Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

Segmentation fault (core dumped)
by Tracy Riggins 09 Mar '23

09 Mar '23

External Email - Use Caution Greetings FS experts: We are trying to run recon-all -s -qcache on a handful of brains processed in freesurfer v5.1.0. (it's an old dataset...5.1 makes the most sense for our purpose.) The error is below: [image: image.png] -------------------------------------- #@# 1/1 HMN080 Fri Mar 3 12:14:44 EST 2023 -------------- ----------------------- mri_surf2surf --srcsubject HMN080 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.51930/HMN080.1.mgh --sval /export/data/seahorse_ncdl/HMN/data/HMN080/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux seahorse.umd.edu 3.10.0-1160.80.1.el7.x86_64 #1 SMP Sat Oct 8 18:13:21 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HMN080 exited with ERRORS at Fri Mar 3 12:14:48 EST 2023 Can you assist? OR perhaps tell us where to find the core dump file, which may have more information? -- Tracy Riggins, Ph.D. Pronouns <https://secure-web.cisco.com/1WTjrK6XJwG7-24mUYPAFcId6puqiKxHmofCChPCQb4mC-…>: she/her/hers Associate Professor of Psychology 4094 Campus Drive, Biology/Psychology Building 2147J University of Maryland, College Park, MD 20742 Zoom Meeting ID: 6751666548 <https://secure-web.cisco.com/1hviwkViTW16JTEvWH-47gs1rSV1H4pi6BZD9e1QCPEJ2V…> ***************************************************** Research info: http://secure-web.cisco.com/1JWrYfqglbLMQuNvUkCI3__mdHJZE-j2I4GZAMwxbYavfuR… and https://secure-web.cisco.com/1gMMoT_3zpTn_EJwufCskhV5rA9d3a3dfl-3blyeCnoRvf… Black lives matter in academia <https://secure-web.cisco.com/1J1h-u95rDMtqm8NNRIKxQgXcKxqK0HepLClZ-LZRNQ_s5…> LGBTQIA+ Ally <https://secure-web.cisco.com/1gzE6oBTSI-WE3shKwya1t2cvYue63e9MW9Tseqcx37Bos…>

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Substantia nigra segmentation status
by Christian Owen 09 Mar '23

09 Mar '23

External Email - Use Caution Hi, The latest post I could find about substantia nigra segmentation in FreeSurfer is from May 2020 <https://secure-web.cisco.com/1kbKgUj7tgWerg-kNskO0E4pbYddAh99-3abcyl688pSr5…>. As of that post, it was not possible. Is it still not possible? If that's the case: - is substantia nigra segmentation on the roadmap? - is there anything a software engineer could do to help make it happen? I cannot promise any resources atm, but there's a chance we could help out (if it turns out to be enough of a priority). Best, Christian

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freesurfer could not parse freeview-loadable surface label
by Yigu Zhou 09 Mar '23

09 Mar '23

External Email - Use Caution Hello Freesurfer community I am trying to transform a label file obtained in subject native surface space to subject native volume space. This label file was obtained through binarizing the subject lh.sulc morphological data through the function write.fs.label from R package freesurferformats, in the left hemisphere, resulting in a binary label for all sulci in the subject. Visual quality control of the label file through Freeview was adequate: I can load the surface label file with any surface of the subject. Now, I would like to map the corresponding voxels that belong to sulci in the left hemisphere of this subject. I tried to convert the label to volume using mri_label2vol first, but got the following error message could not parse 48510th line '1e+05 -37.5524826049805 -5.55967617034912 18.56817436218261' in label file I then tried to first convert the file to annot format using mris_label2annot and then convert to volume using mri_aseg2aparc. Similarly, mris_label2annot threw the error could not parse 48510th line '1e+05 -37.5524826049805 -5.55967617034912 18.56817436218261' in label file The list described similar errors but no obvious solution that I can access right now e.g. having a developer inspect the label file. I would love to get any pointer as to why the label file may have been unparse-able to Freesurfer tools. Sincerely Yigu

