Freesurfer February 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
83 discussions

Tissue Segmentation
by ERNEST KISSI 12 Feb '24

12 Feb '24

External Email - Use Caution Hello freesurfer team, Please does Freesurfer have a function or a code for tissue Segmentation just like in FSL that you can do tissue based segmentations into GM, WM and CSF and also their partial volume segmentations? Thank you.

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mri_histo_atlas_segmen/ mri_synthseg errors (on MacBook M1 pro)
by Leon D. Lotter 12 Feb '24

12 Feb '24

External Email - Use Caution Dear FreeSurfer Developers, I am trying to run the new “NextBrain" probabilistic atlas mri_histo_atlas_segment model, which internally calls mri_synthseg with additional parameters `--threads 8 --cpu --parc --robust` as a first step. My system: MacBook Pro 2021 with M1 pro chip, currently running macOS Monterey 12.6 I installed the most up-to-date developmental FS version: freesurfer-macOS-darwin_arm64-dev-20240211-4e530af Currently, I am definitely getting stuck on the mri_synthseg step, so for now my issue is related to SynthSeg, not to the NextBrain package. This is what I did so far, assuming I am in the SUBJECTS folder: 1. The example for mri_hist_atlas_segment, `mri_histo_atlas_segment bert/mri/orig.mgz bert/mri/histo_atlas_segmentation/ 1 8` will return an error without displaying the error message. 2. I reproduced the error by running it’s analysis steps one by one: SynthSeg returns an error right after running it with any kind of configuration (e.g., `mri_synthseg --i bert/mri/orig.mgz --o mri/synthseg.mgz`): `module 'numpy' has no attribute ‘float128’. This is traceable to line 1595 of freesurfer/dev/python/scripts/mri_synthseg. The error generally seems to be a known issue on Apple chips. I fixed it with replacing `np.float128` with `np.longfloat`. 3. Now, SynthSeg starts to set itself up but quits with: ``` Node: 'model_1/unet_bn_down_0/FusedBatchNormV3' Detected at node 'model_1/unet_bn_down_0/FusedBatchNormV3' defined at (most recent call last): File "/Applications/freesurfer/dev/python/scripts/mri_synthseg", line 2642, in <module> main() File "/Applications/freesurfer/dev/python/scripts/mri_synthseg", line 162, in main predict( File "/Applications/freesurfer/dev/python/scripts/mri_synthseg", line 323, in predict post_patch_segmentation = net.predict(image) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2554, in predict tmp_batch_outputs = self.predict_function(iterator) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2341, in predict_function return step_function(self, iterator) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2327, in step_function outputs = model.distribute_strategy.run(run_step, args=(data,)) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2315, in run_step outputs = model.predict_step(data) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2283, in predict_step return self(x, training=False) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 569, in __call__ return super().__call__(*args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/base_layer.py", line 1150, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/functional.py", line 512, in call return self._run_internal_graph(inputs, training=training, mask=mask) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/functional.py", line 669, in _run_internal_graph outputs = node.layer(*args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/base_layer.py", line 1150, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/layers/normalization/batch_normalization.py", line 597, in call outputs = self._fused_batch_norm( File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/layers/normalization/batch_normalization.py", line 990, in _fused_batch_norm output, mean, variance = control_flow_util.smart_cond( File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/control_flow_util.py", line 108, in smart_cond return tf.__internal__.smart_cond.smart_cond( File "/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/layers/normalization/batch_normalization.py", line 979, in _fused_batch_norm_inference return tf.compat.v1.nn.fused_batch_norm( Node: 'model_1/unet_bn_down_0/FusedBatchNormV3' 2 root error(s) found. (0) INVALID_ARGUMENT: input must be 4-dimensional[1,256,256,256,24] [[{{node model_1/unet_bn_down_0/FusedBatchNormV3}}]] [[model_1/model/gaussian_blur/ExpandDims_27/_546]] (1) INVALID_ARGUMENT: input must be 4-dimensional[1,256,256,256,24] [[{{node model_1/unet_bn_down_0/FusedBatchNormV3}}]] 0 successful operations. 0 derived errors ignored. [Op:__inference_predict_function_4927] resuming program execution ``` 4. After further messing around with the mri_synthseg script, I can get past that point by changing all lines that call the `unet` function from `net = unet(nb_features=24, input_shape=[None, None, None, 1], ...)` to `net = unet(nb_features=24, input_shape=[1, None, None, None, 1], ...)` or similar (e.g. line 627, 645, 667, 684, …). However, then it crashes at a later point with other errors apparently related to data dimensionality. I would really appreciate any suggestions! I know that running the analysis on a MacBook might not be the best choice anyways, but before I try to set it up on our institute HTC (which might be a whole other challenge), I though I try it that way. Also, I figured someone might be interested in the error report. Thanks a lot! Best wishes, Leon ____________ Leon D. Lotter, MD Clinician Scientist PhD candidate INM-7: Brain and Behaviour, Research Centre Juelich Institute of Systems Neuroscience, University Hospital Duesseldorf Max Planck School of Cognition, Leipzig https://secure-web.cisco.com/1dp_Q8wZIqLOEUSqDix0kribzUPxw3EWu7oCDRmyzTKfFU… leondlotter(a)gmail.com l.lotter(a)fz-juelich.de

