Freesurfer

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17 participants
30130 discussions

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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.lta vs .dat questions
by Corinna Bauer 08 Nov '23

08 Nov '23

External Email - Use Caution Hi all, Can someone please explain the difference between .lta and .dat and why the registration looks different using the two file types? If bbregister outputs were already checked and edited (if needed) using the .dat file, is there a way to convert it to .lta? Thanks Corinna

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TR: Issues at the "tailarach_avi" transformation step of recon-all
by Hensenne, Eva (Stud. FHML) 08 Nov '23

08 Nov '23

External Email - Use Caution ________________________________ De : Hensenne, Eva (Stud. FHML) <e.hensenne(a)student.maastrichtuniversity.nl> Envoyé : mercredi 18 octobre 2023 14:41 À : freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Objet : Issues at the "tailarach_avi" transformation step of recon-all Dear Freesurfer Developers, I am currently running recon-all on a UNI scan. This scan has already been partly preprocessed by a script called "presurfer". This presurfered scan should work with recon-all (and it indeed works for my colleagues). However, I have systematically an error when I try to run recon-all on those files. The error says: "talairach_avi log file is transforms/talairach_avi.log... Error:mpr2mni305 failed, see transforms/talairach_avi.log Command exited with non-zero status 1". I attached you the talairach_avi.log and the recon_all.log files. 1. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2. Platform: Unbuntu 22.04 3. Recon-all.log: attached Best wishes, Eva Hensenne

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Atrophy Maps on Coronal Slices
by Daniel Gutstein 08 Nov '23

08 Nov '23

External Email - Use Caution Is there a methodology in FreeSurfer for creating atrophy maps and displaying them on individual coronal slices? Thank you. Daniel Gutstein Research Data Analyst Northwestern University | Mesulam Center for Cognitive Neurology & Alzheimer's Disease 300 E. Superior Street | Tarry 8-734 | Chicago, IL 60611 daniel.gutstein(a)northwestern.edu<mailto:daniel.gutstein@northwestern.edu> | (312) 503 - 8150

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Common space
by Alberto Del Cerro Leon 08 Nov '23

08 Nov '23

External Email - Use Caution Good morning, I would be interested in observing regional differences in cortical thickness without using predefined regions. However the results offered by FreeSurfer arrange the thickness results etc. in an individual space which is difficult to compare between subjects before labeling. Is there a possibility to transform the results to a common mesh (like a template) in order to perform an exploratory analysis?

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