Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

username and password
by Yamada, Takashi 01 Oct '19

01 Oct '19

External Email - Use Caution Hi, I'm subscribers of freesurfer. However, I am about to reading the mail exchange about the Q&A of freesurfer, I was asked to input the username and password, then I cannot read them. How should I proceed for that? Best, Takashi Yamada -------------------------------------------------------------------------------------------------------------------------------- Takashi Yamada, MD & PhD Postdoctorial Research Associate Department of Cognitive, Linguistic and Psychological Sciences (CLPS) Brown University Box 1821 190 Thayer Street Providence, RI 02912 TEL : +1 401 863 9488 FAX : +1 401 863 2255 Email: takashi_yamada(a)brown.edu --------------------------------------------------------------------------------------------------------------------------------

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Hippocampal and Amygdala Segmentation Error - Incorrect Path and Missing Files
by Chen, Christine 01 Oct '19

01 Oct '19

External Email - Use Caution To whom it may concern, I am attempting to run the hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) on the development version of FreeSurfer. However, I am running into a couple errors when running the segmentHA_T1.sh script. The first error is that the script is looking for segmentSubjectT1_autoEstimateAlveusML in the wrong directory. It is currently looking for this command in /usr/local/freesurfer/bin/ however I need to change this path to /g5/dcn/freesurfer_testing/HippoSegment_Test/freesurfer/bin/. I couldn't find where to change this path in run_segmentSubjectT1_autoEstimateAlveusML.sh. Where is this path defined so I can change it? Secondly, the error output states that I am missing the following files in the subject's mri folder: lh.hippoSfVolumes-T1.v21.txt lh.amygNucVolumes-T1.v21.txt rh.hippoSfVolumes-T1.v21.txt rh.amygNucVolumes-T1.v21.txt I believe these files are created using recon-all -all -s [subjectname]. I ran this command before segmentHA_T1.sh using MPRAGE dicoms, and it seemed to have run without noticeable error, but these four files are still missing. How would I go about resolving this to create these files? Thank you in advance for the help! Best, CC ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: [Freesurfer] CUDA 9.1 with freesurfer
by fsbuild 30 Sep '19

30 Sep '19

External Email - Use Caution Hello Vasudev, With the 6.0 source, you can use options to the configure command to point to a coda distribution and try to build freesurfer..  See the post by user buildqa at this link, https://github.com/freesurfer/freesurfer/issues/107#issuecomment… followed by the posts from user melrobin.  User melrobin reported he was able to get it to work with coda 9.1. - R. On Sep 30, 2019, at 09:57, Dev vasu <vasudevamurthy.devulapally(a)gmail.com> wrote:        External Email - Use Caution        Dear HCP team ,Could you please let me know how i can configure CUDA 9.1 with freesurfer 6.0 or Freesurfer 5.3.0 -HCPIt is taking a long time by using openmp to run recon-all.please let me know if you have any suggestions for parallelization.ThanksVasudev_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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CUDA 9.1 with freesurfer
by Dev vasu 30 Sep '19

30 Sep '19

External Email - Use Caution Dear HCP team , Could you please let me know how i can configure CUDA 9.1 with freesurfer 6.0 or Freesurfer 5.3.0 -HCP It is taking a long time by using openmp to run recon-all. please let me know if you have any suggestions for parallelization. Thanks Vasudev

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Matlab crash dump when running the segmentation of longitudinal hippocampal subfields
by Liu Guodong 30 Sep '19

30 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze longitudinal hippocampal subfields for many subjects on a server, but when I run the command longHippoSubfieldsT1.sh, for some subjects, I get the error for Matlab and a file called matlab_crash_dump. I've searched the list and no similar request have been submitted. Does anyone have any thoughts on how to solve this problem? Also, Ive attached the matlab_crash_dump file. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: CentOS release 7 3)matlab_crash_dump file: see attached Best regards, Guodong

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Libraries not found Freeview ubuntu 18
by Renew Andrade 29 Sep '19

29 Sep '19

External Email - Use Caution Dear FreeSurfer experts: I have a problem with Freeview running I ubuntu. Some libraries missing. I read this thread “https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63255.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63255.html>” and my question is regarding the installation of the libraries. Do I need to install manually one by one or is there any package to install most of them? Plus I couldn´t find any of them by the name in "sudo apt-get install *”. Some of them are OpenGL, qtscript, volumerendering, vtkftgl, vtkhybrid, vtkIO, vtkDICOMParser, ...

