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mri_glmfit error: matrix is rank-deficient by 18
by Shawn Flanagan 04 Oct '24

04 Oct '24

External Email - Use Caution *Hi FreeSurfer Developers,* *I am attempting to compute group analysis as described in the FS tutorial and it appears to run but with the following message at the end for each contrast:* Writing results CON-ACLleft maxvox sig=-2.57471 F=9.30914 at index 155198 0 0 seed=1728409464 Computing efficiency /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 CON-ACLright maxvox sig=2.75772 F=10.1304 at index 31842 0 0 seed=1728409464 Computing efficiency /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 CON-ACLtar maxvox sig=2.22177 F=7.75177 at index 69873 0 0 seed=1728409464 Computing efficiency /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 mri_glmfit done *I have searched the list and no similar errors have been reported. Does anyone have thoughts or insights about this? If it is helpful, I have attached the fsgd file, contrast files, script file, and a representative mri_glmfit log file. * *1) FreeSurfer Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460* *2) Platform: Mac Studio M2* *3) Script: * #!/bin/tcsh set study = $argv[1] foreach hemi (lh rh) foreach smoothness (0 5 10 15 20 25) foreach meas (volume thickness) mri_glmfit \ --y ${hemi}.${meas}.${study}.${smoothness}.mgh \ --fsgd FSGD/${study}.fsgd dods \ --C Contrasts/CON-ACLleft.mtx \ --C Contrasts/CON-ACLright.mtx \ --C Contrasts/CON-ACLtar.mtx \ --surf fsaverage ${hemi} \ --cortex \ --glmdir ${hemi}.${meas}.${study}.${smoothness}.glmdir \ --eres-save end end end *Appreciate your time and advice!* *Best,* *Shawn* -- *Shawn Flanagan, PhD* Associate Professor Director, Human Performance Laboratory Department of Podiatric Medicine and Surgery Dr. William M. Scholl College of Podiatric Medicine Neuroscience Program School of Graduate and Postdoctoral Studies shawn.flanagan(a)rosalindfranklin.edu <shawn.flanagan(a)rosalindfrankln.edu>

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Hybrid combination
by Maja Nikolova 01 Oct '24

01 Oct '24

External Email - Use Caution Hi, I want to do tractography on Olfactory bulb in Parkinson Patients but if I use Desikan and Killiany atlas I can't define well Olfactory bulb but cortical parcelation from Desikan is perfect for Neurodegenerative disorders . For functional disorders AAL2 and define Olfactory Bulb is good. My question is can I combine this two atlases and to have *Combine Parcellations:* - *Cortical parcellations* from Desikan-Killiany via FreeSurfer. - *Subcortical and white matter parcellations* from the AAL2 atlas Meaby sound crazy but I think of this and I like to ask does this is possible any way? Thanks in advance, Best Maja

1 0

PetSurfer, PVC uptake of ROI relative to Pons
by zeno Zeng 01 Oct '24

01 Oct '24

External Email - Use Caution Hi Freesurfer experts, Instead of adjusting the 'PVC uptake of ROI relative to the Pons,' I want to adjust it to the 'whole cerebellum.' Are there any parameters I should modify in the command for this? Also, which parcellation or segmentation method would you recommend for this adjustment? Thank you!

2 1

PhD position available/sensory thalamus/developmental dyslexia
by Katharina von Kriegstein 01 Oct '24

