On Jun 15, 2021, at 06:34, 林鈺庭 <ytlin923@g.ntu.edu.tw> wrote:
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_______________________________________________Dear Eugenio,
We checked the RAM setting of the Docker container and found it was default using 2GB RAM! Then we set the Maximum RAM up to 16GB and work all done!!Thank you for your patience helping so much! Wish you have a great day!
Best regards,Josephine
<freesurfer-request@nmr.mgh.harvard.edu> 於 2021年6月12日 週六 上午12:01寫道：
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Today's Topics:
1. Re: T1 hippocampal subfields exited with ERRORS
(Iglesias Gonzalez, Juan E.)
2. Open Position: Postdoc or PhD Student for Deep Learning based
Lesion Recognition in human MRI (Dr. rer. nat. Johannes Jungilligens)
3. Finding equivalent vertices on fsaverage_sym lh and rh
surfaces (Tim Sch?fer)
4. Re: memory allocation error (Bernardoni, Fabio)
5. Issues with recon-all hanging (Michael Datko)
6. Re: how to visualize statistical maps in FS7.1?
(Bernardoni, Fabio)
----------------------------------------------------------------------
Message: 1
Date: Fri, 11 Jun 2021 11:52:08 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] T1 hippocampal subfields exited with ERRORS
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2E162B79-9558-4942-8B6E-55A7B384D524@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Dear Josephine,
This is unusual. Could it be possible that you are running out of RAM memory? Do you have 16GB or more available?
Cheers,
/Eugenio
On 11 Jun 2021, at 01:39, ??? <ytlin923@g.ntu.edu.tw<mailto:ytlin923@g.ntu.edu.tw>> wrote:
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Dear Developer and Eugenio,
We encounter the error at the end of the analysis,it looks like this:
Smoothing mesh collection with kernel size 0.750000 .../usr/local/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 499 Killed /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML S013 /data 0.333333333333333333333333333333333333 /usr/local/freesurfer/average/HippoSF/atlas/AtlasMesh.gz /usr/local/freesurfer/average/HippoSF/atlas/AtlasDump.mgz /usr/local/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 right L-BFGS v21 '/usr/local/freesurfer/bin/fs_run_from_mcr /usr/local/freesurfer/bin/' 0
Linux f8e6a6f8a44a 5.10.25-linuxkit #1 SMP Tue Mar 23 09:27:39 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
T1 hippocampal subfields exited with ERRORS at Thu Jun 10 10:22:54 UTC 2021
I've attached the log file here, could you help us with this error? Thank you so much!
Best regards,
Josephine
<hippocampal-subfields-T1.log>_______________________________________________
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------------------------------
Message: 2
Date: Fri, 11 Jun 2021 08:37:35 -0400
From: "Dr. rer. nat. Johannes Jungilligens"
<johannes.jungilligens@rub.de>
Subject: [Freesurfer] Open Position: Postdoc or PhD Student for Deep
Learning based Lesion Recognition in human MRI
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAAOmhOR4w9sjPKaZogzXs2-x+65oMGE+2m-Fdu1ncdH2PAj6WQ@mail.gmail.com>
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*Postdoc or PhD Student for Deep Learning based Lesion Recognition in human
MRI*
available from July 1st, 2021, or later. The position will be embedded in a
three-year project within the Human Centered AI Network (HUMAINE) at
Ruhr-University Bochum (RUB), Germany. The highly interdisciplinary project
deals with the identification and characterization of epilepsy-causing
lesions in MRI images of the brain and their discrimination from
non-epileptogenic lesions. The project is conducted at the epilepsy center
of the university medical center Knappschaftskrankenhaus
(Ruhr-Epileptology, J?rg Wellmer) in close collaboration with the
Bioinformatics group at the Center for Protein Diagnostics RUB (Axel Mosig).
The applicant should hold a degree in computer science, physics, or
comparable studies and have experience along with profound theoretical and
practical knowledge of deep learning in the context of three-dimensional
medical imaging, in particular using state-of-the-art frameworks such as
tensorflow of pyTorch.
