Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Subcortical segmentation voxel error
by Selina Wilson 10 Mar '16

10 Mar '16

Hello all, I am new to Freesurfer and learning as I go/encounter problems. This might be an obvious question, but has anyone had issues with black holes in their subcortical segmentation runs? The wiki page it suggests contacting the freesurfer mailing list before attempting to manually fix the issue to see if there is an automatic procedure that could fix it. The second part of my issue is that the black voxels are not incorrectly labeled as another structure/region. When I place the cursor over the black holes, the TkMedit Tools window reads "Sgmtn label: none" . If I do any of the suggested manual fixes (brushing, flood filling, linear selections) on the "none" voxels and label them as hippocampus, would that assign voxels to a structure, increasing the volume of that structure, when those voxels are not actually there? To be more clear, I am worried that these "none" voxels are the result of movement during the scan or an error in how the scan was read by the computer. I do not want to 'fix' this problem by manually labeling those voxels as part of the hippocampus and find out down the line that this scan was actually unusable. That would mean that the data collected from this scan on hippocampal volume would be erroneous and make the final cross-sectional data analysis invalid/inaccurate. Thank you for your help! Selina Wilson Undergraduate Research Assistant Duke University Class of 2017 (317) 430 - 7404 selina.wilson(a)duke.edu

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Re: [Freesurfer] System crash by extremely much generated output v6 beta
by Gronenschild Ed (NP) 10 Mar '16

10 Mar '16

Hi Bruce, Here it is Cheers, Ed

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Re: [Freesurfer] System crash by extremely much generated output v6 beta
by Gronenschild Ed (NP) 10 Mar '16

10 Mar '16

Hi, Let me explain it again. On a 3 TByte disk I've made a partition of 20 GB to run OSX10.7. When I run recon-all all input and output data are on the large partition which has about 1.5 TByte free space. This means that all temporary and intermediate files that are created by recon-all (e.g. in /tmp) are residing on the 20 GB partition which has a free space of 11 GB initially. And all this free space is consumed (I assume by all these temporary/ intermediate files) by mri-topo-fixer. Cheers, Ed On 10 Mar 2016, at 18:00, <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: Hi Ed, I am a bit confused by your two emails. In one you state that you have a MacPro OSX10.7 installed on a partition of 20 GB with FreeSurfer v6 beta Then in the next post you state that the disk you have is 1.5TB (is that the disk or partition?) I'm also confused, because you stated that at the time you ran into trouble the disk had 11GB. You then said you ran out of disk (I assume that means you had 0GB left). Then you said when you rebooted you had 11GB (no files were created at all?). This is a dangerous way in general to run a machine. If a program core dumps you have less disk space then your RAM. General advice is to keep at least 5% of disk space free (or a bare minimum of > RAM size). It may be worth doing this after a fresh reboot and checking your RAM to make sure you don't have apps that autostart sucking up RAM, causing you to swap. If you try to swap, without enough free space that can easily crash your machine. First, What is the full disk partition setup? Next, run df (on the relevant partition) and show the output before running FreeSurfer. Then run recon-all and if possible show the df output at the crash Then run df on reboot. hth d PS it may be worth pointing out that beta 6 was withdrawn for more development. On 3/10/16 5:09 AM, Gronenschild Ed (NP) wrote: Hi, I'm using a MacPro with 32 GByte RAM. The output of FreeSurfer is written to a disk with 1.5 TByte free space. At the time I ran into trouble the free disk space was about 11 GByte. When I wanted to inspect the progress after a few hours I noticed that the disk has ran out of space. I couldn't do anything but restarting the MacPro. Then the disk space was again about 11 GByte. So I reran the subject with recon-all -autorecon2 -autorecon3 and it happened again. Inspecting the log files I noticed that both times the problem occurred at exactly the same stage in the pipeline: mris-topo-fixer. Cheers, Ed On 10 Mar 2016, at 10:41, <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: 20 GB is not a lot for a full macos install + data, how much room was free before you ran recon-all? What is the hardware? CPU, RAM etc. hth d On Wed, Mar 9, 2016 at 12:09 PM, Gronenschild Ed (NP) <ed.gronenschild(a)maastrichtuniversity.nl<mailto:ed.gronenschild@maastrichtuniversity.nl> <mailto:ed.gronenschild@maastrichtuniversity.nl>> wrote: Hi developers, Could you please help me out on this problem. Should I upload the data? Cheers, Ed Begin forwarded message: From: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl<mailto:ed.gronenschild@maastrichtuniversity.nl> <mailto:ed.gronenschild@maastrichtuniversity.nl>> Subject: System crash by extremely much generated output v6 beta Date: 7 March 2016 12:57:57 CET To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>> Hi developers, My environment: MacPro OSX10.7 installed on a partition of 20 GByte; FreeSurfer v6 beta During processing recon-all on 4 subjects in parallel using 4 terminal windows, the 20 GByte partition got full. This happened twice and I managed to trace down the offending stage in the pipeline: topology fixing, in particular the tool mris_topo_fixer. Most probably it went into an endless iteration loop generating so much output the disk got full. Cheers, Ed