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password to unzip virtual machine
by Pierpaolo Croce 09 Mar '23

09 Mar '23

External Email - Use Caution I would like the password to unzip the virtual machine installation -- Ing. Pierpaolo Croce, PhD. Institute for Advanced Biomedical Technologies - ITAB and Department of Neuroscience and Imaging University of Chieti "G. D'Annunzio" Via dei Vestini, 33 66013 Chieti, Italy

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Re: [Freesurfer] SynthSeg with CT images.
by Gonzalo Rojas Costa 08 Mar '23

08 Mar '23

External Email - Use Caution Hi Benjamin: I tested with the clipping, and it works ok with a CT image. Sincerely Gonzalo Rojas Costa El mié, 8 de mar de 2023, 14:39, Benjamin Billot <bbillot(a)mit.edu> escribió: > Yes, agreed. > > Gonzalo: Also, if SynthSeg still gives you a bad result after clipping, > you might want to check that the image header is not corrupted. > > Best > > Benjamin > ------------------------------ > *From:* Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Sent:* 08 March 2023 12:25 > *To:* Gonzalo Rojas Costa; freesurfer(a)nmr.mgh.harvard.edu > *Cc:* Benjamin Billot > *Subject:* Re: SynthSeg with CT images. > > > Dear Gonzalo, > > Can you please try clipping the input to Hounsfield between 0 and 80? That > should do the trick. If you have trouble with this, feel free to send me > scan so I can take a look. > > Benjamin: maybe we should add this as a flag, as we do in SynthSR… > > Cheers, > > /E > > > > -- > > Juan Eugenio Iglesias > > http://secure-web.cisco.com/1oY_Ta7QUv3TybD8UgzuVG9Dc0uElb0r5sAAb2tL8RYcVO1… > > > > *From: *Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> > *Date: *Wednesday, March 8, 2023 at 12:04 > *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Cc: *"Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Subject: *SynthSeg with CT images. > > > > * External Email - Use Caution * > > Hi: > > > > I tried SynthSeg using CT images, but I got very bad results... CT > images must have some specific characteristics? I tried with axial > acquisition and volumetric one.... > > > > Sincerely, > > > > > > Gonzalo Rojas Costa > > Department of Radiology > Clínica las Condes > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > > https://secure-web.cisco.com/1dx-ON0IVqdFsAlkwbnFP-5CWyzUsWOqcXmV2sh2Kowfhn… > <https://secure-web.cisco.com/1X4JTWBblTD8tld8oBtoX_hRATMKAHXt1kz8xQ7YPlXYPC…> > https://secure-web.cisco.com/1WfM5q5JiWue1joAWuZpJ-2gnXIfCTH4jF5i5mncbvG8VT… > <https://secure-web.cisco.com/1jIR1VD1EGr6FdxqTGgScWCn_mHW5DPrMZAjfRggLiGtOa…> > > https://secure-web.cisco.com/18CztnN9siLRgJ0-UmgEchKrQq1yBr_pJu3oqRmA8vMLAA… > <https://secure-web.cisco.com/1yA9l7ISJLI6AsyMtjg6tqVLF4b_n1UlUVhia2mXbDUAX5…> > http://secure-web.cisco.com/1wJM_skjI0l0zygtqAs442I6qKn4WaYZxNrNXu6J9to22-8… > <http://secure-web.cisco.com/1WbHoWnrfeHvPRvJjfNf_577rSGYT1ApJAnQKa2Hbt1Jxqb…> > https://secure-web.cisco.com/1cCGpAkoZIpj8dp3v1C-VWfKKTjUqACatHALHubNHZqPhL… > <https://secure-web.cisco.com/1ZasoGFuD7Kwh5m95aUJSJ7Cq9E3amXs01l9LmTC_TxXWG…> > > 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/1Mc_8xJ_hTrW0ec0dAEqEMWEeqF1_jDIzgw0QhAg6eBMmS… . > > 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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Clinical Research Coordinator position at Penn FTD Center, Univ. of Pennsylvania, Philadelphia
by Jeff Phillips 08 Mar '23

