Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

dt_recon question
by Mirsol Choi 09 Nov '23

09 Nov '23

External Email - Use Caution Hi there, I am currently going through the dt_recon tutorial on your website and I just have a quick question regarding the recon-all and dt_recon commands on freesurfer. For me to process dt_recon, my understanding is that I must process recon-all first. But where my confusion lies is: - do I perform recon-all on the actual dwi.nii.gz image, then dt_recon with the same dti files (including the bval and bvec of the same dwi.nii.gz file) OR - should I have two separate sets of data, one T1 and one DTI, and perform recon-all on T1 images and take DWI images from the same subject to perform dt_recon? My understanding was that the second bullet is the right way to go since the dt_recon uses the outputs from T1 recon-all to register properly. Please let me know which one is correct, and if I am missing something. Thank you so much for your help, I really appreciate your time. M

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SynthSEG continued developments
by Dawn Matthews 09 Nov '23

09 Nov '23

External Email - Use Caution Thank you for all of the work of the FreeSurfer team in continuing to make advances to the Freesurfer suite of tools. I wondered if you could comment on (a) any work or plans to include hippocampal subfield, brainstem subfield, or corpus callosum subfield segmentations, and (b) the robustness of SynthSEG to defacing/refacing software as compared to Freesurfer? Thanks very much.

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PETsurfer kinetic modeling
by Dawn Matthews 09 Nov '23

09 Nov '23

External Email - Use Caution Congratulations to the FreeSurfer team in the continued progress made in the FS tool set. I wondered if you could comment on whether it is feasible to create a custom reference region (other than specifying, for example, cerebellar cortex or another predefined FS mask) for PETsurfer kinetic modeling (e.g. a cerebellum subfield) or whether there perhaps is an existing cerebellar subfield atlas that can be run with PETSurfer (e.g. crus2)? In addition, can you please confirm whether the Logan model can be run using a reference region (i.e. without requiring arterial input)? Thanks very much and kind regards.

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Unsubscribe Mailing List
by yunus soleymani 09 Nov '23

09 Nov '23

External Email - Use Caution Hi Freesurfer Team Please unsubscribe my email from the list Email: soleymani.yunus(a)yahoo.comThanksYunus --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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TRACULA Stat error: no pathway reconstructions found
by Lauren Stephens 08 Nov '23

08 Nov '23

External Email - Use Caution Hi FreeSurfers, I have successfully run trac-all -prep, -bedp, and -path on all of my files. However on two of my files when i ran trac-all -stat -c /Users/corpuscallosum/Desktop/TRACULA/RRD/R007A/R007A.txt and trac-all -stat -c on /Users/corpuscallosum/Desktop/TRACULA/RRD/R006B/R006B.txt I got the errors: no pathway reconstructions found. For both files I went to dpath and they both have the correct information and files present. I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6. The log files were too large to attach to this email. Any suggestions for getting the stats files extracted? Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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extracting measurements from segment_subregions
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 08 Nov '23

08 Nov '23

External Email - Use Caution Hi all, First time using FS7.4 for subfields specifically hippo/amy. I've used segment_subregions this time around, and it seems the function for concatenating the volumes, quantifyHAsubregions doesn't work anymore. I suspect its because the .v21 got removed. What is the new function to use now? And could you make it clear in the wiki? Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1QwN_OAI7oG3gbr_OYdwJ9T0dJh1oMH38-joi_EsdgSKHnh… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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parallel processing of long-run fails
by P Pieperhoff 08 Nov '23

08 Nov '23

External Email - Use Caution Dear FreeSurfer developers, when I execute a long-run with parallel processing by calling recon-all -sd <directory> -threads 64 -openmp 64 -parallel -long <imageid> <template_id> -all it fails in step "autorecon3" at the surface registration. But when I start it again without the option "-parallel", it finishs without errors. I'm using FreeSurfer version 7.4.1 with Linux CentOS. I have attached the log file to this mail. Best regards, Peter

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Loading surfaces
by Nicole Rychagov 08 Nov '23

08 Nov '23

External Email - Use Caution Dear team: I am reaching out as I have encountered an error when loading surfaces on Freesurfer and am unsure what it means or how to address the error. I am including the error message below, and I would greatly appreciate any assistance you can provide. mrisReadTriangleFile(/mnt/d/chtt_edited_long_subjects_corrected/090324_CH8357/surf/lh.pial): surface doesn't match /mnt/d/chtt_edited_long_subjects_corrected/090324_CH8357/surf/lh.white No such file or directory mrisReadTriangleFile failed. No such file or directory Converting main surface: 100% done. Converting main surface: 100% done. mrisReadTriangleFile(/mnt/d/chtt_edited_long_subjects_corrected/090324_CH8357/surf/rh.pial): surface doesn't match /mnt/d/chtt_edited_long_subjects_corrected/090324_CH8357/surf/rh.white No such file or directory mrisReadTriangleFile failed. No such file or directory reading colortable from MGH file... colortable with 14176 entries read (originally /fslhome/aaclouse/compute/research_bin/version7_2/freesurfer/FreeSurferColorLUT.txt) Thank you so much for your time! Sincerely, Nicole

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fsxvfb error: Falling back to using screens root_visual
by Dani Del Rubin 08 Nov '23

08 Nov '23

External Email - Use Caution Hello Developers, I’m trying to use fsxvfb to run freeview and save some snapshots, but I can’t get it to run. The command I’m executing is: “fsxvfb freeview -v brainmask.mgz -ss pic1.jpg --quit" The output I get is: this pid 23712 setting display to 86 [1] 23721 pid 23721 Starting command freeview -v brainmask.mgz -ss pic1.jpg --quit Falling back to using screens root_visual. Falling back to using screens root_visual. Falling back to using screens root_visual. Falling back to using screens root_visual. Segmentation fault (core dumped) Program exited normally. No image is saved. If I run the command without fsxvfb, it executes successfully ending up with a saved image, although it still gives an error: X server does not support XInput 2 QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id: 133, major code: 130 (Unknown), minor code: 47 QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id: 133, major code: 130 (Unknown), minor code: 47 Also, I can successfully run the AFNI command @snapshot_volreg to output an image, and that script also uses xvfb, so I don’t believe it’s a general problem with xvfb. Finally, my environment by default uses freesurfer version 6.0.0, but I’ve run the commands “export FREESURFER_HOME=/usr/global/freesurfer/7.4.1” followed by “source /usr/global/freesurfer/7.4.1/SetUpFreeSurfer.sh” to temporarily change the version. Other info: 1. Freesurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 2. Platform: Ubuntu 16.04.7 LTS 3. uname -a: Linux [nodename] 4.4.0-206-generic #238-Ubuntu SMP Tue Mar 16 07:52:37 UTC 2021 x86_64 x86_64 x864_64 GNU/Linux 4. I am connecting remotely via X2Go to a MATE setup, which then connects to the compute node. I only saw 5 questions referring to xvfb on the archive, and most questions about xvfb I found online seem to not apply to my situation. Thanks very much for any help! Dani -- Dani Del Rubin, Ph.D. (he/him) Research Data Analyst, Psychiatry Oregon Health & Science University c: 301-437-7660 | rubinstd(a)ohsu.edu

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mri_cvs_register failure
by Antonín Škoch 08 Nov '23

08 Nov '23

External Email - Use Caution Dear experts, I have encountered an failure of mri_cvs_register --mov my_subject --mni The resulting output file final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz looks like in the attachment. Could you please give me a hint, where could be a problem, or how to troubleshoot the mri_cvs_register routine? Regards, Antonin Skoch

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Freesurfer November 2023