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Map label from lh to rh
by Makaretz, Sara Johanna 10 Mar '16

10 Mar '16

Hi, I want to map a label from one hemi to the other (all on fsaverage). I tried mri_label2label: mri_label2label --s fsaverage --srchemi lh --trghemi rh --srclabel lh.a.label --trglabel rh.flipped_lh.a.label --regmethod surface but I think I need to specify a reg file to go between hemispheres, does this exist somewhere? an error message kindly pointed out that this one does not exist: /usr/local/freesurfer/stable5_3_0/subjects/fsaverage/surf/rh.lh.sphere.reg

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Working with non-FreeSurfer derived meshes and labels
by Slater David 10 Mar '16

10 Mar '16

Hi, I have some mesh and label files I would like to use with my Freesurfer data however they are in an alternative format (connectome workbench). I would like to get the labels into the space of a typical Freesurfer subject (e.g. fsaverage), followed by pushing the labels to subject native space and creating volume label files (similar to the aparc native space parcellations). Is it possible to register an isolated mesh file to the fsaverage subject? How can I convert labels on a .gii mesh file to a standard Freesurfer subject? Thanks, David p.s. The goal of this would be to use the following parcellation scheme with my freesurfer data: Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cereb. Cortex bhu239-.

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v5.3.0 pial crossing into ventricals
by Smaragdi A. 10 Mar '16

10 Mar '16

Hi mailing list, regarding a previous issue with the v5.3.0 and the pial boundary crossing into the ventricles (below), i have run the subjects in the beta version and the problem does not appear. My question to the experts is now, considering it is not advised to switch versions in a data set, how 'bad' would it be to run 7 subjects in the beta version, and the other 190 or so in the v5.3.0 version? It is after all a very small number of the total sample, would this be ok, or would you still advise against it? Many thanks, Areti ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Smaragdi A. [A.Smaragdi(a)soton.ac.uk] Sent: 12 January 2016 18:27 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject) Hi Bruce, thanks for the quick reply, I am running v5.3.0 from a Linux, but more than 2/3 through my data set so don't really want to swap to 6.. Where can I get the beta and how would it help? Thanks, Areti ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: 12 January 2016 16:24 To: Freesurfer support list Subject: Re: [Freesurfer] (no subject) what version are you running? I believe that this is a bug that has been fixed. Hopefully we will get version 6 out soon and upgrading will fix this, but you can download a beta and try to make sure if you want cheers Bruce On Tue, 12 Jan 2016, Smaragdi A. wrote: > Hi mailing list, > > I have encountered this problem in Freesurfer a number of times now and I wondered if any of you had any solutions. > > It seems that sometimes after a recon-all has been run, there is a large overlap of the pial boundary and wm boundary, in the same region each time near the lateral ventricles (it can be on either hemisphere or both). I have attached a print screen of the issue, this time in the LH. As you can see, we have tried adding CPs and have also added WM, but after re-running it, the problem still exists. We have also tried running the randomness, but this has had no effect. > > Any suggestions as to what we could do to fix this would be great - thank you! > > > > > _______________________________________________ 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_fuse_segmentations error in longitudinal stream
by Sandra Preißler 10 Mar '16

