Freesurfer April 2024

freesurfer@nmr.mgh.harvard.edu

54 participants
64 discussions

Re: [Freesurfer] Support for GPU on Freesurfer
by fsbuild 03 Apr '24

03 Apr '24

External Email - Use Caution  Use of parallelization depends upon the order of how the data needs to be processed.  The recon-all command is not  single command, but a wrapper command that runs a sequence or pipeline of many lower level freesurfer commands in a certain order.   It’s not unexpected for recon-all of the subject bert data to take ~8 hours on a consumer (non-server, non-cluster), stand-alone machine, e.g. recent Intel I9 chip with 8 physical (performance) ~3 GHz cores, 8 virtual cores, 32G of DDR4 RAM and an SSD drive.  If you have access to a computing cluster, you could try running recon-all there - which should reduce the processing time. - R. On Apr 3, 2024, at 14:58, Camargo, Aldo <ACamargo(a)som.umaryland.edu> wrote:        External Email - Use Caution        Hi there,I was wondering if there is support for GPU on FreeSurfer. I really would like to use it on GPU because is taking 9 hours per subject to recon-all.Thanks a lot and have a nice day,Aldo CamargoSenior Postdoctoral Fellow at the University of Maryland, Baltimore_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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Question about mris_compute_lgi error: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied")
by XinRan Wu 03 Apr '24

03 Apr '24

External Email - Use Caution I am a researcher currently working with the Freesurfer 7.1.1 version for a research project. I have encountered an issue while trying to compute the local gyrification index (LGI). We have pre-existing Freesurfer analysis results, and we want to use the mris_compute_lgi script to calculate the LGI values. However, we are facing difficulties in the first step of running the mris_fill command to generate the ?h.pial.filled.mgz file. After the command completes, we are unable to read the generated ?h.pial.filled.mgz file, and we receive the following error: reading filled volume... /bin/bash: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh for reading ERROR: loading lh.pial.filled.mgz as MGH Dot indexing is not supported for variables of this type. Error in make_outer_surface (line 25) volume=vol.vol; We have also tried to read the lh.pial.filled.mgz file generated by mris_fill using the load_mgh function individually, but we are still unable to read it successfully. Could you please provide us with some guidance on how to resolve this issue?

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Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds
by fsbuild 01 Apr '24

01 Apr '24

External Email - Use Caution  You can try using the Silicon Mac development build on the M2 machine..  The download links is, https://secure-web.cisco.com/1sX8Y1I4GPyZJYzijtfGnav0Xe1MBg-Yv4HzZ07-_su8lv… Right click on the pkg installer and then select the “open with installer.app …” option. - R. On Apr 1, 2024, at 20:40, Martin Juneja <mj70481(a)gmail.com> wrote:        External Email - Use Caution        Hi Koen and Doug,I am trying to do similar analysis but when I run run_samseg command, it gives me error "Illegal Instruction: 4"I am using the FreeSurfer 7.4.1 version on Apple M2 Max MacBook Pro 14.4.1.Is it because run_samseg is incompatible with Apple M2? If so, could you please suggest any solution (if available) how I can run run_samseg on my Apple M2 computer?Thanks.

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recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")
by 彭翠仪 01 Apr '24

01 Apr '24

External Email - Use Caution Hello FreeSurfer Developers, I'm writing to ask for help while using "recon-all" command. I have converted some dcm format files to to nii format. Then I ran the command "recon-all -s maoyipeng -i first_sT1W_3D_TFE_tra_MR350895.nii -all", an error appeared: mri_convert /home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe similar/first_sT1W_3D_TFE_tra_MR350895.nii /usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz mri_convert: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz") type mri_convert -u for usage Command exited with non-zero status 1 @#@FSTIME 2024:04:01:09:09:04 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 100% M 5972 F 0 R 236 W 0 c 0 w 1 I 0 O 0 L 0.43 0.24 0.19 @#@FSLOADPOST 2024:04:01:09:09:04 mri_convert N 3 0.43 0.24 0.19 Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s maoyipeng exited with ERRORS at Mon Apr 1 09:09:04 HKT 2024 I've searched the list and didn't find a similar question. I'm a bit new to FreeSurfer, so I am unsure how to resolve this issue. I've attached the recon-all.log if that might help. 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b 2) uname -a: Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 3) recon-all.log: see attached

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Freesurfer April 2024