Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Crash in mri_register_ca during recon-all -base id -tp id1 -tp id2 -all
by Knut J Bjuland 17 Jul '13

17 Jul '13

Hi, I have some trouble running recon-all longitudinal pipelines. When recon-all comes to mri_register_ca it crashes without giving a message, even tough 8g ram was available. I have run the program with -debug. Is there any other option I may use? The system is running Rocks 6.0 (Mamba), and it uses Slurm queue system. Can I use the FreeSurfer 5.3 longitudinal process with data processed with FreeSurfer 5.1? I wish to use the new Longitudinal linear mixed effects model MATLAB tools. Knut J

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Re: [Freesurfer] SWI acquisition question
by Fotiadis, Panagiotis 17 Jul '13

17 Jul '13

Hi Bruce, Don't worry about it! In addition, I was wondering about something else as well. I've been using MRIcron to analyze some of my Susceptibility Clinical Scans and even though they used to open fine, some of them (like the one I have attached in this email) appear distorted in a way. In the images I attached the "Original" one is how the Susceptibility clinical image should appear like, and the "Distorted" is how it appears for some of my subjects. Would you happen to know why is this happening? Thanks again for your time and help! Best, Panos ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Wednesday, July 17, 2013 11:54 AM To: Fotiadis, Panagiotis Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] SWI acquisition question Hi Panos sorry, I think this is pretty far outside our expertise, and it would be hard in any case to try to figure out what happened to give you these strange looking results. I certainly don't have any insight sorry, Bruce On Wed, 17 Jul 2013, Fotiadis, Panagiotis wrote: > Hi FS Community, > > I was wondering whether anyone had a chance to look into this. Thanks again for your time! > > Best, > Panos > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis > Sent: Tuesday, July 16, 2013 2:00 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] SWI acquisition question > > Hi FreeSurfer community, > > I am analyzing some SWI scans of some old subjects. For most of my subjects when a SWI was acquired, the resulting files that I would get would be a Magnitude image, a Phase image, a mIP image, and the SWI image. However, I have a couple of subjects for whom I get only the mIP and the SWI images, and the SWI image looks more blurry than it's supposed to be. I was wondering: > > 1) Why do I get only the mIP and the SWI images for those subjects and not the magnitude and phase images as well, > 2) Is it normal for the mIP to look like that? Usually it looks different, and > 3) Why is the final SWI image more blurry than usual? By looking at the image, I believe that maybe the head coil was not properly connected to the scanner at the time of the acquisition but I don't know whether that would be a sufficient explanation. > > I have attached two attachments: One of the resulting mIP and one of the equivalent blurry SWI of the same subject. > > Thank you in advance for your help and time! > > Best, > Panos >

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kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files
by Jasmeet Hayes 17 Jul '13

17 Jul '13

Dear Freesurfer experts, I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left & right stats) but the only information in the text files is the subject ID number. However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script. Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files). We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz > volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd ..

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Missing flirt.fsl file in bin folder
by Gundran, Andrew 17 Jul '13

17 Jul '13

Hello freesurfers, I’ve been trying to run tracula on freesurfer and it seems that when I get to the point where it uses FSL’s flirt I receive an error. I looked into it further and it seems I am missing a file to run flirt: $FREESURFER_HOME/bin/flirt.fsl It seems that I somehow do not have that file to complete tracula. I was hoping someone could help with this or perhaps send me the file? I am using freesurfer- Darwin-snowleopard-i686-stable-pub-v5.3.0- MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Hope to hear from someone soon, Andrew

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Re: [Freesurfer] SWI acquisition question
by Fotiadis, Panagiotis 17 Jul '13

