Freesurfer January 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
132 discussions

Re: [Freesurfer] Missing transformation files in
by Nederpelt, D. van (David) 25 Jan '21

25 Jan '21

External Email - Use Caution Hi Douglas, I'm sorry I did not see the reply. However, according to this FSwiki page (https://secure-web.cisco.com/1ewSiiCxfbK4xZi1tAuiwuw5w7OeKME66LJV0CpSAaOHVv… , see the information I found below) the transform file should be in the longitudinal directory, if I'm not mistaken. I ran FS 6.0.1 for a previous project and the transform files were present there. Now with FS 7.1.1 they are not present. I ran the recon-all -all -3T pipeline on two different OS and didn't get the needed .lta files. The transform files are missing for each subject I ran (448) To be sure I've attached the recon-all.log file for the cross, base and longitudinal run for one subject. Thank you for your help! Kind regards, David cd $SUBJECTS_DIR/<tpid>.long.<baseid>/mri mri_convert -ait transforms/<tpid>_to_<tpid>.long.<baseid>.lta \ -rl $SUBJCECTS_DIR/<tpid>/mri/rawavg.mgz \ -rt nearest -odt uchar \ aseg.mgz aseg-in-rawavg.mgz Message: 1 Date: Fri, 15 Jan 2021 09:24:33 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FW: Missing transformation files in longitudinal pipeline To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <821a58f9-2fa0-4db1-56fc-75e63c997019(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Are you looking in the base/mri/transforms folder? If it is not there, can you send the recon-all.log file for the base run On 1/14/2021 11:12 AM, Nederpelt, D. van (David) wrote: > > ????????External Email - Use Caution > > Hi FS-team, > > I ran a longitudinal recon-all stream(FS version 7.1.1) ?and trying to > convert the aseg.mgz back to native space. However, in the transform > file the <tpid>_to_<tpid>.long.<baseid>.lta is missing. > > This is the case for every subject I ran, while the recon-all.log > showed freesurfer finished without errors. I?ve attached the .log > file. The base dir does have the needed transform files. > > How can I resolve this and transform ROI to native space? > > Thank you in advance, > > Kind regards, > > David ******************************************* ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/1LR8PaInq9faioBV4wOz8RSwnKDDD3kmimYFmZTyHAZ63Ee… AMC disclaimer : http://secure-web.cisco.com/17sYewASoS_ayfu7I7ZppvxN_xtGM_aIVV2MP-PJ1Ab-Gxu…

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Error Using samseg
by Jesper Folsted Kallehauge 23 Jan '21

23 Jan '21

External Email - Use Caution Dear All, I have encounter an error when running samseg for a fraction of my subjects. I am very new to FreeSurfer so there is a good chance it is a rookie mistake. The error message I get is the following: Traceback (most recent call last): File "/home/frog/freesurfer/python/scripts/run_samseg", line 166, in <module> reg_only=args.reg_only File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 132, in segment return self.postProcess() File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 239, in postProcess posteriors, biasFields, nodePositions, _, _ = self.computeFinalSegmentation() File "/home/frog/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 778, in computeFinalSegmentation posteriors = self.gmm.getPosteriors(data, priors, self.classFractions) File "/home/frog/freesurfer/python/packages/freesurfer/samseg/GMM.py", line 183, in getPosteriors posteriors = posteriors / np.expand_dims(normalizer, 1) MemoryError: Unable to allocate 7.15 GiB for an array with shape (21800066, 44) and data type float64 The it finishes without a segmentation. Does anyone know the solution to this issue ? King regards Jesper Kallehauge

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Taking screenshots on different views with tksurfer
by Simone Cauzzo 23 Jan '21

23 Jan '21

External Email - Use Caution Dear all, I have a lot of different surface analyses to display. For each test that I performed, I have to take a screenshot of the left and right medial surfaces and left and right lateral surfaces (4 screenshots for each analysis). Since there's a lot of screenshots to take and I'd like to test different thresholds, I'd like to do it from the command line without using GUIs. At the moment I'm using tksurfer mni152.fnirt lh inflated -ov *********.nii.gz -fminmax 5 8 -truncphaseflag 1 -snap *************.tif But this only helps me with lateral views. Is there any way to automatically take a snap of the medial view? Thanks Simone

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Mapping labels created in fsaverage_sym into subjects.
by Jose Graterol 21 Jan '21

21 Jan '21

External Email - Use Caution Hello, I have a question regarding label mapping. I did a whole-brain analysis in the fsaverage_sym space and extracted some of the clusters that I obtained as labels. I would like to use those labels to obtain the mean cortical thickness values for each participant. The approach that I thought of is the following: Mapping the labels with mri_label2label --srcsubject fsaverage_sym --trgsubject subject. And then extracting the thickness with mris_anatomical_stats. Some labels are lh and some rh, so I would need to flip them in the fsaverage_sym space with mris_apply_reg, although the hemispheres are the same, to be able to map them into the subjects. Would this be the recommended way to do it? Or is there something better that I can apply? I would really appreciate your help and thank you in advance José

