freesurfers, I recently read the paper titled "SYNTHSR: A PUBLIC AI TOOL TO TURN HETEROGENEOUS CLINICAL BRAIN SCANS INTO HIGH-RESOLUTION T1-WEIGHTED IMAGES FOR 3D MORPHOMETRY" and need more information regarding table 2 (attached). Pearson Correlation values were given for SEGMENTATION structures but not PARCELLATION structures. Surely these values must be available somewhere? Could you please post the PARCELLATION correlation values? Thanks, Ken.

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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

1 0

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

2 6

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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