We offer an inspiring working environment in well-established
interdisciplinary structures, providing state-of-the-art IT infrastructure
in a highly dynamic interdisciplinary setting with project partners
covering the whole range between medicine, machine learning, sociology, and
business. The salary is that of a full-position scientist according to
German payment standards.
For further information and application, feel free to contact J?rg Wellmer (
Joerg.Wellmer@kk-bochum.de) and Axel Mosig (axel.mosig@rub.de).
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------------------------------
Message: 3
Date: Fri, 11 Jun 2021 16:01:44 +0200 (CEST)
From: Tim Sch?fer <ts+ml@rcmd.org>
Subject: [Freesurfer] Finding equivalent vertices on fsaverage_sym lh
and rh surfaces
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1290876552.38407.1623420104997@ox.hosteurope.de>
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Dear FreeSurfer experts,
for the 'fsaverage_sym' template that comes with FreeSurfer, I would like to find a mapping between equivalent vertices (i.e., vertices in the same anatomical position) between the left and right hemispheres.
By "equivalent" I mean identical anatomical positions. I noticed, for example, that vertex 500 in the file fsaverage_sym/surf/lh.white and vertex 500 in the file fsaverage_sym/surf/rh.white are not at equivalent anatomical points.
I feel this mapping must be documented somewhere or there is an obvious way to get it that I am currently overlooking, so I thought I'd ask here.
Thanks in advance,
Tim
--
Dr. Tim Sch?fer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
------------------------------
Message: 4
Date: Fri, 11 Jun 2021 15:10:41 +0000
From: "Bernardoni, Fabio" <Fabio.Bernardoni@uniklinikum-dresden.de>
Subject: Re: [Freesurfer] memory allocation error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <4b5ecebd01af4ac8b5317c9c24f5f146@uniklinikum-dresden.de>
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dear all,
is there any progress on this issue? can I send more information to help with debugging? judging from the other entries of the mailing list this is not an issue that concerns only me.
thank you for your attention,
bests
fabio
Dr. Fabio Bernardoni
wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1dOZP5j8XdDioY7tViTW7NqEi9mrvvba6PAbK6uv63gP7Q8bNrlLCYFkKfvXXNpcvR7MIg3L5wRfoQWO66UdM1HtJA4W7iKqfq4FhnnE9W2R2KwGDIaI7MjIpsOL5VryAdycFZZismV1CFp4rNE47COVEcaN7m-ypDnjnXobdlMmq5EirIKZSBuBmmU3BrEdMYwD-BFb3nS8AdCafRfCfvjcSJaTNtkXlb52Ab49xmqiAfSbLVpAV32A2F_b5QaItKY0wLlYGCGD0ZC1nbr_gag/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1C5zQD6S2aQEn7dMGBOKijRrWY8INlUWuanF5g6gCvX_Y1b1F-tAXUd55vvYP2ExpFYOE4G_Gf0Ujo0hS1Y2GnTUxWS4Q-Hw7ryBf9XfzTCb8akQhMElGzETBV9Y9Dx77zF8x-MJ9GUD0FyloeWVletfQc1s8UEKQ3yoaKTFfJ2V8wWshKFJa_JP1qacQoSHNmMiXI_FcftEAwml4E2oNwVLDD4wbGRONmoBUwVEiXo5dl7kMXPeg0RsJWGcPzoL3tA375bU9hNlgebAeMlJOhg/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
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USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
________________________________________
Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Bernardoni, Fabio <Fabio.Bernardoni@uniklinikum-dresden.de>
Gesendet: Donnerstag, 20. Mai 2021 11:17:05
An: Freesurfer support list
Betreff: Re: [Freesurfer] memory allocation error
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dear Andrew,
I was allowing 8, 16, ~36GB of memory in different runs, so I would exclude that this was the problem.
