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Re: [Freesurfer] error glm-fit-sim (message 11)
by Caroline Beelen 10 Oct '18

10 Oct '18

External Email - Use Caution Few clusters survive glm fit. No clusters seem to survive glm-fit-sim (when visualizing). However, I'm not sure if I should also see this in a text file. Opening cache.th40(or 30).abs.sig.cluster.summary it seems to have found no clusters. At least, under the line ClusterNo Max VtxMax Size MNIX MNIY etc. nothing is written. But does a lack of significant clusters also explain the weird messages of "colortable with 1 entries read (originally none)" (& "CTABisEntryValid: index -1 was OOB" & "Resource temporarily unavailable") that show up in the terminal? Thanks very much, Caroline -----Oorspronkelijk bericht----- Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens freesurfer-request(a)nmr.mgh.harvard.edu Verzonden: dinsdag 9 oktober 2018 18:00 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 176, Issue 9 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. FW: RE: error glm-fit-sim (Caroline Beelen) 2. Re: output values of vertices on surface into a textfile (Sims, Sara A) 3. Re: output values of vertices on surface into a textfile (Bruce Fischl) 4. Re: output values of vertices on surface into a textfile (Sims, Sara A) 5. Re: Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab (Pradeep) 6. Re: Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab (Iglesias Gonzalez, Eugenio) 7. hippocampal subfields (Marcel Heers) 8. Re: hippocampal subfields (Iglesias Gonzalez, Eugenio) 9. Re: Difference between 6.0.1 and 6.0.0 (Dicamillo, Robert) 10. Talairach failed in monkey brain (Frehiwot Woldeyes) 11. Re: FW: RE: error glm-fit-sim (Greve, Douglas N.,Ph.D.) 12. Mri Convert Help (Justin Arnett) 13. Re: Mri Convert Help (Greve, Douglas N.,Ph.D.) 14. Re: Recon-all with/without T2 give the same stats (Greve, Douglas N.,Ph.D.) 15. Re: Recon-all with/without T2 give the same stats (Jianzhong Chen) 16. m.khalilian(a)sutech.ac.ir sent you files via WeTransfer (WeTransfer) 17. very bad result using "mris_ca_train" and "mris_ca_label" (Maedeh Khalilian) 18. Re: Talairach failed in monkey brain (Greve, Douglas N.,Ph.D.) 19. Re: Recon-all with/without T2 give the same stats (Greve, Douglas N.,Ph.D.) 20. Re: very bad result using "mris_ca_train" and "mris_ca_label" (Bruce Fischl) 21. Re: Extract individual vertex thickness values from cortical parcellations (Greve, Douglas N.,Ph.D.) 22. Re: nu_correct disk i/o issues (Greve, Douglas N.,Ph.D.) 23. Re: masking cortical thickness (Greve, Douglas N.,Ph.D.) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Oct 2018 16:12:06 +0000 From: Caroline Beelen <caroline.beelen(a)kuleuven.be> Subject: [Freesurfer] FW: RE: error glm-fit-sim To: "freesurfer-bounces(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu>, "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4051d561c94b40e0b641202b7bad7192(a)ICTS-S-EXMBX25.luna.kuleuven.be> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution The command: gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot -viewport 3d The output: reading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) The command with a bit less strict significance level: gop@gop-linux:~/freesurfer$ freeview -f $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=3,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot -viewport 3d The output: reading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) (and then it says no more). Both commands visualize the data, but no clusters are found. Is this how it should be? Does it mean that there is a problem with reading colortables or not? Best, Caroline Message: 2 Date: Mon, 1 Oct 2018 17:10:28 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] error glm-fit-sim 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>> Message-ID: <504d6069-399f-163d-39a9-dcc6c02d32f9(a)mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d32f9@mgh.harvard.edu>> Content-Type: text/plain; charset="Windows-1252" What says that? What command are you running? What is the other terminal output? On 10/01/2018 04:54 AM, Caroline Beelen wrote: > > ????????External Email - Use Caution > > Dear FS, > > I followed the group analysis page for glm analysis and it worked fine > until the final step. I?m using version 5.3. After performing > glm-fit-sim it says ?glm-fit done? (for all files), but when trying to > open these it says: > > ?Reading colortable from annotation file? > > Colortable with 1 entries read (originally none) > > Colortable with 1 entries read (originally none) > > CTABisentryvalid: index -1 was 00B > > Resource temporarily unavailable > > CTABisentryvalid: index -1 was 00B > > Resource temporarily unavailable > > Resource temporarily unavailable? > > (etc..) > > It opens, but nothing is visible and I have the feeling it cannot open > color files?? > > MRI glmfit gives positive clusters for some values. I therefore used > the abs sign for glm-fit-sim. > > What might be wrong? > > Thanks. Caroline

