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30070 discussions

No flt available for tract training files
by Stylianos Charalampous 12 Jun '23

12 Jun '23

External Email - Use Caution Hello, I am trying to to run trac-all and I am getting the following error when using the FSL Flirt registration in the prior fitting step, due to the flt files not being available for the tract training subjects: WARN: Could not open /path/trctrain/hcp/mgh_1001/syn/acomm.flt.prep.trk for reading WARN: Error was: Can not open file WARN: Skipping to next subject Note: The reason I am using Flirt is because BBRegister requires the lh.white and rh.white files which I don't have available as I have used third party software for the brain parcellation. I have also had an issue with the fs_temp_file function which gives an error in cases where the subject is given as a nested folder, e.g. subject_1/subject_1_visit_1, subject_1/subject_1_visit_2 instead of subject_1_visit_1, subject_1_visit_2. This error was only noticed in the prior fitting step where the ntest was appended before subjid thus creating a file /tmp/1.subject_1/subject_1_visit_1.txt for instance causing an error. -- Kind regards, Stylianos Charalampous

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Re: [Freesurfer] Longitudinal SAMSEG with multi-contrast data
by Cerri, Stefano,PHD 12 Jun '23

12 Jun '23

External Email - Use Caution Hi Gonzalo, Assuming that you have run mri_robust_template and obtained longitudinally registered images (e.g., tp0_t1_reg.mgz, tp1_t1_reg.mgz, etc...), then you can co-register each additional contrast of each time point with the commands: mri_coreg --mov tp0_flair.nii --ref tp0_t1_reg.mgz --reg tp0_FLAIRtoT1.lta mri_vol2vol --mov tp0_flair.nii --reg tp0_FLAIRtoT1.lta --o tp0_flair_reg.mgz --targ tp0_t1_reg.mgz for time-point 0 and mri_coreg --mov tp1_flair.nii --ref tp1_t1_reg.mgz --reg tp1_FLAIRtoT1.lta mri_vol2vol --mov tp1_flair.nii --reg tp1_FLAIRtoT1.lta --o tp1_flair_reg.mgz --targ tp1_t1_reg.mgz for time-point 1, etcetera. Stefano [Freesurfer] Longitudinal SAMSEG with multi-contrast data<https://secure-web.cisco.com/1wqAljGN-HfqNgjoB_GLYISZdkqc0_9NrBWKfoyXxioxHK…> Gonzalo Rojas Costa<https://secure-web.cisco.com/17xEk5nL7zi1KleESqeBlN3BTHFcZZZ5aIVXY_BJb6V_Lk…> Mon, 12 Jun 2023 10:21:51 -0700<https://secure-web.cisco.com/1emebkgy5p75OaE8PVfVUI7Bh8WG2NzT6RocEeQ_clhqM6…> External Email - Use Caution Hi: How can I generate "tp1_flair_reg.mgz" image appeared in command "run_samseg_long --timepoint tp0_t1_reg.mgz tp0_flair_reg.mgz --timepoint tp1_t1_reg.mgz tp1_flair_reg.mgz --timepoint tp2_t1_reg.mgz tp2_flair_reg.mgz --output outputDir/" ? Sincerely, Gonzalo Rojas Costa _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1gm8Mo90Xz5BNWI2qCZ6Q3l2guFyqznXM3Mc10zV67LMsh… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/12Agmx53cqZKs72ZRcgmLh2khJsG4EHKL-2xt0JtfedpJH… <https://secure-web.cisco.com/12Agmx53cqZKs72ZRcgmLh2khJsG4EHKL-2xt0JtfedpJH…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Longitudinal SAMSEG with multi-contrast data
by Gonzalo Rojas Costa 12 Jun '23

12 Jun '23

External Email - Use Caution Hi: How can I generate "tp1_flair_reg.mgz" image appeared in command "run_samseg_long --timepoint tp0_t1_reg.mgz tp0_flair_reg.mgz --timepoint tp1_t1_reg.mgz tp1_flair_reg.mgz --timepoint tp2_t1_reg.mgz tp2_flair_reg.mgz --output outputDir/" ? Sincerely, Gonzalo Rojas Costa

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VM password
by Chad Haines 12 Jun '23

12 Jun '23

External Email - Use Caution Hello. I would like the password to the Ubuntu VM that has Freesurger installed on it. Thank you.