bests
fabio
Dr. Fabio Bernardoni
wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/187My4Jucq7g2iOhroEKk8K8OFGoFoeORTu-mXzokMtuySZfRpdmpBUHAWrZs3PiUgTJQxvI4t7mF19Q65QoVRPm9HIRo1ga6iFYC3emunkTnsx44xyypE8RQ7se9eW1WnrqXrI_Z3OCRQDKjl_O6YrVXw8u2fxs-M2rmDvVwA1c8A6B-TCU2kRIeB7oIt49DW_DM1zE6Vs2u2KvWqA9-ZtIcGYVGPwCKGzShIT5OOvNrJjUldtN0AoNqCDk2gUFd6DjRtozUhmyNbDtaEpIJOQ/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15nLSigNtaEzdHxIpWerC4ukwoFMkkmjnCaSZHFWvxZoHCXH4XhBy49dgkjt_Vq9EFKvYq9xxQ4wmBIAl28GFHwhUJe7IfUAQkVKEMD5fvpyeYO8Shfw1PZr2zy9p7hm86gBaVav8UarY5wXbQ2FUH7lzmO3kgv-sylrFq8rFfmbsx-WSHLLJyi6zQDOV0A7vxj7uJyZDym-vCiDaPrxTdvo7Tws6y8FnBWgAvc-2BMa-GAAkHZJOPrvFuJw9Nh5WXnTa0wo5mD-Qgvp8aHL22A/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
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Anstalt des ?ffentlichen Rechts des Freistaates Sachsen
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Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
________________________________________
Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Hoopes, Andrew <AHOOPES@MGH.HARVARD.EDU>
Gesendet: Mittwoch, 19. Mai 2021 20:38:45
An: Freesurfer support list
Betreff: Re: [Freesurfer] memory allocation error
Hi Fabio,
How much memory are you allowing for this process? You might want to just try increasing the limit on the slurm job to see if that works.
Best
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bernardoni, Fabio <Fabio.Bernardoni@uniklinikum-dresden.de>
Date: Tuesday, May 11, 2021 at 4:22 AM
To: freesurfer mailing list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] memory allocation error
External Email - Use Caution
Sorry I forgot the attachment.
Dr. Fabio Bernardoni
wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
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Anstalt des ?ffentlichen Rechts des Freistaates Sachsen
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http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
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Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
________________________________________
Von: Bernardoni, Fabio
Gesendet: Dienstag, 11. Mai 2021 10:20:19
An: freesurfer mailing list
Betreff: AW: memory allocation error
Dear Freesurfers,
when running the longitudinal preprocessing on a subject, I get the same error as described here (see recon-all.log attached):
https://secure-web.cisco.com/1my6XFSQF3uEj1ZrgriH6ZF1WxWnqfBMBdiuPDNdXZfq_XO9uhiKwZPYEvG3NS0vJSxZM7hcmTWq1hUXJUt2_XigG_UONfGk8UL_5FWLEktb3qrFvDpcgohhnKOb1j6uAWMIE10PVwXrnLZx4Gf441Olp7jcMNX8eLVVNtPMcFPE5OH3N4cODD6Z83hDSq2HPzZH7tQ78HFekvVecIFyNfG7sKdlEVUVjwFGX6pd4c9fRkVgt6eCj-kuSxbdQrF2OBr2Vi1IX-Bz_UzXD9ZcLyw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57542.html
my FS version is:
recon-all -version
freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e
and I did not perform any editing, so there is no control points to remove as suggested in the above post (which also refers to version 6). Therefore, if I understand correctly, my problem is a different one. Any clue what I might be doing wrong?
Other possibly useful information:
uname -a
Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
Thanks for any hint/help
Fabio Bernardoni
Dr. Fabio Bernardoni
wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
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an der Technischen Universit?t Dresden
Anstalt des ?ffentlichen Rechts des Freistaates Sachsen
Fetscherstra?e 74, 01307 Dresden
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Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
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Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
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------------------------------
Message: 5
Date: Fri, 11 Jun 2021 11:46:23 -0400
From: Michael Datko <mikedatko@gmail.com>
Subject: [Freesurfer] Issues with recon-all hanging
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Cc: "Datko, Michael" <mdatko@mgh.harvard.edu>,
stohyama@mgh.harvard.edu
Message-ID:
<CACDOVXeZSTX7Ai5xx3gBKVqw8vGKsQoBKRkLx3h5xeCk1+4a4w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello,
I have been collecting data on a 7T scanner, with functional EPI data
collected with 1.5mm voxels, and I have been having an issue with some of
our data where recon-all just hangs after producing only a small amount of
outputs. For instance, it might get to a point where it has generated 5-10
of the ?lh? left hemisphere outputs in the surf folder, and then appears as
if it continues to run for hours or days but no other outputs get produced
and eventually the process times out and quits. I estimate that this
happens for about 5-10% of the participants we have collected so far. If
it doesn?t work for a particular participant, it will do the same thing
again if I delete their temporary working folder and any outputs and try to
run again from scratch.