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Re: [Freesurfer] Disjointed thalamic nuclei segmentation
by Iglesias Gonzalez, Eugenio 10 Oct '18

10 Oct '18

External Email - Use Caution Thanks, Niels. It is definitely a matter of hyperintensity of voxels close to the lateral boundary, particularly in the anterior region (which has a fuzzy boundary with the white matter in first place). Whether these hyperintensities are due to MS pathology, that I do not know (I’m really not the person to tell…). These could be cleaned up with postprocessing (e.g., filling holes, or using a Markov Random Field), but the impact on the volumes would be negligible. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: Niels Bergsland <theniels(a)gmail.com> Date: Wednesday, 10 October 2018 at 15:42 To: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Subject: Re: [Freesurfer] Disjointed thalamic nuclei segmentation Hi Eugenio, Thanks for the lightning fast response! :) I've attached them here. It looks like it might actually be the opposite in this case in that the voxels here are darker. Some of the cases are MS patients and so it's conceivable that they have thalamic lesions. Admittedly though, I have not really spent time in the past looking for thalamic lesions on T1-weighted images and this hasn't been an issue in the past since the thalamic segmentation in the aseg doesn't end up being affected by these voxels with lower intensities. If you would like to look at some other cases or need other outputs, just let me know and I'm happy to send them along! Thanks again, Niels On Wed, Oct 10, 2018 at 4:30 PM Iglesias Gonzalez, Eugenio <e.iglesias(a)ucl.ac.uk<mailto:e.iglesias@ucl.ac.uk>> wrote: External Email - Use Caution Thanks, Niels. I suspect the problem is that, for some reason, such voxels have much brighter intensity than their surroundings, and are classified as white matter / reticular nucleus. But that shouldn’t be happening that far from the lateral boundary of the thalamus… Can you please send us norm.mgz and the thalamic segmentation file, so I can take a look? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Niels Bergsland <theniels(a)gmail.com<mailto:theniels@gmail.com>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 10 October 2018 at 15:22 To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Disjointed thalamic nuclei segmentation External Email - Use Caution Hi Eugenio, Thank you again for the fantastic thalamic nuclei segmentation tool! I'm going through and QC'ing a batch of subjects that were processed through the pipeline. Data was originally processed with freesurfer-6.0.0 and then processed through the thalamic nuclei stream (dev-20180818-e30e6f9). I have found that for some cases, there are some isolated patches of voxels that are disconnected and seemingly in the wrong place. I've noticed it primarily for the MDm and my impression is that it tends to happen more in the right hemisphere. I've attached a sample image to show you what I mean. The red cross has been placed on a set of these voxels. It is not the case that they are connected in 3D. Any input is appreciated and thanks again! If it can be useful, I'm happy to upload the data -Niels _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Disjointed thalamic nuclei segmentation
by Niels Bergsland 10 Oct '18