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Emerging Topics in Artificial Intelligence 2021 Conference
by Joana Braga Pereira 21 Jan '21

21 Jan '21

External Email - Use Caution Dear all, We are organizing the second edition of the conference “Emerging Topics in Artificial Intelligence”, which will take place from 1-5 August 2021 in San Diego, USA. The aim of this conference is to bring together experts from different fields to discuss new applications of artificial intelligence to biomedicine, neuroimaging, microscopy, active matter and photonics. Importantly, this conference will also count with the participation of industry to foster commercialization and utilization opportunities. Please find more detailed information about the topics that will be covered at: http://secure-web.cisco.com/1CslSK-vNS5mb8ErSEP5niowyyr_RmPbKemszI6ldTcFq-U…. Despite the ongoing pandemic situation and its unusual online format, the 1st edition held in 2020 was a major success with more than 3000 visualizations and 70 video talks. We hope to replicate and even advance this success in the new edition of the conference. At the moment we are planning to make the conference in person but, depending on the circumstances, we might change it to a virtual format. The period for abstract submission is now open. Please forward this information to anyone who might be interested. Best wishes, Joana B. Pereira (Karolinska Institute) Giovanni Volpe (Gothenburg University) Aydogan Ozcan (University of California) Daniel Brunner (Institut Franche-Comte Electronique Mecanique Thermique et Optique) Follow us on twitter: @ETAIconference

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Postdoctoral Fellowship in advanced multi-parametric imaging in Parkinson’s disease, Alzheimer’s disease, and healthy aging.
by Maurizio Bergamino 20 Jan '21

20 Jan '21

External Email - Use Caution My Lab, at Barrow Neurological Institute (Phoenix, AZ), is looking for a Postdoc. The study will be mainly focused on task-based fMRI and resting-state fMRI. *A postdoctoral fellowship position (fully funded for up to three years) is available at Barrow Neurological Institute (BNI) working with Ashley Stokes, PhD, and Ryan R. Walsh, MD, PhD, as part of a rapidly growing collaborative research effort between the Division of Neuro-Imaging Research, Department of Neurology, and Muhammad Ali Parkinson Center. The position will primarily focus on the development, application, and analysis of advanced MRI methods in the context of both Parkinson’s disease and Alzheimer’s disease, as well as dementia with Lewy bodies and healthy cognitive aging, expanding upon recent novel approaches developed by this multi-modal lab. These methods include advanced functional, diffusion, perfusion, and structural imaging methods, with an emphasis on novel mathematical/signal processing approaches to provide a more comprehensive understanding of neurodegenerative diseases and normal brain aging across structural, functional, and perfusion signatures, including their mutual interdependence.BNI is the world’s largest dedicated neurological disease treatment and research institution, and the Muhammad Ali Parkinson Center at BNI is a recognized leader in the field. Outstanding institutional resources, including 1.5T and 3T Philips clinical MRI, a research-dedicated Philips 3T MRI, a 7T preclinical Bruker MRI, microCT, microPET, and optical imaging scanners are available at BNI. The Division of Neuro-Imaging Research has a strong history of imaging excellence and is currently expanding. BNI is a major hub for neuroscience research, including both basic and translational neuroscience, with a wide range of internationally-recognized neurology subspecialties. Barrow Neurological Foundation provides robust philanthropic support exceeding $18M per annum, 100% of which benefits patient care, research and education at BNI.Applicants should have a PhD in physics, engineering, mathematics, computer science, or a related discipline. Competitive candidates will have expertise in signal processing and/or functional MRI and be interested in developing novel approaches to analysis of MRI-based signals. This position is available immediately and offers competitive compensation and benefits.Phoenix is the 5th largest metropolitan in the United States and the 2nd fastest growing city. Phoenix is a beautiful place to live and work, boasting more days of sunshine and a lower cost of living than most comparable cities. A rich culture, including theatre, concerts, museums, sports, and great food, are easily found in Phoenix. With a moderate climate most of the year, many Phoenicians enjoy an active lifestyle of hiking, cycling, rock climbing, swimming, and golf.* *Interested applicants should send a current CV, including the names of three references, to both:Ashley M. Stokes, Ph.D.Assistant Professor - Division of Neuro-Imaging Research Barrow Neurological Institute Ashley.Stokes(a)BarrowNeuro.organd/orRyan R. Walsh, M.D., Ph.D., FAANAssociate Professor - Muhammad Ali Parkinson Center Department of Neurology - Barrow Neurological Institute Ryan.Walsh(a)BarrowNeuro.org*

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Re: [Freesurfer] Error in longitudinal pipeline
by vittal korann 20 Jan '21