This is not happening with data from the same participants collected from a
3T scanner with 3mm EPI voxels, with recon-all run at 2mm. The only
difference is the resolution of the data and therefore the resolution at
which we are running recon-all. Our 7T functional EPI data is collected at
1.5mm resolution, so for those scans we run recon-all at 1mm resolution.
Do you have any advice for how to get these participant?s data to finish
with recon-all at 1mm?
Thank you,
Mike Datko
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Message: 6
Date: Fri, 11 Jun 2021 15:53:38 +0000
From: "Bernardoni, Fabio" <Fabio.Bernardoni@uniklinikum-dresden.de>
Subject: Re: [Freesurfer] how to visualize statistical maps in FS7.1?
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <233ce09ccbac40a7b3fb34db82438319@uniklinikum-dresden.de>
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dear all
even though on the official webpage it is advised to use freeview to display statistical maps because tksurfer is considered obsolete/not maintained in freesurfer 7, I am unable to reproduce the same figures, even when using tksurferfv.
one feature that is missing but can be reproduced using mri_fdr is FDR thresholding. however, it is not clear to me how to produce a decent color scale given a threshold computed by mri_fdr or any other means, which indicates the threshold.
could someone please suggest how to edit the color scale in freeview? or whether there is an alternative software to display the overlays/statistical maps produced by freesurfer?
thank you very much in advance!
fabio
Dr. Fabio Bernardoni
wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1NUA3Kn39JuhF9hBZYddG5zC7EUE779Ca85qGI3CWyMQGgtceMJDZRWhouZ5WGjYJWj9bwKrD2fD8s-hYFwlM9Zb7PnHApqOOdsXMN_UqKlRrAimZGaAbHyNmcB9eQc5bFAwPScLDl6teibcOsvSTEnICFgvqooR9lO2wtAQTJ5FeXCgJ_SpT53obkUl22C99Qs40AAaX_Wl-lb7XLeXtAn2E4QG0UtoS7p7UeyqVg_TLcctdVMNC-o4N0Uy1K879qlpx8J4ph1VuwogyQIlbGA/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/14qCxqn3snsuFXdZvB5lycE4FPyFND_EXl-CJ4_Vot9lSJiTnBFfpJazexQgemAFSqoGm7CBIyEnExxeRG6zWhYfzffjDt7l2n5yMtZAefgBXdkiV56cfJbXtHdHuWPQFlvInkSQIulWLx6mp6mbDfqfTojWarCOggU4inOp1-_BNPn9sKuPQxbme2JtgDgI3jrhzF1cGekZtMUl4O9mmuQgm5kH9QvITIy1-mBcFsoBz1x2MSpGocBouBWImztww-pm8hUehycRbu2-ob0_I6w/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
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an der Technischen Universit?t Dresden
Anstalt des ?ffentlichen Rechts des Freistaates Sachsen
Fetscherstra?e 74, 01307 Dresden
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Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
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Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
________________________________________
Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Bernardoni, Fabio <Fabio.Bernardoni@uniklinikum-dresden.de>
Gesendet: Freitag, 14. Mai 2021 17:35:25
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] how to visualize statistical maps in FS7.1?
External Email - Use Caution
Ok I found a solution using separately mri_fdr
thanks anyway!