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Bayesian Segmentation with Histological Atlas - FreeSurfer Version
by Adrian Korbecki 12 Feb '24

12 Feb '24

External Email - Use Caution Good morning, I recently came across the Bayesian Segmentation with Histological Atlas feature during my FreeSurfer research, and I'm very interested in trying it out. However, I found that my current FreeSurfer version is from June 2023, and it appears that this feature requires a version released after October 26, 2023. Could you advise on how I can obtain this newer version of FreeSurfer to utilize this module? Kind regards, Adrian Korbecki MD, PhD

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Academic posts in MRI physics - University of Manchester and UK biobank
by Hamied Haroon 10 Feb '24

10 Feb '24

External Email - Use Caution Dear all, Please share with anyone you think might be interested! Also posted on LinkedIn<https://secure-web.cisco.com/1jDTsSIfcrw7IcQGNzSJSGVwV1pQOqWyqshPbwGz8_StzY…> and Twitter<https://secure-web.cisco.com/1HkvPwIQH_B9DboW5qhjc--GteS7iuUPkogmzFk60U65sc…>. An exciting opportunity in Manchester: 2 PERMANENT ACADEMIC POSTS IN MRI PHYSICS Do you want to work on the largest imaging project in the World? Come and join us! The UK Biobank Imaging Study is a "first of a kind", significantly larger than any previous imaging study. The unprecedented scale, detail and quality of the project has enabled unique discoveries about the development of many diseases in older age. The post-holders will work seamlessly across the University of Manchester and the UK Biobank (approximately on 50% each). You will develop a highly competitive program of research linking with your Biobank role. This could be related, but not limited, to areas of strategic importance such as technological advances in neuroimaging. To apply (deadline 28 Feb): https://secure-web.cisco.com/1Mp50NFo-hHPbosu0KgfnbdtWzFYpaFDZlKS0mGny5AKWi… For informal enquiries please contact: Prof. Laura Parkes Laura.Parkes(a)manchester.ac.uk<mailto:Laura.Parkes@manchester.ac.uk> ____________________________________ Prof. Laura Parkes (She/Her) Lead for Manchester Neuroimaging Zochonis building room 124d University of Manchester Laura.Parkes(a)manchester.ac.uk<mailto:Laura.Parkes@manchester.ac.uk> sites.manchester.ac.uk/mcrneuroim<https://secure-web.cisco.com/1icY_AfRQUFWeTEBK2-xlnqdxUY82AcygPpI-CHvfPq-Pm…> @McrNeuroIm [twitter.com]<https://secure-web.cisco.com/18DXTZWvT6uMDu6t_rIsYgfcm3JkWfxvEvoAAQ9UXNmx_Q…>

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Re: [Freesurfer] mpr2mni305 failed
by fsbuild 09 Feb '24