10 Mar '16

Dear freesurfer experts, I am running freesurfer “freesurfer-Linux-centos7_x86_64-dev-20150728”. On a Linux terminal: “Linux cortical 3.16.6-2-default #1 SMP Mon Oct 20 13:47:22 UTC 2014 (feb42ea) x86_64 x86_64 x86_64 GNU/Linux” After normal processing of the data cross sectional. Followed by the creation of the within-subject template (DTprae_P01) I get an error message running the longitudinal command (-long). The command line I used was: recon-all -long DTprae_P01 DT_P01 -all The subject directory is: /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT The subprocess ending with the error and the error message were the following: mri_fuse_segmentations -a aseg.presurf.mgz -c aseg.auto_noCCseg.mgz -n norm.mgz DTprae_P01.long.DT_P01 DTprae_P01 DTpost_P01 aseg.fused.mgz mghRead(/mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01/mri/aseg.presurf.mgz, -1): could not open file using aseg.presurf.mgz as aseg volume using aseg.auto_noCCseg.mgz as aseg no-CC-label volume using norm.mgz as norm volume reading /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01.long.DT_P01/mri/norm.mgz and processing 2 timepoints, writing to aseg.fused.mgz loading data for subject DTprae_P01 ... mri_fuse_segmentations: could not read input volume /mnt/bp01dat_castor/Studie158_Phantom_Bein/Daten/MRT/DTprae_P01/mri/aseg.presurf.mgz Linux cortical 3.16.6-2-default #1 SMP Mon Oct 20 13:47:22 UTC 2014 (feb42ea) x86_64 x86_64 x86_64 GNU/Linux recon-all -s DTprae_P01.long.DT_P01 exited with ERRORS at Tue Mar 8 17:52:40 CET 2016 I checked the folder (DTprae_P01/mri) and there is no data called aseg.presurf.mgz. in which step is this data produced? How can I fix this problem? I hope you could help me. Kind regards, Sandra

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Re: [Freesurfer] System crash by extremely much generated output v6 beta
by Gronenschild Ed (NP) 10 Mar '16

10 Mar '16

Hi, I'm using a MacPro with 32 GByte RAM. The output of FreeSurfer is written to a disk with 1.5 TByte free space. At the time I ran into trouble the free disk space was about 11 GByte. When I wanted to inspect the progress after a few hours I noticed that the disk has ran out of space. I couldn't do anything but restarting the MacPro. Then the disk space was again about 11 GByte. So I reran the subject with recon-all -autorecon2 -autorecon3 and it happened again. Inspecting the log files I noticed that both times the problem occurred at exactly the same stage in the pipeline: mris-topo-fixer. Cheers, Ed On 10 Mar 2016, at 10:41, <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: 20 GB is not a lot for a full macos install + data, how much room was free before you ran recon-all? What is the hardware? CPU, RAM etc. hth d On Wed, Mar 9, 2016 at 12:09 PM, Gronenschild Ed (NP) <ed.gronenschild(a)maastrichtuniversity.nl<mailto:ed.gronenschild@maastrichtuniversity.nl>> wrote: Hi developers, Could you please help me out on this problem. Should I upload the data? Cheers, Ed Begin forwarded message: From: Ed Gronenschild <ed.gronenschild(a)maastrichtuniversity.nl<mailto:ed.gronenschild@maastrichtuniversity.nl>> Subject: System crash by extremely much generated output v6 beta Date: 7 March 2016 12:57:57 CET To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Hi developers, My environment: MacPro OSX10.7 installed on a partition of 20 GByte; FreeSurfer v6 beta During processing recon-all on 4 subjects in parallel using 4 terminal windows, the 20 GByte partition got full. This happened twice and I managed to trace down the offending stage in the pipeline: topology fixing, in particular the tool mris_topo_fixer. Most probably it went into an endless iteration loop generating so much output the disk got full. Cheers, Ed

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adc brainstem-subs
by Thomas Potrusil 10 Mar '16

10 Mar '16

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Re: [Freesurfer] Using external software to perform brain extraction, multiple T1s
by Chris Adamson 09 Mar '16

09 Mar '16

There was a post in 2015 from Richard Parker talking about using SPM brainmasks instead of the Freesurfer ones. I would like to do this but in some cases I have multiple T1s and I get the motioncor step to make a registered template. What steps do I need to perform to get a brainmask from one of the images into the template space created by motioncor? Apologies if this has already been asked. [cid:image001.jpg@01D17AC3.302C3530] Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adamson(a)mcri.edu.au www.mcri.edu.au<http://www.mcri.edu.au/> [cid:image002.png@01D17AC3.302C3530]<https://www.facebook.com/MurdochChildrensResearchInstitute>[cid:image003.png@01D17AC3.302C3530]<https://twitter.com/MCRI_for_kids>[cid:image004.png@01D17AC3.302C3530]<http://instagram.com/murdoch_childrens>[cid:image005.png@01D17AC3.302C3530]<http://www.youtube.com/user/MurdochChildrens/videos>[cid:image006.jpg@01D17AC3.302C3530]<https://donate.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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