10 Oct '18

External Email - Use Caution Hi Eugenio, Thank you again for the fantastic thalamic nuclei segmentation tool! I'm going through and QC'ing a batch of subjects that were processed through the pipeline. Data was originally processed with freesurfer-6.0.0 and then processed through the thalamic nuclei stream (dev-20180818-e30e6f9). I have found that for some cases, there are some isolated patches of voxels that are disconnected and seemingly in the wrong place. I've noticed it primarily for the MDm and my impression is that it tends to happen more in the right hemisphere. I've attached a sample image to show you what I mean. The red cross has been placed on a set of these voxels. It is not the case that they are connected in 3D. Any input is appreciated and thanks again! If it can be useful, I'm happy to upload the data -Niels

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Postdoctoral Fellowship Positions in Traumatic Stress Disorders
by Emma Brown 10 Oct '18

10 Oct '18

External Email - Use Caution POSTDOCTORAL FELLOWSHIPS IN TRAUMATIC STRESS DISORDERS Collaborating research groups at the VA Boston Healthcare System anticipate up to two NIMH-funded postdoctoral fellowships to begin by September 2, 2019. These two-year training positions are designed to prepare researchers for academically-oriented careers in the psychology and neurobiology of stress-related disorders. Previous fellows have launched successful careers in universities and academic medical settings. Candidates with backgrounds in neuroimaging and/or genetics are encouraged to apply. The fellowship program is affiliated with Boston University School of Medicine and is located primarily at the Jamaica Plain Campus of VA Boston. Affiliated centers include the Behavioral Science and Women's Health Sciences divisions of the National Center for PTSD, the Translational Research Center for TBI and Stress Disorders, the Neuroimaging Research for Veterans Center, the VA National Center for PTSD Brain Bank, and the Center for Healthcare Organization and Implementation Research. These programs offer outstanding resources including existing datasets, technical support personnel, well-equipped laboratories, advanced computing facilities, and a broad range of professional expertise. The anticipated salary and benefits package is competitive, and supplemental funds will be available to support further coursework and other educational opportunities, conference attendance, and travel. The program offers training in several core areas. Candidates may contact the following program leaders prior to application for more information about the specific cores:Clinical Neuroscience and Neuroimaging(David Salat salat(a)nmr.mgh.harvard.edu) Molecular Biomarkers and Genetics (Mark Miller: mark.miller5(a)va.gov) Assessment, Diagnosis, and Epidemiology (Brian Marx:brian.marx@va.gov), Treatment Development and Optimization (Denise Sloan:denise.sloan@va.gov), and Implementation and Dissemination (Terry Keane:terry.keane@va.gov). Fellows will have the opportunity to participate in ongoing research projects conducted by program faculty, initiate independent research projects, conduct secondary analyses on existing data sets, prepare grant applications to federal and other funding agencies, and learn about all aspects of laboratory management. Each fellow will have a senior faculty member assigned to serve as a primary mentor. For license-eligible clinical psychology fellows, arrangements are available outside the program to provide direct clinical services to patients under the guidance of a clinical supervisor. Materials will be reviewed and interviews arranged on a first-come basis. Preliminary applications should include a statement of interests and goals, a curriculum vita, and three professional references that should be sent directly by the recommendation writer. Applicants must be U.S. Citizens and have completed all requirements for their doctoral degree prior to starting the program. Minority candidates are strongly encouraged to apply. Applications should be submitted electronically no later than December 3, 2018 to Denise Sloan, Ph.D. (denise.sloan(a)va.gov) The VA Boston Healthcare System is an equal opportunity employer.