09 Feb '24

External Email - Use Caution  The recon-all log contains this entry, ERROR: mpr2mni305 failed, see transforms/talairach_avi.log If you go to where that log file is, which I think would be, $ cd $SUBJECTS_DIR/mri/transforms … then look in that log file to see what the error is.  It is usually at the end of the log file. - R. On Feb 9, 2024, at 07:16, Francesco Lomi <francesco.lomi(a)unifi.it> wrote:        External Email - Use Caution        Unfortunately I've tried to change the directory but I've encountered the same error, as shown in the log file. Best,FrancescoIl giorno gio 8 feb 2024 alle ore 17:59 Huang, Yujing <YHUANG43(a)mgh.harvard.edu> ha scritto:This is from your recon-all.log: “setenv SUBJECTS_DIR /home/ubuntu/freesurfer/subjectsFREESURFER_HOME /home/ubuntu/freesurferActual FREESURFER_HOME /home/ubuntu/Freesurfer“Your SUBJECTS_DIR points to your Freesurfer install directory - /home/ubuntu/freesurfer/subjects. I’m not sure if this is the reason for the failure. But it is a good idea to set SUBJECTS_DIR to some other directory where you have write permissions. Can you re-set SUBJECTS_DIR and try again? Best, Yujing   From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Francesco LomiSent: Thursday, February 8, 2024 11:44 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] mpr2mni305 failed         External Email - Use Caution        Yes, sure. This is the fileThanks.  Il giorno gio 8 feb 2024 alle ore 17:03 Huang, Yujing <YHUANG43(a)mgh.harvard.edu> ha scritto:Can you re-send recon-all.log as attachment? From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Francesco LomiSent: Thursday, February 8, 2024 10:58 AMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] mpr2mni305 failed         External Email - Use Caution        Hello everybody, I'm new on Freesurfer and I've installed the software on my Ubuntu 20.04 machine. The installation should be fine. just tried to run recon-all on my subject data but i got stuck on the following error you can see on the screenshot: <image001.png> Any idea on how to fix this?Thank you in advance Best,Francesco_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XbsZgwTnI3onjdYJVFjoCKwtbD8UOXL2chYPX… 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1AWr9-RI-XVYXogeF7gwubnfYP8OHUBQfXOW1x… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PLDGVmlJ15D7C2mdizQggSFTGmzd-UMuECjke…; .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._______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XbsZgwTnI3onjdYJVFjoCKwtbD8UOXL2chYPX… 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1AWr9-RI-XVYXogeF7gwubnfYP8OHUBQfXOW1x… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PLDGVmlJ15D7C2mdizQggSFTGmzd-UMuECjke…; .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. <recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Assistant/Associate/Full Professor, Radiology, Human Ultra-High-Field MR
by Jennifer Elam 09 Feb '24

09 Feb '24

External Email - Use Caution *Assistant/Associate/Full Professor, Radiology, Human Ultra-High-Field MR * *Division: *Radiological Sciences *Track: *Tenure *Rank: *Commensurate w/Experience *Position Description: * The Mallinckrodt Institute of Radiology (MIR) at the Washington University School of Medicine in St. Louis -- consistently ranked among the top five departments in NIH radiology funding (fourth in 2020, second in 2021, and third in 2022) -- invites applications for two full-time faculty positions on the investigator (tenure) track in human ultra-high field (UHF) MR imaging and spectroscopy. Applications are particularly encouraged from candidates with research interests focused on UHF RF coil and hardware development or novel acquisition and reconstruction methods. *Qualifications: * - PhD, MD/PhD or equivalent degree in the physical sciences or engineering; - Experience and skill in the development of UHF MR hardware or data acquisition and reconstruction methods; - Demonstrated potential or success in obtaining extramural funding; - Demonstrated potential or success in mentoring graduate students and post-doctoral fellows; - Outstanding communication, writing, and interpersonal skills. *Biomedical MR Center (BMRC): * The selected candidates will join the Biomedical Magnetic Resonance Center (BMRC), one of five research centers housed within MIR. The BMRC comprises approximately 20 faculty members and 50 students, postdoctoral fellows, staff, and clinical fellows. BMRC investigators are pioneers in the development and application of MR techniques and data analytics, providing an understanding of the complex microstructure and biophysical and physiological determinants that govern healthy and diseased tissues. The BMRC offers a collaborative environment for diverse interdisciplinary research initiatives. More information about the BMRC can be found here: https://secure-web.cisco.com/1nSa0o7OBhpVJOO3EbXEa-9SNtFPhm8gCZ2DJcyYm5_3gd… The selected candidates will be encouraged to collaborate with the BMRC faculty and the broader imaging community in MIR and other departments at Washington University in St. Louis. *Facilities: * MIR is a preeminent research institute with excellence in magnetic resonance imaging, optical imaging, neuroimaging, PET tracer development and translation, and imaging informatics. MIR has extensive collaborations with other top-ranked departments across the School of Medicine and the University. MIR supports world-class research imaging facilities, including magnetic resonance, nuclear, molecular, and optical imaging resources, and cyclotrons for preclinical and translational research. Human MR research scanners include a Siemens whole-body Terra.X 7T (anticipated delivery in summer 2024), four Siemens Prisma 3T, a Siemens Vida 3T, a Siemens Biograph mMR PET/MR, and two PET/CT (Vision). The MIR small-animal imaging resources include 9.4 T, 4.7 T, and 11.74 T MR scanners, PET/CT and simultaneous PET/MR scanners, and a GE SPINlab hyperpolarization unit. MIR radiologists serve nine hospitals, including the nationally ranked Barnes-Jewish and St. Louis Children's Hospitals, bridging cutting-edge MRI science with clinical excellence. *Benefits: * Washington University provides faculty with generous benefits that include health, life, disability coverage, retirement, and tuition assistance. In addition to these competitive benefits, the university offers a variety of time off and quality-of-life programs. We are a diverse group and wholly encourage diversity to reflect the rich community in which we live and serve. We are committed to promoting an environment that is inclusive and welcoming to all individuals. All qualified applicants will receive consideration for employment without regard to race, color, age, religion, sex, sexual orientation, gender identity or expression, national origin, veteran status, disability, or genetic information. *Application Instructions * Candidates are invited to submit their applications through Opportunity Details - Faculty Opportunities (wustl.edu) including a cover letter detailing qualifications and career goals, a research plan, and a curriculum vitae addressed to Dr. Pam Woodard, Elizabeth E. Mallinckrodt Professor and Chair of the Department of Radiology. *Contact for questions * Hongyu An, D.Sc, Chair of the Search Committee hongyuan(a)wustl.edu 314-3625805 http://secure-web.cisco.com/1sJF6ys1OMuD8BKVdzY_hxlGAXIiE2BJ84epS5n49kUQ7tJ… -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu http://secure-web.cisco.com/10X4eqA4EeOjIrPj1lwKKIkO0LWWuqGi0mtRPBn1u9DnAfg…