01 Oct '24

External Email - Use Caution We are seeking an enthusiastic PhD student with a particular interest in understanding sensory mechanisms of human communication. Task: The task of the successful candidate involves using high-resolution neuroimaging to test for predictive coding mechanisms in the human sensory pathway in typically developed populations as well as in populations with developmental dyslexia. The project is based on prior work of our group listed here<https://secure-web.cisco.com/1eYkFNwS9FN7zHVolDH0xnf7Dq2PeToz4b3PaGM5L5bup8…>. The setting: TU Dresden is one of eleven German Universities of Excellence. The successful candidate will be based at the Chair of Cognitive and Clinical Neuroscience<https://secure-web.cisco.com/1qGAH2dJu90pNwxoYbS7Y6juvJSqgDQ-kidjwgQ3pm48NC…>. The Chair is part of ReDyslexia,<https://secure-web.cisco.com/1PA3bsEfLY6OZN-kdgPonD-JPj0_q_3Pmuu0ibq3J-gqgi…> which is a research consortium of neuroscientists and clinicians that have the aim (1) to better understand sensory pathway dysfunction in developmental dyslexia, and (2) to directly use this knowledge for improving treatment strategies. ReDyslexia includes studies in humans with developmental dyslexia as well as experiments in animal models. Experiments will be performed at the TUD Neuroimaging Centre (NIC<http://secure-web.cisco.com/1B9euS7RTbWQs6UhieoP1iAfAPZQtKflzEo6zYBPMzf0SuZ…>). The NIC is equipped with a research-only MRI machine (Siemens 3T Prisma), MRI-compatible EEG, eye-tracking and noise-cancellation headphones, and a neurostimulation unit including TMS, tDCS, and tFUS. The experimental facilities are supported by experienced physics and IT staff. The TU Dresden Graduate Academy <https://secure-web.cisco.com/1ThIXhNwzW-Vhe99NSgvkuSueEU_Q9xZUZjW1I_bxTtLme…> offers a comprehensive training programme and individual career advice for early career researchers. The Dresden-concept Welcome Centre<https://secure-web.cisco.com/1lIFaP6lw1NR_zF5f6l4e99SbQKbaTDH3MUX7n-gS6mFrx…> facilitates the start in Dresden for international researchers. The position: The PhD position is fully funded (E13 TV-L 75%) and available at the next possible date. More information: The official job advertisement can be found here PDF<https://secure-web.cisco.com/1jNiBTkw1M6UJAE-Ib7raXVeRlcY1PsBKW7TaNOY0czV14…>. If you have questions or for informal enquiries on the post please contact Katharina von Kriegstein (katharina.von_kriegstein(a)tu-dresden.de<mailto:katharina.von_kriegstein@tu-dresden.de>) _ _ Katharina von Kriegstein Professor of Cognitive and Clinical Neuroscience Vice-Dean Faculty of Psychology TUD Dresden University of Technology Chemnitzer Str. 48b, 01187 Dresden Phone +49 (0) 351-463-43145 https://secure-web.cisco.com/1CzroRXZF2PJEcrPWVAU4xGHcirslcxHmAHQJuWAMqWJDv… https://secure-web.cisco.com/1laJ-TJJIUcBtWBNrNJIWkJF0ayhUIJHmzIkWw3ciMwg2a…

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petsurfer using brainstem subfields
by Sneha Pandya 01 Oct '24

01 Oct '24

External Email - Use Caution Dear team, We need to use PVC brainstem subfield which we intend to use as high binding region for MRTM based kinetic analysis. Can we run mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation? Or is to possible to combine gtmseg and brainstem subfields and use this combined segmentation for mri_gtmpvc (will be using GTM or RBV for PVC). Thank you, Sneha

2 5

BEDPOSTX Tracula Error
by Daniel Salinas 30 Sep '24

30 Sep '24

External Email - Use Caution Hello, I hope this email finds you well. I submitted this command to run the second part of tracula trac-all -bedp -c $SUBJECTS_DIR/tracula/tracula_config.txt And, before it would process, but then I was looking into SLURMS and somehow misconfigured it. Now I get: I tried to reconfig the file and got it running again, but still get the error: ----------------------------------------------------------------------------------- (base) danielsalinas@danielsalinas-linux:~$ trac-all -bedp -c $SUBJECTS_DIR/tracula/tracula_config.txt INFO: SUBJECTS_DIR is /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer INFO: Diffusion root is /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output Actual FREESURFER_HOME /usr/local/freesurfer ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output/NCANDA_S00033/dmri/nodif_brain_mask.nii.gz WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 -model 1 /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output/NCANDA_S00033/dmri subjectdir is /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output/NCANDA_S00033/dmri Making bedpostx directory structure Queuing preprocessing stages srun: error: Invalid --mail-type specification Queuing parallel processing stage ----- Bedpostx Monitor ----- srun: error: Unable to allocate resources: Job dependency problem Queuing post processing stage srun: error: Unable to allocate resources: Job dependency problem ----------------------------------------------------------------------------------- I remade the config file: # Basic settings ControlMachine=danielsalinas-linux ClusterName=BakerLabCluster AuthType=auth/munge SlurmdPort=6818 SlurmctldPort=6817 SlurmUser=slurm SlurmdUser=root StateSaveLocation=/var/spool/slurmctld SlurmdSpoolDir=/var/spool/slurmd # Add or modify in your slurm.conf JobCompType=jobcomp/filetxt JobCompLoc=/var/log/slurm/jobcomp.log # Node settings NodeName=danielsalinas-linux CPUs=8 RealMemory=94000 Sockets=1 CoresPerSocket=4 ThreadsPerCore=2 State=IDLE # Partition settings PartitionName=normal Nodes=ALL Default=YES MaxTime=INFINITE State=UP

