Freesurfer

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Question on using thalseg_1.1.h5
by Georgios Argyropoulos 08 Apr '24

08 Apr '24

External Email - Use Caution Dear Colleagues, Hope you're well. I have been trying to use the thalseg_1.1.h5 patch (MRI Segment Thalamic Nuclei CNN model v1.1 update). I use the following command: mri_segment_thalamic_nuclei_dti_cnn --t1 mri/norm.dwispace.mgz --aseg mri/aseg.dwispace.mgz --fa dmri/dtifit_FA.nii.gz --v1 dmri/dtifit_V1.nii.gz --o outputSegmentation.nii.gz --vol measuredVolumes.csv --model /usr/local/freesurfer/7.4.1/models/thalseg_1.1.h5 --threads 3 However, I have been encountering the following error message. I was wondering whether you may be able to help. many thanks georgios Using user-specified model: /usr/local/freesurfer/7.4.1/models/thalseg_1.1.h5 DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) Traceback (most recent call last): File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 2551, in <module> main() File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 164, in main predict( File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 258, in predict net = build_model(model_file_segmentation=path_model_segmentation, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 661, in build_model net = unet(nb_features=24, ^^^^^^^^^^^^^^^^^^^^ File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 942, in unet dec_model = conv_dec(nb_features, ^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 1125, in conv_dec input_shape = last_tensor.shape.as_list()[1:] ^^^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'shape' -- Georgios P. D. Argyropoulos PhD, CPsychol, FHEA Division of Psychology, Faculty of Natural Sciences; University of Stirling; FK9 4LA Scotland UK *Personal Website <https://secure-web.cisco.com/1bHuyxjaHSXaNhBW47ORm6M_ZgtAKVjOaFDyrDvTlvpzMG…>*

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WMH-SynthSeg - Torch module not found
by Corinne Alison Donnay 06 Apr '24

06 Apr '24

External Email - Use Caution Good Afternoon! I was working with my IT department to install the development version of FreeSurfer on our server so that I could use WMH-SynthSeg<https://secure-web.cisco.com/13uSpbM7Qfplsr0IlNG1yQzvDu3TL4ODjz8qdEUly_QzsK…>. IT installed development version 2024-04-14. After loading the freesurfer development module, and running source $FREESURFER_HOME/SetUpFreeSurfer.sh, I still get the following error: [cid:image001.png@01DA8780.B1BD2E60] Is there any way to fix this or figure out what is wrong? Thank you! Corinne

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recon-all exits with errors
by William Graves 05 Apr '24

05 Apr '24

External Email - Use Caution Dear FreeSurfer Developers, I’m trying to run recon-all as a pre-processing step in the AFNI resting-state analysis pipline, using the command: recon-all -subject $subj -i $anat_cm -all -parallel So far it has successfully run on about 20 participants in my sample, but for the current participant it’s now suddenly throwing this error: PIDs (691564 691567) completed and logs appended. Linux demeter 6.2.0-26-generic #26~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Jul 13 16:27:29 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s R21-24 exited with ERRORS at Fri Apr 5 16:29:23 EDT 2024 I searched through the log file, tried Googling the error, and searched your email list archive, but couldn’t find anything to address this. The log file is attached, along with: 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2) Platform: Ubuntu 22.04.3 LTS I’d appreciate any help or advice you could give! Best, Will --- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ 07102 http://secure-web.cisco.com/1YyXSJSQDDL3zr4YbJxaYRG9TNwpk7Xc_p79GM8FJGBDWWV…

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Recon-All Clinical Stream: Image Output Observations in Creating ENIGMA QC Images
by Sam Sievertsen 05 Apr '24

05 Apr '24

External Email - Use Caution Good Afternoon, I hope this email finds you well! My name is Sam Sievertsen, the research coordinator for Dr. Jennifer Forsyth at the University of Washington. We are utilizing the recon-all clinical processing stream from FreeSurfer 7.4.1 on Rocky Linux (within our institutions HPC environment) to process subjects with decreased T1 image quality, and for whom previously processing with the standard recon-all pipeline resulted in missed grey matter during segmentation. Per recommendations in the bug reporting page, I have attached an example recon-all clinical log from this processing in case it is helpful. Following the recon-all clinical processing of these subjects, we are using an existing (ENIGMA cortical QC) pipeline to take screenshots of the external cortical reconstruction <https://secure-web.cisco.com/19i9TSlgNlNnONXLIpqTWX3BCSsnOf-EugV08XsKq72OGs…> / aparc+aseg segmentation overlaid on internal images <https://secure-web.cisco.com/13TQ3PwQQ9BI4s2aBpZBhunwgJsJT6-yH3IIqx3cliLqe4…> . We are able to successfully generate external (reconstruction) cortical QC images using the recon-all clinical output, but encounter an error when attempting to generate the internal (T1 with aparc+aseg.mgz overlay) QC images. Specifically, there is a conditional check within the internal QC image generation script linked above that halts the process if the Nx*Ny*Nz dimensions in the T1 image and the Nx*Ny*Nz dimensions in aparc+aseg.mgz do not align, which is where our process is throwing the error. Manual examination of the recon-all clinical image output (e.g., "native.mgz", "synthSR.norm.mgz", and "aparc+aseg.mgz") suggests that the aforementioned dimensions are all different in those images. Conversely, the dimensions in the processed images and segmentations (e.g., "orig_nu.mgz", "aparc+aseg.mgz") from the standard recon-all pipeline appear to be uniform (256) for those same subjects we are processing in this cohort. To hopefully assist with clarity, I have attached the script we are using ("func_make_corticalpngs_ENIGMA_QC.m") to construct these internal QC images, and example output files from the same subject using the standard recon-all pipeline output ("internalQC_standard_recon_all.txt") and recon-all clinical pipeline output ("internalQC_recon_all_clinical.txt"), which show a discrepancy in the aforementioned dimensions. Following up on the above information, I am wondering if "SynthSeg: to obtain a volumetric segmentation and linear registration to Talairach space"on the recon-all clinical page <https://secure-web.cisco.com/1ysMZeQggBLaLzKrZvbENqA_ienVNIRzPan5TKDtzxTjvk…> about registration to talairach space implies that the recon-all clinical output should have uniform dimensions, or if I am misunderstanding that and there is anything that stands out from this description that we may be doing incorrectly/that other users have encountered as well? Would also be very appreciative of any other suggestions you may have for attempting to troubleshoot this issue, thank you very much in advance for your time! Happy to answer any resulting questions or follow up with additional information should it be helpful. All the best, *Sam Sievertsen * Research Coordinator I Department of Psychology, GRaND Lab [image: logo]

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Support for GPU on Freesurfer
by Camargo, Aldo 04 Apr '24

04 Apr '24

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 Camargo Senior Postdoctoral Fellow at the University of Maryland, Baltimore

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Re: [Freesurfer] Question about mris_compute_lgi error: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied")
by fsbuild 03 Apr '24

03 Apr '24

External Email - Use Caution  The permissions on /scratch may not be set to allow you to write files there.  If it does not work from the terminal window to create a plain file there via the command, $ touch /scratch/foo - then you will get the same permission denied error. If the above fails, then you should contact whoever setup the machine, your IT department, etc. and ask them to provide write permission there. - R, Begin forwarded message:From: XinRan Wu <wxr1173199759(a)gmail.com> Subject: [Freesurfer] Question about mris_compute_lgi error: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied") Date: April 3, 2024 at 12:14:38 EDT To: freesurfer@nmr.mgh.harvard.edu Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> ERROR: could not open /scratch/

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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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