17 Jul '13

Hi FS Community, I was wondering whether anyone had a chance to look into this. Thanks again for your time! Best, Panos ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Tuesday, July 16, 2013 2:00 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] SWI acquisition question Hi FreeSurfer community, I am analyzing some SWI scans of some old subjects. For most of my subjects when a SWI was acquired, the resulting files that I would get would be a Magnitude image, a Phase image, a mIP image, and the SWI image. However, I have a couple of subjects for whom I get only the mIP and the SWI images, and the SWI image looks more blurry than it's supposed to be. I was wondering: 1) Why do I get only the mIP and the SWI images for those subjects and not the magnitude and phase images as well, 2) Is it normal for the mIP to look like that? Usually it looks different, and 3) Why is the final SWI image more blurry than usual? By looking at the image, I believe that maybe the head coil was not properly connected to the scanner at the time of the acquisition but I don't know whether that would be a sufficient explanation. I have attached two attachments: One of the resulting mIP and one of the equivalent blurry SWI of the same subject. Thank you in advance for your help and time! Best, Panos

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Propagating changes to segmentation
by Liane Hunter 17 Jul '13

17 Jul '13

Hello, I have a question about propagating changes to segmentation. Once I have saved my edits what is the appropriate command to propagate these changes for both cortical and subcortical changes that I have made. The workflow instructs that after segmentation edits are made to run -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3 to the wm. mgz file. However the instructions indicate to open brainmask.mgz to make edits. Should I make changes on the wm.mgz file? Any clarification on this topic would be much appreciated. -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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ROI center of gravity
by Tyler Manning 16 Jul '13

16 Jul '13

Hi, I'd like to use freesurfer to determine the center of gravity of an ROI from a functional overlay in surface space. I've tried looking for some sequence of commands to do this with no luck. Any suggestions? Thanks in advance for your help. All the best, Tyler

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Tracula problem in pre-processing
by Gundran, Andrew 16 Jul '13

16 Jul '13

Helo all, I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file. ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 I have also attached the trac-all log.

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freesurfer does not recognize white matter or the brain
by Christine Smith 16 Jul '13

16 Jul '13

I have a subject for whom we have had consistent difficulties within freesurfer. The difficulties existed for a single scan from 2008 and also for a pair of scans (averaged together) that were collected in 2013. The difficulty is that freesurfer will fail to label white matter as white matter. The problem is not small like the one listed in the troubleshooting area of the wiki. In some cases an entire lobe is not labeled. There are also instances where freesurfer will delete areas of brain out of the brainmask. Again, these are large areas of the brain, including regions where we have control points. I have included a picture of what is happening. We are going on 4000+ control points for this person. I should mention that after we address one problem in one part of the brain (by adding hundreds of control points and also drawing in the white matter underneath on the the wm.mgz) it will still fail to capture the brain properly. It will also then decide that another part of the brain (which had been parcellated perfectly before) is now not considered part of the brainmask or has no white matter. The picture shows these problems perfectly. Any advice about how to get this to work? Regards, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

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Re: [Freesurfer] motion dependent resolution: bbr vs flt
by Gerit Pfuhl 16 Jul '13