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Repost: NextBrain Segmentation PyTorch-GPU Compatibility Error
by AmirHussein Abdolalizadeh 30 Sep '24

30 Sep '24

External Email - Use Caution Hi, I am reposting an issue with NextBrain that I asked about a few months back: https://secure-web.cisco.com/1Ep1FaXAlpDcDJk3cT-fDgniEdtHQ5Fy30s9xstmgNRrAE… "NVIDIA H100 with CUDA capability sm_90 is not compatible with the current PyTorch installation. The current PyTorch install supports CUDA capabilities sm_37 sm_50 sm_60 sm_70 sm_75 sm_80 sm_86." There is a PyTorch incompatibility with the newer H100 nVidia GPUs. I had the same issue with FastBrain which was resolved by updating their torch dependencies in their release. See the discussion here: https://secure-web.cisco.com/1iI7S9ydIJfS44SEVzbqqTAOd5_M_tzx6bBulJhDsE0KOd… I think this can be a solution for this issue as well since many HPCs are moving towards these kinds of GPUs. Best, Amir

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Efficient printing of freeview screenshots through freeview [HPC]
by Camilo Castelblanco Riveros 30 Sep '24

30 Sep '24

External Email - Use Caution Hi, I am trying to print screenshots of MR images efficiently with the freesurfer reconstruction with Freeview in an HPC. For an unknown reason, this code works for iterating over sagittal, not coronal or axial coordinates. It does not iterate over the coordinates in the coronal and axial cases even though the cmd file looks okay. Any help would be appreciated. -------- # Define the MRI and surface files for the current subject T1_IMAGE="${SUBJECT_DIR}/mri/T1.mgz" WM_IMAGE="${SUBJECT_DIR}/mri/wm.mgz" BRAINMASK_IMAGE="${SUBJECT_DIR}/mri/brainmask.mgz" ASEG_IMAGE="${SUBJECT_DIR}/mri/aseg.mgz" LH_WHITE="${SUBJECT_DIR}/surf/lh.white" LH_PIAL="${SUBJECT_DIR}/surf/lh.pial" RH_WHITE="${SUBJECT_DIR}/surf/rh.white" RH_PIAL="${SUBJECT_DIR}/surf/rh.pial" # Define number of slices and step size for each view (sagittal, coronal, axial) STEPS=15 # Increase this value for more plots/slices SAGITTAL_START=20 SAGITTAL_END=200 CORONAL_START=20 CORONAL_END=200 AXIAL_START=20 AXIAL_END=200 # Create a fresh cmd.txt file for the current subject echo "-v $T1_IMAGE \ $WM_IMAGE \ $BRAINMASK_IMAGE \ $ASEG_IMAGE:colormap=lut:opacity=0.2" > "$CMD_FILE" echo "-f $LH_WHITE:edgecolor=blue \ $LH_PIAL:edgecolor=red \ $RH_WHITE:edgecolor=blue \ $RH_PIAL:edgecolor=red" >> "$CMD_FILE" # Loop through slices in each dimension and add commands to cmd.txt #==================> Sagittal view slices (changes in X-coordinate) for ((i = 0; i <= STEPS; i++)); do slice=$(bc <<< "$SAGITTAL_START + ($SAGITTAL_END - $SAGITTAL_START) * $i / $STEPS") echo "-viewport sagittal -slice $slice 127 127 -viewsize 800 800 -ss ${ OUTPUT_DIR}/sagittal_slice_${slice}.png -noquit" >> "$CMD_FILE" done # Reset the view and Freeview instance to avoid cache issues between views echo "-quit" >> "$CMD_FILE" echo "Processing sagittal slices..." # Debug message freeview -cmd "$CMD_FILE" > freeview_log.txt 2>&1 sleep 2 # Wait for Freeview to close