Dr. Fabio Bernardoni
wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/15vnpAEjrPYiKn6yEt0jIUfHx8_4Erx_TvQU05r-dRGFvX5o0_mKiLNQoOoY_DiUFEu3Zb0adehInmHSUaelrON7US4wQ_sWBoQxe2WEPWflAevksiDhq9xUM0HpqhFyVYQ_E6lAcMbhVCVy7BrdLpkrKVNjZklIfxcHcWr5x_R8nAnO3kseYCYgupaYK0YfQU5rXE3-xyfRoCRuDtLtXKnJmnAG9REL9uq0BV_7ZXuM239yt3PhScBv-jdmCWqnVKhzsluD3IrIBTh6UsOy7mQ/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou9CYrXL4wwpARdd5jBIoEyyH6WRwiGcI2zF0MEzpoexufmjhvKmf_TJMFBg6Cielu-V9qKgk7jDZWTcDm2ciqEtHGLSlLLw-eqLWYalhfAFef1y44MmoHa3utLtAl3loyhlAUlPlAjROXw1deJfxT8nmYTPE19cdW9XGZWokm5kWZ2Nqc_Stox4LWVgzrO1P3Dxj11oUM0MCPkWo0tV7otPW3zFFqjc20pMEyZRA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universit?tsklinikum Carl Gustav Carus
an der Technischen Universit?t Dresden
Anstalt des ?ffentlichen Rechts des Freistaates Sachsen
Fetscherstra?e 74, 01307 Dresden
http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
________________________________________
Von: Bernardoni, Fabio
Gesendet: Freitag, 14. Mai 2021 17:28:18
An: freesurfer@nmr.mgh.harvard.edu
Betreff: AW: [Freesurfer] how to visualize statistical maps in FS7.1?
Dear Greve,
thanks for your reply.
These are my steps (I corrected the second):
1) I open the inflated surface:
tksurferfv fsaverage lh inflated
(this successfully displays the inflated left hemisphere of the average subject)
2) I now load the overlay from the freeview window (sig.mgh from a mri_glmfit)
(this successfully overlays the -log(p) statistical map)
3) I would like to threshold the map using FDR<.05. This was possible in tksurfer:
https://secure-web.cisco.com/14RYweM71AH5pQm4yA5snEHYyrEVoKp3gpJ8mUW3BNypi7NSOhmp_YRd_jgi1SujzPXH9cIwy0Jernwep4nXrHFntFwpmUGWaIX6TS3NaUOhiQOpi-4w3nsq0bzphVsDjhFHhzNZiBY2LmWmseyLnHL2_5Ush2yKkKt5RdI2Rb74ulrrCLToWDqAnLUM0q_qlRi1RA239cuSMcBgPwpPvJtGGN411DfZewDIyQVbpNY2MLzO1iONzbuI6zyeP0zy7lFjVCoM-4HlMIAnGtBBf0Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkSurferGuide%2FTkSurferWorkingWithData%2FTkSurferOverlay
however no such option appears in tksurferfv / freeview
Any hint at this point?
Thanks a lot
Fabio
Dr. Fabio Bernardoni
wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/15vnpAEjrPYiKn6yEt0jIUfHx8_4Erx_TvQU05r-dRGFvX5o0_mKiLNQoOoY_DiUFEu3Zb0adehInmHSUaelrON7US4wQ_sWBoQxe2WEPWflAevksiDhq9xUM0HpqhFyVYQ_E6lAcMbhVCVy7BrdLpkrKVNjZklIfxcHcWr5x_R8nAnO3kseYCYgupaYK0YfQU5rXE3-xyfRoCRuDtLtXKnJmnAG9REL9uq0BV_7ZXuM239yt3PhScBv-jdmCWqnVKhzsluD3IrIBTh6UsOy7mQ/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou9CYrXL4wwpARdd5jBIoEyyH6WRwiGcI2zF0MEzpoexufmjhvKmf_TJMFBg6Cielu-V9qKgk7jDZWTcDm2ciqEtHGLSlLLw-eqLWYalhfAFef1y44MmoHa3utLtAl3loyhlAUlPlAjROXw1deJfxT8nmYTPE19cdW9XGZWokm5kWZ2Nqc_Stox4LWVgzrO1P3Dxj11oUM0MCPkWo0tV7otPW3zFFqjc20pMEyZRA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universit?tsklinikum Carl Gustav Carus
an der Technischen Universit?t Dresden
Anstalt des ?ffentlichen Rechts des Freistaates Sachsen
Fetscherstra?e 74, 01307 Dresden
http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
________________________________________
Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Gesendet: Donnerstag, 13. Mai 2021 17:11:29
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] how to visualize statistical maps in FS7.1?
your tksurferfv command line is wrong
On 5/12/2021 6:06 AM, Bernardoni, Fabio wrote:
> External Email - Use Caution
>
> Dear Freesurfers
>
> I recently moved to FS7.1 and I was trying to reproduce my workflow I had with FS5.3.
