Freesurfer October 2018

freesurfer@nmr.mgh.harvard.edu

113 participants
156 discussions

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

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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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very bad result using "mris_ca_train" and "mris_ca_label"
by Maedeh Khalilian 09 Oct '18

09 Oct '18

External Email - Use Caution Dear Dr.Bruce Fischl Thank you very much for your great sense of responsibility. Sure, i have sent you a zip file named "Maedeh_results"(it was a rather big sized one so i had to send it through Wetranser). Hope you have received it. However, a general question is that, according to freesurfer help the required arguments for "mris_ca_train" are : mris_ca_train [options] <hemi> <canon surf> <annot file> <subject 1> <subject 2> ... <output file> as it seems it gets one surf file(e.g sphere.reg),and one annotation file, but several subjects...so what does this surface file refer to?should i make an average of all subjects' .reg files? and also for the annotation file ! just one .annot is enough or i have to make an average of several annotation files? if yes, how should i do that? i would be grateful if you could help me. Best regards Maedeh,

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Talairach failed in monkey brain
by Frehiwot Woldeyes 09 Oct '18

09 Oct '18

External Email - Use Caution Hello Freesurfers, I was attempting to reconstruct a monkey brain, i encountered an error during talairach registration step, i have used tkregister2 to manually edit the registration but i have gotten error there too: tkregister2 --targ /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --mov /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --reg /usr/local/freesurfer/subjects/A004_crop.mhd.nii tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii movable volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii reg file /usr/local/freesurfer/subjects/A004_crop.mhd.nii LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 regio_read_register(): No such file or directory Could not open /usr/local/freesurfer/subjects/A004_crop.mhd.nii ERROR: reading /usr/local/freesurfer/subjects/A004_crop.mhd.nii Do you have any thoughts on how to troubleshoot this one? Regards, frehiwot

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m.khalilian@sutech.ac.ir sent you files via WeTransfer
by WeTransfer 09 Oct '18

09 Oct '18

External Email - Use Caution m.khalilian(a)sutech.ac.ir sent you some files 1 file, 378 MB in total ・ Will be deleted on 16 October, 2018 Download link: https://wetransfer.com/downloads/9370a847d04b46d6fcbc4faec24f094e2018100911… Message: Dear Dr.Bruce Fischl Thank you very much for your great sense of responsibility. Sure, i have attached a zip file named "Maedeh_results"(it was a rather big sized one so i had to send it through Wetranser). It contains my initial annotation files(as the input of 'mris_ca-train') by which i have made my atlas(?h.Desikan100.annot), my atlases for both hemispheres(?hDesikan100.gcs), a color LUT, my subject directory "test1" which i have used as the input of "mris_ca_train", another subject diectory "subj1", on which i have used to test my atlas, and finally my results "?h.finalDesikan100.annot" .(actually the result of applying my atlas on subj1) i myself guess that the main problem is that i am using just one subject as the input of "mris_ca_train", but i dunno how to get multiple subjects... that would be perfect if you could help me. Cheers Maedeh. 1 file Maedeh_results.zip [Get more out of WeTransfer, get Plus](https://wetransfer.com/plus?trk=WT201704_email&utm_campaign=WT_email_… About WeTransfer: https://wetransfer.com/about Help: https://wetransfer.zendesk.com/hc/en-us Legal: https://wetransfer.com/legal/terms To make sure our emails arrive, please add noreply(a)wetransfer.com to [your contacts](https://wetransfer.zendesk.com/hc/en-us/articles/204909429).

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Mri Convert Help
by Justin Arnett 08 Oct '18

08 Oct '18

External Email - Use Caution Hello Everyone, I hope you are doing well! I am trying to recon-all a DICOM file, for the ultimate hope of being able to identify the location of M1 via parcellation. I have successfully been able to do so for 2 subjects already, though for some reason I am having a problem with the MRI convert stage from the .dcm file to the .nii.gz file. I copied/pasted the terminal shell I tried performing above. I am using a Mac (Yosemite 10.10.5) with FreeSurfer V6.0.0 Further, I think it might be helpful to note that I am a very extreme novice in computer science/coding--I have completed recon-all's of 2 subjects by following, essentially line-by-line, the "FreeSurfer Download and Install Page," and this process was the first time I ever used the terminal shell. (In this way, I would absolutely LOVE if anyone might be able to explain where I went wrong as simplistically as possible). Thank you all so much for the help- I hope you have a great start to the week! - Justin DBI 05 MRI Convert Error Justins-Computer:~ justinarnett$ export FREESURFER_HOME=/Applications/freesurfer Justins-Computer:~ justinarnett$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects -bash: [: /Users/justinarnett: binary operator expected grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory MNI_DIR /Applications/freesurfer/mni Justins-Computer:~ justinarnett$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/DBI05MRI Justins-Computer:~ justinarnett$ cd /Applications/freesurfer/subjects/DBI05MRI Justins-Computer:DBI05MRI justinarnett$ cp $FREESURFER_HOME/subjects/DBI05MRI/Image1.dcm usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory Justins-Computer:DBI05MRI justinarnett$ mri_convert Image1.dcm Image1.nii.gz /Applications/freesurfer/FreeSurferEnv.sh: line 226: [: /Users/justinarnett: binary operator expected grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory grep: /Users/justinarnett: Is a directory grep: 1/matlab/startup.m: No such file or directory mri_convert.bin Image1.dcm Image1.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from Image1.dcm... Starting DICOMRead2() dcmfile = /Applications/freesurfer/subjects/DBI05MRI/Image1.dcm dcmdir = /Applications/freesurfer/subjects/DBI05MRI Ref Series No = 401 Found 824 files, checking for dicoms WARNING: tag ImageNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR WARNING: tag SeriesNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR WARNING: tag image orientation not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR ERROR: GetDICOMInfo(): dcmGetDWIParams() 10 DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR break DICOMRead.c:5228 Found 164 dicom files in series. WARNING: tag ImageNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR WARNING: tag SeriesNumber not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR WARNING: tag image orientation not found in /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR ERROR: GetDICOMInfo(): dcmGetDWIParams() 10 DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR break DICOMRead.c:5228 First Sorting Computing Slice Direction Vs: -120.054 -103.192 34.4639 Vs: -0.741 -0.636922 0.212719 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 165 ndcmfiles = 165 MRIallocSequence(0, 0, 165, 1): bad parm No such file or directory ERROR: mri alloc failed

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Freesurfer October 2018