08 Mar '23

External Email - Use Caution Dear colleagues, The Penn Frontotemporal Degeneration Center is seeking a Clinical Research Coordinator to manage our ongoing NIA-funded PET and MRI studies of atypical, early-onset Alzheimer's disease and frontotemporal dementia patients. This position is ideal for aspiring researchers looking to gain experience with neuroimaging, Alzheimer's disease and related dementias, and clinical trial management. Please share this link with your talented trainees or colleagues--I'm happy to respond to direct inquiries: https://secure-web.cisco.com/12wO4MVCs84118ysL8fy6xvbYNtL9LzfpZBTronQnSEbQR… Thanks so much, Jeff Phillips Research Assistant Professor of Neurology Penn Frontotemporal Degeneration Center Philadelphia, PA

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Database of longitudinal freesurfer subjects
by KennethSPrice 08 Mar '23

08 Mar '23

External Email - Use Caution Hello all, Is there a database of longitudinal data anywhere that have already been processed? There are some databases with longitudinal data but to run recon-all on them would take an entire month! Thanks, Ken

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SynthSeg with CT images.
by Gonzalo Rojas Costa 08 Mar '23

08 Mar '23

External Email - Use Caution Hi: I tried SynthSeg using CT images, but I got very bad results... CT images must have some specific characteristics? I tried with axial acquisition and volumetric one.... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/124lTzPUFk2g93tIiOP_RZIKtO7aB_xIAzR3n-NFnpRUBD… https://secure-web.cisco.com/1j0ISp47eIFtrb1e8T61MHEGaGOjjkY7X7EP3tl6QI9uUy… https://secure-web.cisco.com/1Y56xwcQwRV4t77xO4h4FW-bL40P_UtP-sWKcOdTY6xL_b… http://secure-web.cisco.com/1jDmtFL__LFuOoeWvIVy_NxznOAMBVzwNnvweeEquHeNDvB… https://secure-web.cisco.com/1zOogV6Olu-Gbu6J9GAYf7iYCLr5rTveKf3HrLVn5jSdNR…

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Re: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation
by Zollei, Lilla,Ph.D. 08 Mar '23

08 Mar '23

Hi Inga, Could you share some screenshots and the age-at-scan of your subjects? Thanks, Lilla ________________________________ From: Harting, Inga <Inga.Harting(a)med.uni-heidelberg.de> Sent: Wednesday, March 8, 2023 10:18 AM To: Zollei, Lilla,Ph.D. <LZOLLEI(a)mgh.harvard.edu>; freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: AW: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation External Email - Use Caution Hi Lilla, I got infant_recon_all to run through, but the segmentation did not produce the subcortical results I was hoping for. Looking stepwise at results it seemed as if the registration process “bloated” the central structures = basal ganglia, internal capsules (email and your answer below). I’d be happy if you have any suggestions looking at the label fusion step. Best regards, Inga Von: Zollei, Lilla,Ph.D. <LZOLLEI(a)mgh.harvard.edu<mailto:LZOLLEI@mgh.harvard.edu>> Gesendet: Montag, 6. März 2023 17:18 An: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: Harting, Inga <Inga.Harting(a)med.uni-heidelberg.de<mailto:Inga.Harting@med.uni-heidelberg.de>> Betreff: Re: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation Hi Inga, Sorry, I missed this message on the mailing list. This is a new issue to me, so I will take a look at the label fusion step. And yes, we are working on including T2w images in the pipeline as at the newborn stage it would help with the GM/WM segmentation accuracy. Best, Lilla ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Inga Harting <inga.harting(a)gmx.de<mailto:inga.harting@gmx.de>> Sent: Monday, October 31, 2022 3:11 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Inga_klinik <inga.harting(a)med.uni-heidelberg.de<mailto:inga.harting@med.uni-heidelberg.de>> Subject: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation External Email - Use Caution Hello experts, I've begun using infantFS for neonates and I'am interested in the subcortical segmentation. I noticed that the internal capsule is delineated in the manseg-tsubj2subj.NIFTYREG volumes (irrespective of the template's having gmwm or not), but that ist lost after mri_label_fusion when the thalamus has suddenly increased, swallowing PLIC and corona radiata, the basal ganglia have also expanded and the corpus of the caudate nucleus is large and pushed upwards. Is there a way to preserve the subcortical anatomy? Would labelling e.g. capsula interna help? Is there a way to include 2D T2axial to help with gmwm contrast? Best regards, Inga. -- Dr.med. Inga Harting Dpt. Neuroradiology Heidelberg University Medical Center INF 400 69120 Heidelberg inga.harting(a)med.uni-heidelberg.de<mailto:inga.harting@med.uni-heidelberg.de> Mühltalstr. 124b 69121 Heidelberg inga.harting(a)gmx.de<mailto:inga.harting@gmx.de> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1s0ysBlCft27Tx_i8N73qUOkTNobR8v2yZnptqd2cp5sgb…> 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://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1LI_y60Z9xdsi_MfBPpNQMIcMItnhcFBE7Wa4lwhsnZXS2…> . 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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Fwd: infant Freesurfer - subcortical/white matter segmentation
by Inga Harting 08 Mar '23