20 Jan '21

External Email - Use Caution Hi Kersten Thank you for kind response. I think we need to talk about the design matrix X first (sorry, I did not look at your xlsx file; I think it's probably better to send simple csv files if at all). I attached longitudinal data in csv format. Besides the covariates that you mention, the matrix needs to contain an intercept, a variable for ?time?, a variable for ?group? (assuming you have a control group also), and a group-by-time interaction term in order to asses differential change over time (again, if you have a control group). I do not have a control group. Right now I have only schizophrenia patients who underwent 2 scans: first is baseline and second one is after 3 months of yoga therapy. Wish to know the how can I proceed with my availabe data. Just to make sure: ?age? should be ?age at baseline? (i.e. constant across time per subject), otherwise it will be confounded with time. Yes, I used same across the study. Could you review (and possibly adapt) your design matrix X with respect to which columns it contains, and write it in the reply? I tried but couldn't get there. Any help would be greatly appreciated! Thanks, Vittal

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BIDS-PET extension request for comments - closes on Friday, Feb. 12
by Franklin Feingold 19 Jan '21

19 Jan '21

External Email - Use Caution We are happy to announce that the Positron emission tomography BIDS extension is finally nearing it’s completion. Hence, we are seeking final community feedback for the PET BIDS standard. We are looking for feedback on GitHub and specifically to the BIDS-PET extension proposal ( https://secure-web.cisco.com/18Ho2R5GZxtyWMrxs5QijrXyOtATKVsoJi_C5x9ERZG379… ). We have also developed an extension for the validator ( https://secure-web.cisco.com/1DgfuUr_8N83-nl-GVdF77jT1sDjVqo-4lsli0XrQ3TOkX… ) and added PET examples into BIDS examples ( https://secure-web.cisco.com/1wcZumOdpBZTibGDOVnAaiUqg8mWF2RuYFeqp6qHGuwgbx… ). The community review will close on Friday (Feb. 12) at 11:59pm PT (pacific time). This BIDS extension seeks to establish how PET data and additional metadata are organized within the BIDS structure. This encompasses the recent guidelines for brain PET data in publications and in archives provided in the consensus paper (Knudsen et al. 2020, https://secure-web.cisco.com/1MIWMgeigCAuC-K3Vo4dwvsJCklRfo3-nj_Avatf4FkWMO… ), including blood and metabolite data. The final review entails a two week period for public commenting, with a possibility of extension for unresolved discussion. Once public comments are concluded, there will be a one week freeze, during which only critical issues will be considered. (Please see our release protocol for more details, https://secure-web.cisco.com/1YsYtZpSMYV6IeNX0JH4epLt99zW9k-K7bPF3XTD3j9llS… ) We are looking forward to hearing from you, Melanie Ganz (BEP 009 lead) and team

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Recon-all log
by Bohorquez Montoya, Luisa 19 Jan '21

19 Jan '21

External Email - Use Caution Good morning freesurfer, I am new using recon all. Would you mind to help me with this error I am getting? What should I do? Attached is the log and here is my command. recon-all \ -subject ${ANATDIR} \ -i ${ANATDIR}/${subject}/*Ax_FSPGR_3D_GR.nii.gz \ -T2 ${ANATDIR}/${subject}/*Ax_T2_FLAIR_SE_IR.nii.gz \ -T2pial \ -parallel -openmp 12 \ Thank you so much for your time Luisa Bohorquez, PhD. Department of Psychiatry, Medical College of Wisconsin.

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Re: [Freesurfer] Recon-all Error
by Garcia Pallares, Erendira Xenia 19 Jan '21

19 Jan '21

Hi Dimitri, Could you indicate the recon command that you ran? You could try rerunning the recon-all command in the directory with one of the dicom files for the T1 image. I’ve posted an example command below: recon-all -all -i I50 -s Subj001 • The file after the “-i” flag indicates your input dicom file (I50) • The file after the “-s” flag represents the output directory (Subj001) after you have run recon-all If you have more than one dicom file that you’d like to run through the recon pipeline you can add -i flags for each additional dicom. You can find additional information on the Freesurfer<applewebdata://2215FD5C-E547-4E06-A0A9-A6F106A2BD18/that%20you%20can%20also…> wiki Let me know if you have more questions. Best regards, Ren From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Date: Wednesday, January 6, 2021 at 21:34 To: Freesurfer(a)nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all Error External Email - Use Caution Hello! I’m experiencing an error while I try to use recon-all in a T1 MRI image, the following error message appears: “[...] using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... error: mghRead(/home/developer/Desktop/BIBE_2020/Simulated_MRI/HC/rf0/t1_icbm_normal_1mm_pn1_rf0/mri/norm.mgz, -1): could not open file error: mri_normalize: could not open source file norm.mgz” Thanks!

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Freesurfer January 2021