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mpr2mni305 failed
by Francesco Lomi 09 Feb '24

09 Feb '24

External Email - Use Caution Hello everybody, I'm new on Freesurfer and I've installed the software on my Ubuntu 20.04 machine. The installation should be fine. just tried to run recon-all on my subject data but i got stuck on the following error you can see on the screenshot: [image: Schermata del 2024-02-08 16-55-08.png] Any idea on how to fix this? Thank you in advance Best, Francesco

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make_average_subject command error
by Asuka Toyofuku 09 Feb '24

09 Feb '24

External Email - Use Caution Dear Freesurfer experts, We're trying to make an average subject for group analysis using Freesurfer 7.1, but the make_average_subject command exits with errors after calling make_average_surf: MakeAverageSurf(): 129 lh pial sphere.reg talairach.xfm 1 1 It appears to be trying to find the lh.pial surface for the first participant, but this file is named "lh.pial.T1". (In FS 5.3 and 6.0, this file was labelled "lh.pial", but with FS7.1, it seems to be named lh.pial.T1). Does anyone have a suggestion for how to fix this problem? (We want to avoid changing all the file names to "lh.pial" from "il.pial.T1") Should we call make_average_subject again with -no-surf-to-surf ? Best regards, Asuka

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Re: [Freesurfer] Synthsr command !
by fsbuild 08 Feb '24

08 Feb '24

External Email - Use Caution The python distribution in the 7.4.1 release cannot run all the python based tools on a Silicon Mac (M1, M2, M3 chip) because at that time we did not have a python distribution that was completely compatible with the arm64 architecture. We currently have a development build for the Silicon Mac, and you can download/try the installer package from: https://secure-web.cisco.com/1iKFStD8SwFv0R2HIbwHmO8r1CRu1iDcQPEOYPG7jJvIjr… But we cannot recommend this build for ongoing work as it is currently unstable and not a tested release. - R. On Feb 7, 2024, at 17:05, Martin Juneja <mj70481(a)gmail.com> wrote:        External Email - Use Caution        Dear Juan and FreeSurfer developers,I am trying to run the mri_synthsr command on a MacPro M2 Max chip (OS 13.6.4) - but somehow, I am getting the following error when I try to run this command. I am using FreeSurfer's 7.4.1 version.Illegal instruction: 4I would greatly appreciate any help in getting this resolved.Thanks._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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if: Expression Syntax - preproc-sess with -nomc option
by Stefano Delli Pizzi 08 Feb '24

08 Feb '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run preproc-sess with -nomc option preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -force if: Expression Syntax. This error occurred before to create the file with slice timing correction The error did not occur when I run the preproc-sess command line without the -nomc option. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Platform: Darwin Kernel Version 21.6.0

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