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Generate Stats File for fornix.mgz in T1 weighted MRI ?
by Ahsan Ali 12 Jun '23

12 Jun '23

External Email - Use Caution Dear Sir/Madam, I'm having a ADNI T1 weighted MRI database. I have run the recon-all command successfully and got a couple of default stats files in the stats folder. Then fornix.mgz is estimated using command "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f folder_name" successfully. Now what can be done to generate the stats for fornix.mgz? I've been struggling with this for a long time, please help me with this. I'm using ubuntu. [image: IMG-20230526-WA0000.jpg] With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552

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trac-all ERROR: Option syn/acomm.flt.prep.trk unknown
by Stylianos Charalampous 12 Jun '23

12 Jun '23

External Email - Use Caution Hello, I am attempting to run white matter tractography using TRACULA, as described in the tutorial, however, using a brain parcellation acquired using an external algorithm. I have put the aparc+aseg.mgz file in the subject directory in folder mri but I am getting the following error: ERROR: Option syn/acomm.flt.prep.trk unknown Linux GS63VR-6RF 5.19.0-43-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon May 22 13:39:36 UTC 2 x86_64 x86_64 x86_64 GNU/Linux I also get the following error in the start of the prior fitting step in case they are linked: #@# Priors Mon Jun 12 11:43:04 AM BST 2023 error: Could not create temporary file in /tmp $slistfile: Ambiguous. The error occurs when running the prior calculation step using the prep command: trac-all -c config_file -prep. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this one? 1) FreeSurfer version: freesurfer-7.3.2 2) Platform: ubuntu-22.04.02

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Huge difference between volumes for Freesurfer vs CAT12
by Michael Mc Laughlin 10 Jun '23

10 Jun '23

External Email - Use Caution I have used both CAT12 and Freesurfer to segment a particular brain scan and I get completely different volumes. CAT12 (cc) Freesurfer 7.3.2 (cc) Left Cerebral White Matter volume(cc): 209 Left hemisphere cerebral white matter volume 242 Left Cerebral Cortex volume(cc): 444 Left hemisphere cortical gray matter volume 269 Left Lateral Ventricle volume(cc): 28 Left-Lateral-Ventricle 43 Right Cerebral White Matter volume(cc): 208 Right hemisphere cerebral white matter volume 242 Right Cerebral Cortex volume(cc): 440 Right hemisphere cortical gray matter volume 270 Right Lateral Ventricle volume(cc): 20 Right-Lateral-Ventricle 28 Total 1350 Total 1095 Total volume (cc): 1618.09 Brain Segmentation Volume 1309 Estimated Total Intracranial Volume 1852 What could be causing this difference? The brain scan was done with MPRAGE protocol with 176x256x256 voxels of size 1mmx0.976mmx0.976mm Which one is correct? The scan is of a normal adult male aged 62 with chronic migraine. Michael McLaughlin,

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Cortical thickness of elephant brain
by Malav Shah 09 Jun '23

09 Jun '23

External Email - Use Caution Dear freeSurfer team, I am trying to extract cortical thickness in a postmortem elephant (structural) MRI scan. I initiated the process with the segmentation of white (wm) and pial matter, using MATLAB image processing tools. Having satisfied white and pial matter labels, I "tesselated" these volumes to generate pial and wm surfaces. Then, with 'mris_smooth' command, I smoothed these surfaces. When attempted to estimate cortical thickness between these surfaces (lh.pial.smth5 and lh.wm.smth5), I get the following error. command: mris_place_surface --thickness lh.pial.smth5 lh.wm.smth5 20 5 lh.thickness error: No such file or directory error: ERROR: MRISreadVertexPositions(/Volumes/experiment/share/Malav/Ele_ana_cortexMRI/pipelines/dumba_piece/lh.wm.smth5): surfaces differ. Main: 177753 verts 365096 faces, lh.wm.smth5: 145095 verts 298436 faces Surfaces may be out-of-date I understand there is a mismatch in the number of nodes of these surfaces. How can I rectify this issue to get to the thickness? Thanks and regards, malav Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

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different results for gtmpvc with different tracers
by Federica Di Antonio 09 Jun '23

09 Jun '23

External Email - Use Caution Dear experts, I hope this email finds you well. I run the pvc correction with mri_gtmpvc for subjects data obtained with two different PET tracers. In gtm.stats.dat, for every subject and every region, the number of voxels evaluated for amyloid tracer is approximately twice the volume evaluated for the second tracer. I'd expect that the volume of a region for the same subject doesn't change with the tracer. Do you think this error can result from previous errors in the analysis? Or is it in some way plausible? Thank you for your patience, Federica

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trac-all error aparc+aseg_mask.bbr not found
by Stylianos Charalampous 07 Jun '23

07 Jun '23

External Email - Use Caution Hello, I am attempting to run white matter tractography using TRACULA, as described in the tutorial, however, using my own data and brain parcellation acquired using external algorithm. I have put the aparc+aseg.mgz file in the subject directory in folder mri but I am getting the following error: Error : No image files match: /diffusion/root/subject/visit/dlabel/diff/aparc+aseg_mask.bbr The error occurs when running the tensor fit step using the prep command: trac-all -c config_file -prep As described in the trac-all documentation (https://secure-web.cisco.com/1OCcv-f3jRdcpwsIbW4XJ0lMpQY1t0rNu6Ec3x47wJ56GO…) the file aparc+aseg_mask.bbr was supposed to be created by the intra step which comes before tensor-fit but upon checking nothing is created. I have also tried running only that specific step using trac-all -intra but nothing is created either. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this one? 1) FreeSurfer version: freesurfer-7.3.2 2) Platform: ubuntu-22.04.02

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