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Fwd: Hippocampal-Amygdala subfields error
by Miguel Ángel Rivas Fernández 10 Oct '18

10 Oct '18

External Email - Use Caution Hi everyone, Here a question and an answer of FreeSurfer experts that would be for interest. - Could there be any difference in accuracy when the recon-all is executed on two Mac computers that have a different processor? that is, it is preferable to execute the recon-all of all the subjects in the same computer?. Sorry for this absurd question but I would be sure about this. - *Regarding the second question: it is a really good one. Would you mind posting it on the FreeSurfer list? Short answer is: same machine. * Best ---------- Forwarded message --------- From: Iglesias Gonzalez, Eugenio <e.iglesias(a)ucl.ac.uk> Date: mié., 10 oct. 2018 a las 11:53 Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error To: Miguel Ángel Rivas Fernández <miguelrivasfdez(a)gmail.com> Cc: Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> Hi again, MA. I totally forgot to attach the binary. The thing is that I don’t have it on my hard drive, so I need to recompile it, but our MAC server seems to be down ggggrrr Andrew: any ideas why breck is not responding? MA: sorry for the delay; we’ll definitely get to the bottom of this. Regarding the second question: it is a really good one. Would you mind posting it on the FreeSurfer list? Short answer is: same machine. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ *From: *Miguel Ángel Rivas Fernández <miguelrivasfdez(a)gmail.com> *Date: *Wednesday, 10 October 2018 at 09:39 *To: *"Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error Hi Eugenio, It´s possible that you have forgotten to attach the file in this email? because I don´t find anywhere. Another question, could there be any difference in accuracy when the recon-all is executed on two Mac computers that have a different processor? that is, it is preferable to execute the recon-all of all the subjects in the same computer?. Sorry for this absurd question but I would be sure about this. Best, El mié., 3 oct. 2018 a las 19:52, Iglesias Gonzalez, Eugenio (< e.iglesias(a)ucl.ac.uk>) escribió: Allrighty, here are the instructions (depending on the location of FREESURFER_HOME, the following commands might need to be preceded by “sudo”) 1. Save the attached file to a directory of your choice. From the terminal, cd into that directory. 2. Decompress with: tar xvf segmentSubjectT2_autoEstimateAlveusML.tar.gz 3. Move existing version of the code: mv $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app.old 4. Replace with new version: mv ./segmentSubjectT2_autoEstimateAlveusML.app $FREESURFER_HOME/bin/ 5. Rerun the code If this doesn’t work, you can revert the changes with: 1. Delete new version with: rm –rf $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app 2. Restore previous version: mv $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app.old $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app If it works: there’s no need to rerun the subjects that didn’t crash. Please let us know what happens! Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ *From: *Miguel Ángel Rivas Fernández <miguelrivasfdez(a)gmail.com> *Date: *Wednesday, 3 October 2018 at 18:32 *To: *"Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error Hi Eugenio, I ran the command with the version *freesurfer-darwin-OSX-ElCapitan* (downloaded from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev) but anyway I can try with the updated executable. If the problem solved, it is necessary to run the command with this updated executable in the subjects in which before I had no problem? I guess it would not be necessary but I would like to be sure about this. Thanks Cheers, El mié., 3 oct. 2018 a las 19:17, Iglesias Gonzalez, Eugenio (< e.iglesias(a)ucl.ac.uk>) escribió: Hi MA, I believe the FreeSurfer course is ongoing this week, which would be taking most of Andrew’s time. Our main hypothesis is that the binary with the bug fixed did not make it to the public distribution for some reason. If you want: I can send you the updated executable; you can then give it a shot, and if it solves the problem, we’ll know what the problem was. Let me know if you want to do this. Otherwise we can wait for Andrew to find time to take a look. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ *From: *Miguel Ángel Rivas Fernández <miguelrivasfdez(a)gmail.com> *Date: *Wednesday, 3 October 2018 at 18:07 *To: *"Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> *Cc: *"ahoopes(a)mgh.harvard.edu" <ahoopes(a)mgh.harvard.edu> *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error Hi Andrew, Did you have chance to review the error that I reported some days ago? Thanks for your help! Cheers, El lun., 1 oct. 2018 a las 9:44, Miguel Ángel Rivas Fernández (< miguelrivasfdez(a)gmail.com>) escribió: Thanks a lot! Miguel, El lun., 1 oct. 2018 a las 8:39, Iglesias Gonzalez, Eugenio (< e.iglesias(a)ucl.ac.uk>) escribió: Thanks a lot! Sent from my phone, please excuse brevity and typos ------------------------------ *From:* Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> *Sent:* Monday, October 1, 2018 4:15:12 AM *To:* Iglesias Gonzalez, Eugenio; Miguel Ángel Rivas Fernández *Subject:* Re: [Freesurfer] Hippocampal-Amygdala subfields error Sure thing, I can look into it tomorrow afternoon. Andrew *From: *"Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> *Date: *Sunday, September 30, 2018 at 10:47 AM *To: *"Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu>, Miguel Ángel Rivas Fernández <miguelrivasfdez(a)gmail.com> *Subject: *FW: [Freesurfer] Hippocampal-Amygdala subfields error * External Email - Use Caution * Hi, Andrew and MA. MA: sorry for the slow response. I’ve been on vacation (today’s my last day). Andrew: Can you please verify that the version for MAC with this bug fixed made it to the server? It’s the only explanation I can find to MA’s problems… Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez(a)gmail.com> *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Date: *Wednesday, 26 September 2018 at 00:09 *To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error * External Email - Use Caution * Hi Eugenio, Did you have chance to review the error that I have reported some days ago when I ran the hippocampal and amygdala command? It was happened only in 17 subjects (sample size 295). I rerun the HippocampalSubfieldsandAmygdalaNuclei command and I got the same error: *Fitting mesh to image data mask took 683.6633 seconds Transforming points Transforming points Wrote image to file image.mgz INFO: dst volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (691, 691, 473) voxel : ( 0.3333, 0.3333, 0.3333) x_(ras) : ( 0.0000, -1.0000, 0.0000) y_(ras) : (-0.0047, 0.0000, 1.0000) z_(ras) : ( 1.0000, 0.0000, 0.0047) c_(ras) : ( 4.2397, 13.6233, 12.2196) file : T2isotropic.mgz volume geometry: extent : (640, 640, 225) voxel : ( 0.3594, 0.3594, 0.7000) x_(ras) : ( 0.0000, -1.0000, 0.0000) y_(ras) : (-0.0047, 0.0000, 1.0000) z_(ras) : ( 1.0000, 0.0000, 0.0047) c_(ras) : ( 4.2397, 13.6234, 12.2196) file : /Applications/freesurfer/subjects/5095/mri/orig/T2.nii Constructing image-to-world transform from header information (asmr1.mgz) Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz) Wrote image to file asmr2.mgz This file does not contain MRI parameters This file does not contain MRI parameters In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT2_autoEstimateAlveusML (line 2147) MATLAB:subsassignnumelmismatch Darwin rmnlab1.inv.usc.es <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 T2 hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de 2018, 15:35:35 CEST For more details, see the log file /Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log* What could be the problem? Thanks in advance. Best wishes, El dom., 16 sept. 2018 a las 19:20, Miguel Ángel Rivas Fernández (< miguelrivasfdez(a)gmail.com>) escribió: Hi Eugenio, It was happened in only in 17 subjects (sample size is 295). I repeated the process several times and I got always the same error. Thank you very much for your help!. Cheers, El dom., 16 sept. 2018 a las 19:14, Iglesias Gonzalez, Eugenio (< e.iglesias(a)ucl.ac.uk>) escribió: * External Email - Use Caution * Wow sorry about this. I have to carefully check whether it’s a different / related bug, or if the fix only made it to the Linux version. Is it happening for all subjects, or only some? I’m traveling / on vacation these days but will take a look as soon as I can. Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez(a)gmail.com> *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Date: *Sunday, 16 September 2018 at 15:52 *To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error * External Email - Use Caution * Hi Eugenio, I have downloaded the most recent dev version ( freesurfer-darwin-OSX-ElCapitan-dev.tar.gz <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-…> ) from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev and I get the same error. My version of Mac is Mac OS High Sierra Version 10.13.3 *Fitting mesh to image data mask took 683.6633 seconds Transforming points Transforming points Wrote image to file image.mgz INFO: dst volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (691, 691, 473) voxel : ( 0.3333, 0.3333, 0.3333) x_(ras) : ( 0.0000, -1.0000, 0.0000) y_(ras) : (-0.0047, 0.0000, 1.0000) z_(ras) : ( 1.0000, 0.0000, 0.0047) c_(ras) : ( 4.2397, 13.6233, 12.2196) file : T2isotropic.mgz volume geometry: extent : (640, 640, 225) voxel : ( 0.3594, 0.3594, 0.7000) x_(ras) : ( 0.0000, -1.0000, 0.0000) y_(ras) : (-0.0047, 0.0000, 1.0000) z_(ras) : ( 1.0000, 0.0000, 0.0047) c_(ras) : ( 4.2397, 13.6234, 12.2196) file : /Applications/freesurfer/subjects/5095/mri/orig/T2.nii Constructing image-to-world transform from header information (asmr1.mgz) Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz) Wrote image to file asmr2.mgz This file does not contain MRI parameters This file does not contain MRI parameters In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT2_autoEstimateAlveusML (line 2147) MATLAB:subsassignnumelmismatch Darwin rmnlab1.inv.usc.es <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 T2 hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de 2018, 15:35:35 CEST For more details, see the log file /Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log* *What could be the problem?* *Thanks in advance, * *Best wishes, * El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio (< e.iglesias(a)ucl.ac.uk>) escribió: * External Email - Use Caution * Hi Miguel Angel, This bug was recently fixed in the dev version. If you download the most recent one, you won’t have this problem. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez(a)gmail.com> *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Date: *Thursday, 13 September 2018 at 21:12 *To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> *Subject: *[Freesurfer] Hippocampal-Amygdala subfields error * External Email - Use Caution * Hello Freesurfer devs, I ran the hippocampal and amygdala subfields command in my sample and I get the following error in several subjects: *Constructing image-to-world transform from header information (asmr1.mgz) Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz) Wrote image to file asmr2.mgz This file does not contain MRI parameters This file does not contain MRI parameters In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing image-to-world transform from header information (asmr1.mgz) Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz) Wrote image to file asmr2.mgz This file does not contain MRI parameters This file does not contain MRI parameters In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)* *MATLAB:subsassignnumelmismatch Darwin rmnlab1.inv.usc.es <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 T2 hippocampal subfields exited with ERRORS at jueves, 13 de septiembre de 2018, 21:37:33 CEST* What would be the reason? Thanks in advance, Best wishes, -- *Miguel Ángel Rivas Fernández* _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- *Miguel Ángel Rivas Fernández* _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- *Miguel Ángel Rivas Fernández* -- *Miguel Ángel Rivas Fernández* -- *Miguel Ángel Rivas Fernández* -- *Miguel Ángel Rivas Fernández* -- *Miguel Ángel Rivas Fernández* -- *Miguel Ángel Rivas Fernández* -- *Miguel Ángel Rivas Fernández*