16 Jul '13

the QC on the T1 data gives no obvious clue. We edit the brainmask when there are surface issues However, we have not quantified this data yet - a closer look may indeed tell us more. Thanks Gerit On 16 July 2013 20:52, Pfuhl, Gerit <Gerit.Pfuhl(a)uniklinikum-dresden.de>wrote: > > ________________________________________ > Von: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Gesendet: Dienstag, 16. Juli 2013 20:51 > An: Pfuhl, Gerit > Cc: Roschinski, Benjamin; freesurfer(a)nmr.mgh.harvard.edu; King, Joseph > Betreff: Re: AW: [Freesurfer] motion dependent resolution: bbr vs flt > > Is the motion in the anatomicals bad enough that it would affect the > quality of the surfaces? Bbregister uses the surfaces, flirt does not. > > The "eddy current correction" is also motion correction - it aligns all > the frames to the first with an affine registration. Rotation and > translation due to head motion, in addition to warping due to eddy > currents, is what cause the frames to be misaligned. It's assumed that by > aligning them you correct for both (approximately). > > On Tue, 16 Jul 2013, Pfuhl, Gerit wrote: > > > Hi, > > > > we have more motion in the anatomical data between the groups (healthy > controls vs patients). > > The difference between 5.1 using flt and 5.2. using bbr is not extreme. > > If I understood correctly, since we use first recon-all and thatis > independent of flt or bbr, any difference musts come how the two algorithms > deal with the dti raw data. Is there any motion correction? > > The preprocessing steps include eddy current correction but I did not > find a step for motion correction. > > > > Regards > > Gerit > > ________________________________________ > > Von: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > > Gesendet: Dienstag, 16. Juli 2013 20:03 > > An: Roschinski, Benjamin > > Cc: freesurfer(a)nmr.mgh.harvard.edu; Pfuhl, Gerit; King, Joseph > > Betreff: Re: [Freesurfer] motion dependent resolution: bbr vs flt > > > > Hi Benjamin - You can see how bbregister works in this paper: > > > http://surfer.nmr.mgh.harvard.edu/pub/articles/greve.2009.ni.63.BBR.pdf > > > > In short it uses the surfaces from the freesurfer recon (which of course > > come from the anatomical) to align the anatomical to an EPI (in this case > > the low-b from the diffusion series). Because bbregister uses the extra > > information about the surfaces (which flirt doesn't), that's why Doug was > > asking if the motion is in the anatomical or the diffusion. > > > > Between 5.1 and 5.2 several things changed in tracula, only one of them > > being the default registration method. You can still switch back to flirt > > with 5.2 though if you want to check if that's what's making the > > difference. The instructions for this are under "Specify the > intra-subject > > registration method" here: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > > > Let me know if you have any other questions. > > > > a.y > > > > On Tue, 16 Jul 2013, Roschinski, Benjamin wrote: > > > >> Hi Doug, > >> > >> thanks for the answer. > >> We did a comparison between the results of TRACULA 5.1 and 5.2. > >> When we compared the two different results (5.1 and 5.2) from health > controls and recovered anroxia nervosa patients for the first time the > results of TRACULA 5.2 seemed to be better than the ones of TRACULA 5.1 > >> Then we did the same with our acute anorexia patients which are less > settled in mri studies. > >> In the end the TRACULA 5.2 outputs were not as good as the results of > TRACULA 5.1 after we included the acute patients. > >> I hope now you understand why we thought that bbr might be more > sensitive for motion. > >> If bbr is pretty robust in anatomical and dti what do you think about > flt. Is it as good as bbr or might be better in case of motion? > >> Another question: we know that bbregister needs to have a high > resolution image reference for its algorithm. > >> Is that the T1? > >> > >> thank you very much > >> > >> Benjamin > >> > >> ________________________________________ > >> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [ > freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von > "Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > >> Gesendet: Montag, 15. Juli 2013 19:41 > >> An: freesurfer(a)nmr.mgh.harvard.edu > >> Betreff: Re: [Freesurfer] motion dependent resolution: bbr vs flt > >> > >> Hi Benjamin, BBR does not need higher resolution. Do you mean motion in > >> the anatomical or motion in the DTI? BBR should be pretty robust in > >> either case. It is hard to know what might be going on without more > >> details of why you think it is getting worse. > >> doug > >> > >> > >> On 07/14/2013 08:01 AM, Roschinski, Benjamin wrote: > >>> Dear freesurfer experts and users, > >>> > >>> we visualize white matter tracts of anorexia nervosa patients which > >>> are characterized by more movements in mri studies. > >>> We have the impression that we get worser TRACULA outputs by using > >>> bbregister than flt. > >>> Could it be possible that bbregister needs a higher resolution than > flt? > >>> So summarizing it is more sensitive for motion? > >>> > >>> kind regards > >>> > >>> Benjamin > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> greve(a)nmr.mgh.harvard.edu > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >> _______________________________________________ > >> 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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Freesurfer July 2013