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Converting .label coordinates to MNI
by Berger, Joel 27 Sep '19

27 Sep '19

External Email - Use Caution Hi friendly Freesurfers, I have seen this question asked, but can't find the answer. When exporting a label from tksurfer for a particular ROI for a subject, the coordinates in the .label document don't match up with any of the coordinates I can view in tksurfer. Is there a way/formula to convert these easily, ideally into MNI coordinates? I tried loading the label into Matlab with freesurfer_read_label.m converting to Talairach with freesurfer_label2tal.m and then also converting those coordinates using tal2mni.m, but the Talairach or the MNI coordinates do not match with the Talairach/MNI coordinates shown for the corresponding vertices in tksurfer. Thank you, Joel ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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TRACULA - input Nifti instead of DICOM?
by Daniel Callow 27 Sep '19

27 Sep '19

External Email - Use Caution Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work? Best, Daniel Callow -- *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Which files do I need to mri_deface to anonymized a subject?
by Tim Schäfer 27 Sep '19

27 Sep '19

External Email - Use Caution Dear FS experts, I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all pipeline to a consortium server, and they require all data to be anonymized. I found mri_deface [1] and wondered which files I would have to apply it to, and whether there are any other things I should be aware of. So far, my plan is to use mri_deface to replace, for each subject, the following files in mri/: * orig.mgz * orig_nu.mgz * T1.mgz * rawavg.mgz It would also be an option to upload only a subset of all the files produced by FreeSurfer, but I do not know which files to exclude and include, so if you have suggestions for this, it would also be very welcome. I will also look at some public datasets to see how they did it. [1] https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Error during processing data. mris_make_surfaces malloc: *** error for object 0x2431900024317: pointer being freed was not allocated.
by Троицкий Антон Александ рович 27 Sep '19

27 Sep '19

External Email - Use Caution Dear Bruce, I don't’ know exactly what happened during the processing. I have 8 Gb of RAM of my Mac. When the freesurfer is working there is approximately 2 Gb free RAM. Unfortunately, I don’t know how to check the working of RAM and was there a memory overflow or memory leaking. It will be great If you could check my data. I want to mention that the same problem was with other data of the same patient. I have uploaded the patient data on my google drive account. So here you can download it https://drive.google.com/file/d/1Rx2HG2ZXTTphrYDMRwguOljz9T4K7av1/view?usp=…. The error appeared for data for 2019-07-22. But the same problem appeared for data for 2019-09-04. mris_fix_topology(5832,0x7fffc83843c0) malloc: *** error for object 0x7fcf88f2ca50: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug 0 defective edges Abort Darwin mac-2ap023-2.fccho-moscow.ru<http://mac-2ap023-2.fccho-moscow.ru> 16.7.0 Darwin Kernel Version 16.7.0: Thu Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64 recon-all -s 2019-09-03_3DBrainView_T1_FSSD_2019-09-26_13-11 exited with ERRORS at Thu Sep 26 17:43:07 MSK 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I saw the system requirements for the freesurfer and there was a mention about 8 RAM. Is it a necessary amount of memory only for freesurfer or for PC station? Best regards, Anton Troitskii. Are you running out of memory on the machine? If not, and you upload the entire subject dir we will see if we can replicate and fix this problem. cheers Bruce On Tue, 24 Sep 2019, Троицкий Антон Александрович wrote: External Email - Use Caution Hello FreeSurfer Developers, during the processing of patient data an error occurred. I don’t clearly understand a reason for this error. Technical description of this error is mris_make_surfaces(10174,0x7fffbf9553c0) malloc: *** error for object 0x2431900024317: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug 000: dt: 0.0000, sse=991989.1, rms=2.913 021: dt: 0.5000, sse=841468.7, rms=1.605 (44.916%) 022: dt: 0.5000, sse=803776.9, rms=1.267 (21.055%) rms = 1.24, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=793308.4, rms=1.242 (1.982%) Abort My suggestion is that the error associated with memory allocation and its reading. Is there any suggestion about why it happened and how can I prevent it in the future? Also, I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0 2) Platform: macOS Sierra 10.12.6 3) uname -a: Darwin mac-2ap023-2.fccho-moscow.ru<http://mac-2ap023-2.fccho-moscow.ru> 16.7.0 Darwin Kernel Version 16.7.0: Thu Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached _______________________________________________

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