08 Mar '23

External Email - Use Caution Gesendet: Mittwoch, 8. März 2023 16:17 An: 'Zollei, Lilla,Ph.D.' <LZOLLEI(a)mgh.harvard.edu>; freesurfer(a)nmr.mgh.harvard.edu Betreff: AW: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation Hi Lilla, I got infant_recon_all to run through, but the segmentation did not produce the subcortical results I was hoping for. Looking stepwise at results it seemed as if the registration process “bloated” the central structures = basal ganglia, internal capsules (email and your answer below). I’d be happy if you have any suggestions looking at the label fusion step. Best regards, Inga Von: Zollei, Lilla,Ph.D. <LZOLLEI(a)mgh.harvard.edu> Gesendet: Montag, 6. März 2023 17:18 An: freesurfer(a)nmr.mgh.harvard.edu Cc: Harting, Inga <Inga.Harting(a)med.uni-heidelberg.de> Betreff: Re: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation Hi Inga, Sorry, I missed this message on the mailing list. This is a new issue to me, so I will take a look at the label fusion step. And yes, we are working on including T2w images in the pipeline as at the newborn stage it would help with the GM/WM segmentation accuracy. Best, Lilla From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Inga Harting <inga.harting(a)gmx.de> Sent: Monday, October 31, 2022 3:11 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Cc: Inga_klinik <inga.harting(a)med.uni-heidelberg.de> Subject: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation External Email - Use Caution Hello experts, I've begun using infantFS for neonates and I'am interested in the subcortical segmentation. I noticed that the internal capsule is delineated in the manseg-tsubj2subj.NIFTYREG volumes (irrespective of the template's having gmwm or not), but that ist lost after mri_label_fusion when the thalamus has suddenly increased, swallowing PLIC and corona radiata, the basal ganglia have also expanded and the corpus of the caudate nucleus is large and pushed upwards. Is there a way to preserve the subcortical anatomy? Would labelling e.g. capsula interna help? Is there a way to include 2D T2axial to help with gmwm contrast? Best regards, Inga. -- Dr.med. Inga Harting Dpt. Neuroradiology Heidelberg University Medical Center INF 400 69120 Heidelberg inga.harting(a)med.uni-heidelberg.de Mühltalstr. 124b 69121 Heidelberg inga.harting(a)gmx.de _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/15NZRlEJ1Qw9lqmqqp06dT_F-2aqPXLCySzGHdV_Dsc1ul… 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/1P3TaHH8y3URhhJQ9UaC-mXSbCjguz_m-Zg7wcruNhxGgF… . 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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Freesurfer March 2023