completely # If Freeview doesn't quit properly, use pkill as a fallback pkill freeview #%%%%%%%%%%%%%%%%%%%% # Create a fresh cmd.txt for coronal slices CMD_FILE="${OUTPUT_DIR}/cmd_coronal.txt" #================> Coronal view slices (changes in Y-coordinate) for ((i = 0; i <= STEPS; i++)); do slice=$(bc <<< "$CORONAL_START + ($CORONAL_END - $CORONAL_START) * $i / $STEPS") echo "-viewport coronal -slice 127 $slice 127 -viewsize 800 800 -ss ${ OUTPUT_DIR}/coronal_slice_${slice}.png -noquit" >> "$CMD_FILE" done ------- Best regards, Camilo *================================* *Camilo Castelblanco Riveros (He/His)* Integrative Neuroscience at Dartmouth (IND) Ph.D. Candidate Robertson Lab <https://secure-web.cisco.com/1QRdD2mxYtydinuoic7wn0eITgFhkqKqoGQdP-IFOAFtu5…> & Bujarski Lab <https://secure-web.cisco.com/1cOiHwMsWx3XS3cX7DjImdJuyBu3ix4ePXcP4xtelQK30A…> Student Interest Group in Neurology (SIGN <https://secure-web.cisco.com/1dq5CGYwmVLVUgtU1lI9vL6j7Qx4yi0AzfTjFxlK___c2G…>) Co-Leader Diversity Student Advisory Board Member e: ccastelblanco.gr(a)dartmouth.edu <camilo.a.castelblanco.riveros.gr(a)dartmouth.edu> Zoom <https://secure-web.cisco.com/14g7m031Cr0kkdNxX-rGazLPRk_s-3aNkJgXOZ6l_5Sf_8…> [image: Integrative Neuroscience at Dartmouth (IND) (@DartmouthNeuro) / Twitter]

2 1

morphometry protocol - cross site/platform?
by Mira Michelle Raman 30 Sep '24

30 Sep '24

External Email - Use Caution Good afternoon, I was looking at the Morphometry Protocol on the wiki and was wondering if anyone has developed matching GE sequences (which they would be willing to share) that could be used in combination with these Siemens sequences (or equivalent) for a multi-site study. My proposed project: -multi-site (Siemens and GE), -participants under sedation (so minimum scan time is ideal), and - minimum images need T1w, T2w, and quantitative T1 at 1mm^3 resolution. Sincerely, Mira _______________________________________________________________________ Mira Michelle Raman BrIDGe Lab, Division of Interdisciplinary Brain Sciences Stanford University 1520 Page Mill Rd, 160.12 Palo Alto, CA 94304

2 1

NextBrain with 333 labels
by Woo-Suk Tae 30 Sep '24

30 Sep '24

External Email - Use Caution Dear FreeSurfer experts I tried to segment my brain MRI using NextBrain.in the most recent FreeSurfer-dev package. I followed the command in https://secure-web.cisco.com/150f92dNZNQHVJBK1fmC5Z4FYOqCYvgP1aIrq7dafQUxfy…, but, I got only the volumes of 101 labels How can I got the 333 labels and volumes using NextBrain? my command as follows mri_histo_atlas_segment ../subject/mri/orig.mgz ..subject/mri/histo_atlas_segmentation/ full 1 -1 Best regards Woo-Suk Tae Seoul, Korea -------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Korea University College of Medicine, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6077 email: woosuk.tae(a)gmail.com, w <woosuk.tae(a)kumc.or.kr>stae(a)korea.ac.kr woostae(a)naver.com --------------------------------------------------------------------

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