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PhD position in Neuroscience of Auditory (Speech) Perception, TU Dresden, Germany
by Katharina von Kriegstein 10 Oct '18

10 Oct '18

External Email - Use Caution We are seeking an enthusiastic PhD student with a particular interest in neuroscience of auditory (speech) perception. The PhD position is part of the Chair of Cognitive and Clinical Neuroscience led by Prof. Dr. Katharina von Kriegstein at the TU Dresden, Germany. The position is funded by the ERC-project SENSOCOM (http://cordis.europa.eu/project/rcn/199655_en.html) The aim of the SENSOCOM project is to investigate the role of auditory and visual subcortical sensory structures in analysing human communication signals and to specify how their dysfunction contributes to human communication disorders such as developmental dyslexia. For examples of our work on these topics see von Kriegstein et al., 2008 Current Biology, Diaz et al., 2012 PNAS, Müller-Axt et al., 2017 Current Biology. TU Dresden is one of eleven German Universities of Excellence and offers an interdisciplinary scientific environment. The Neuroimaging Centre at the TU Dresden (http://www.nic-tud.de) has cutting-edge infrastructure with 3-Tesla MRI, MRI compatible headphones and eye-tracking, several EEG systems, a neurostimulation unit including neuronavigation, TMS and tDCS devices. The PhD position is available at the next possible date. Subject to personal qualification, employees are remunerated according to salary group E 13 TV-L 50%. There will be the opportunity to participate in the TU Dresden graduate academy (https://tu-dresden.de/ga?set_language=en) For more information on the post please see the official advertisement: https://tinyurl.com/ybwe47bc For more information on our research group see: https://tu-dresden.de/mn/psychologie/kknw --- Katharina von Kriegstein Professor of Cognitive and Clinical Neuroscience Technische Universität Dresden Bamberger Str. 7, 01187 Dresden, Germany Phone +49 (0) 351-463-43145 https://tu-dresden.de/mn/psychologie/kknw https://twitter.com/kvonkriegstein

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Thalamic Nuclei segmentation results
by Dev vasu 09 Oct '18

09 Oct '18

External Email - Use Caution Dear all, I have used Freesurfer pipeline for Thalamic Nuclei segmentation, the results of segmentation appear to be very poor, i am annexing the results , please kindly review if there is any thing wrong with the segmentation results. Thanks Vasudev

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recon-all terminated in middle : continuing an analysis of an existing subject
by Dev vasu 09 Oct '18

09 Oct '18

External Email - Use Caution Dear all, I was trying to run recon-all, the pipeline terminated in middle now i would like to know if there is any way i can restart it from the point where it was terminated?. Thanks Vasudev

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nu_correct disk i/o issues
by Jasper van den Bosch 09 Oct '18

09 Oct '18

External Email - Use Caution We are trying to run recon_all inside an fmriprep singularity container, but are running into an issue with nu_correct. It says it cannot write to disk, however there is plenty of space on the tmpdir and output dir. Does this script try to write to any other locations? Because this would fail inside the container, where each writable location has to be 'mounted'. Error message: ncendef: ncid 5: No space left on device Error outputting volume: possibly disk full? nu_evaluate: crashed while running evaluate_field (termination status=139) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct Command ran: nu_correct -clobber ./tmp.mri_nu_correct.mni.1121/nu0.mnc ./tmp.mri_nu_correct.mni.1121/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1121/0/ -iterations 1000 -distance 50 [xxx@yyyy.cluster:/data/BIDS/derivatives/freesurfer/sub-1/mri/] [2018-10-04 14:59:29] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1121/0/ ./tmp.mri_nu_correct.mni.1121/nu0.mnc ./tmp.mri_nu_correct.mni.1121/nu1.imp this issue at the fmriprep repo: https://github.com/poldracklab/fmriprep/issues/1308 possibly related: https://github.com/freesurfer/freesurfer/issues/462 Many thanks for any advice, Jasper van den Bosch

3 4

Extract individual vertex thickness values from cortical parcellations
by lindsay hanford 09 Oct '18

09 Oct '18

External Email - Use Caution Hello Freesurfer Community, I am looking for a way to extract thickness values at the level of each vertex from Freesurfer atlas-based parcellated regions (aparc.annot), or more generally lobes. Is this possible? Using mri_segstats I know it is possible to get more general metrics such as min, max and average thickness values, and # of voxels. Is it possible to use an annot file to read out the raw thickness values? This post was the closest I could find to answering my question, however, this was at the group level and not specified for parcellated regions. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022097.… Thank you in advance, Lindsay -- *Lindsay Hanford, PhD* *The Buckner Laboratory* *|* *Harvard University*

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