>
> To visualize statistical maps, I had always used tksurfer. It seems, however, it is no longer maintained.
>
> When I launch it it fails to find out the tix, tcl, etc libraries. Following this thread:
> https://secure-web.cisco.com/1v7sQGKZgCQ9d6BT0fUpIf9QvmP5selhkoGYWs1-X9TSsF6ebf9WkfXQKwNGkJnbQTNihRlUwkt3d_MtgGepc7G9MM_ZkCKisZX1hKBJ9twis_mX1rWvKXW84_u67FO-1Nf-Nw0XV4e4TaksCUTJbLoVykRInrujR5kv4RuP668hB4uZuRSUTzw5Wv0cdJpuX2G2CxoXrNGsfZPGI9wEQy2xuY0fWpzXbjw3A6IN30dlVGcFiz2RxbN4DmxS9mgJACyaWUAW4XrSh_mrEyukmaw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66219.html
>
> I tried to use tksurferfv. However, when trying to overlay the sig.mgh output of mriglmfit, on an inflated fsaverage surface, the program shuts down, with this error:
>
> freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:curvature=/usr/local/freesurfer/subjects/fsaverage/surf/lh.curv -viewport 3d
> terminate called after throwing an instance of 'int'
> Abort (core dumped)
>
>
>
>
>
> What would you suggest to visualize statistical maps in FS7? Is my problem expected?
>
> Thank you in advance for your attention
>
> Fabio
>
>
> Dr. Fabio Bernardoni
> wiss. Mitarbeiter
>
> Division of Psychological & Social Medicine and Developmental Neurosciences
> http://secure-web.cisco.com/1fJ-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhEyJg3GuHzjb7IPAU-FCiyn7epXi34kENaICaL_blhCQ8oexcOBMTiefsG3_aAP0L5sU_H9y1xYVTw6Wh6hIqLbAa4i4vAgC5EkA-lRurbVwk8nsJ2OkIW9GfadFxibvScxITahbmnRCznxGJlPF-53t2LTXrv5ovrctRRUr3HCbs6q1-FfiwpZbapsJCpLgnVMXDIXmR9FalmQ1tAveKdaDRqfq1X5OnoG5ccMFg/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_rVe8WFPk8CrMRmNwa_OuMhrKZXOFFO-FGw4FoQLrEFxfrO0Bmrs52S58GLUHqIsCPDL1IlMhZljPMxwDvqHheBhbH3FY9WwkZleNf0vOcLN7T--LeyLSKHC_sDn8owSIUefCSKVrRFaCMbFr5M04ZXYBHqA2QiHHZt1TpSnAlfoaQMAYejGip5Lnf_rIw4wUFl8P8g9z1Vi1EDDQW72FYV0DvC7gVAebazbP_AQ/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
> +49 (0351) 458-5245
> Universit?tsklinikum Carl Gustav Carus
> an der Technischen Universit?t Dresden
> Anstalt des ?ffentlichen Rechts des Freistaates Sachsen
> Fetscherstra?e 74, 01307 Dresden
> http://secure-web.cisco.com/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EBtyOQOncARekE9xGU6ufm0K3AsWqpT_QNy_QstYzolatBvaWI4t7eMeALTKskxEvWoxokVkLLB4HMJ0YkwdqKEe8ljROpTHIFtyq1qCflRlJTMWaL3-X3wy0Xoc3l8aqALWtblfOLH8ZWHGuYKuFG4ZDS2lawCB8R4FPsst51f44nwNGvWALB0xsX_5W2NQbQ4wnfuAoIXlyw0pV5MKnAhp5Uh9k6uZlMYG5XgZw/http%3A%2F%2Fwww.uniklinikum-dresden.de
>
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
> Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
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> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
> Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
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End of Freesurfer Digest, Vol 208, Issue 28
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