Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

Hippocampal sufields
by Erik Lindberg 19 Jun '17

19 Jun '17

Dear Freesurfer experts, I am currently running your new pipeline for hippocampal subfield segmentation. However the resolution on my MRI images is too bad for identifying specific cellular layers such as stratum moleculare. My preferred option would be not to divide the different subfields into different cellular layers and only have one volume for the presubiculum for instance. Is there any way I can know how much volume of the molecular layer that should be included into each separate subfield? So forinstance I can add the volume of subiculum with the volume of the molecular layer in the subicula Best Erik

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PhD-position | clinical MR-physics | Germany
by Theodor Rüber 19 Jun '17

19 Jun '17

Dear colleagues, Please note the following PhD-student job offer: http://www.ukb.uni-bonn.de/42256BC8002B7FC1/vwLookupDownloads/PhD_EPI_Ruebe… This is a highly attractive position between the fields of MR-physcis, clinical research and neuroradiology as part of a research project on imaging of the bbb in the appealing research environment of Bonn University. We are looking forward to receiving your application! Best, Theodor. on behalf of Elke Hattingen, Tony Stöcker, and Christian E. Elger Theodor Rüber, MD .............................................................. Department of Epileptology Bonn University Hospital .............................................................. Sigmund-Freud-Str. 25 53127 Bonn Germany .............................................................. theodor.rueber(a)ukbonn.de www.epileptologie-bonn.de

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e: recon-all exits with error at surf/lh.thickness, mghRead looks for .mgh/.mgz filename extension
by Anup Bidesi 18 Jun '17

18 Jun '17

Thanks Bruce, recon-all finished process without error. Regards, Anup Date: Wed, 14 Jun 2017 10:25:20 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all exits with error at surf/lh.thickness, mghRead looks for .mgh/.mgz filename extension To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1706141024260.28087(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Anup I suspect the problem is choosing a subject with ".mgz" in the ID. I wouldn't include any of ".nii" ".mgz" or ".mgh" in a subject ID. Try rerunning and just using fsMM cheers Bruce On Wed, 14 Jun 2017, Anup Bidesi wrote: > > Hello FreeSurfer Users, > > New to Freesurfer, I'm attempting to recon-all using : > > recon-all -all -i T1.nii -s op.nii.mgz (Attached recon-all log) > > The automated process begins normally and seems to run Autorecon Prrocessing > Stages 1-25, but at step 26 > (I think) and then exits with Error, per log as seen below: > > ------------------------------------------------------------- > > mghRead(/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.th > ickness, > -1): could not open file. > Filename extension must be .mgh, .mgh.gz > or .mgz > > ------------------------------------------------------------- > > Within the subject .mgz folder in Surf there was a tmp.pctsurfcon.14807 fold > er with > a file named lh.wm.mgh (size 569 kb). > > I ran this process a couple of times and the autorecon process would exit at > same step.I > tried looking up the Archive for any similar previous error messages but did > not find any. > Please advise. > > 1) FreeSurfer version: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > 2) Platform: Ubuntu 14.04 > > 3) uname -a: Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic > #164-Ubuntu > SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > 4) recon-all.log: see attached > > Thanks for your help, > > Anup

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Re: [Freesurfer] TRACULA: Motion measures only
by Yendiki, Anastasia 16 Jun '17

16 Jun '17

Yep, you can use the dmri_motion command. Run it without any arguments to see usage info. It needs: * Your original, unprocessed DWIs * b-value table * Output from your FSL eddy correction (*.ecclog from eddy_correct or *.eddy_parameters from eddy) Hope this helps, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Buckless, Colleen" <Buckless(a)kennedykrieger.org<mailto:Buckless@kennedykrieger.org>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, June 16, 2017 at 10:22 AM To: "'freesurfer(a)nmr.mgh.harvard.edu<mailto:'freesurfer(a)nmr.mgh.harvard.edu>'" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA: Motion measures only Hi All, I have already preprocessed data in FSL and only want to use TRACULA to get the motion measures to match subjects based on motion. Is there any way I can get out the motion measures without doing all of the other preprocessing steps in TRACULA? Thanks, Colleen Buckless ________________________________ 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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TRACULA: Motion measures only
by Buckless, Colleen 16 Jun '17

16 Jun '17

Hi All, I have already preprocessed data in FSL and only want to use TRACULA to get the motion measures to match subjects based on motion. Is there any way I can get out the motion measures without doing all of the other preprocessing steps in TRACULA? Thanks, Colleen Buckless ---------------------------------------------------------------------- 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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FA ROI analysis using 6-gradient-dir DWIs
by Yong Li 16 Jun '17

16 Jun '17

Dear Bruce, Dear Anastasia, I would like to investigate white matter changes in a group of elderly patients. The acquired DWI data are 6-gradient-direction+1-non-DWI images by a clinic routine (not by me unfortunately). The meaningful analyses may be ROI-based DTI model considering FA, MD etc. measures to perform group comparisons. Subcortical ROIs like thalamus, putamen in aseg as well as white matter bundles like *h.cst_AS etc. in TRACULA are of my research interests. I would like to kindly ask the following questions: 1. To compute FA/MD of thalamus for instance, shall I simply apply individual thalamus mask extracted from aseg to wmparc then output the results in .stats files? 2. TRACULA analysis works with my DWI data (6 gradient-direction) so I could extract masks of the 18 tracts, which serve as ROIs in the FA/MD group analysis. I wonder whether there exists a better alternative to extract fiber bundle masks? The practical issue is that it takes >20 hours to process single patient and I have hundreds and it's accumulating. 3. Is there a new development to enable adding new labels to the TRACULA atlas? I would like to include Corona Radiata, Inferior Fronto-Occipital Fasciculus, Olfactory Tract etc. So far I only found this post to do it manually: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31955.html. Thank you all very much in advance! Kind regards, Yong

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web image preprocessing
by tom parker 16 Jun '17

16 Jun '17

Dear Freesurfer experts, Does anyone know if there is a web portal where i can upload my T1 images to preprocess them with freesurfer and download the preprocessed files? Thank you so much!

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Design matrix for local gyrification index in QDEC
by marco mcsweeney 16 Jun '17

16 Jun '17

Dear all, I have a quick question regarding the appropriate design (DOSS, DODS, SOSS, SODS) to be used with QDEC when comparing LGI values for 2 groups (patients and healthy controls). I have noted that a number of publications have used DODS when comparing LGI values between 2 groups while controlling for age and gender, but I was just wondering if this is the correct design to use for this type of analysis. I am aware that only DODS and DOSS can be used with QDEC but that it may be possible to use SOSS or SODS with mri_glmfit. I would like to be 100% sure about which is the most appropriate design to use. I have 2 groups with 29 subjects in each group (N = 58). The reason I ask this is because I am wondering whether it would be better to use SOSS (same offset same slope) when looking at LGI because, as I understand it, cortical folding patterns are roughly determined in the first few months of life and remain relatively stable into adulthood, unlike cortical thickness which is much more dynamic. If the results of this analysis are significant after FDR correction I would assume that this suggests that cortical folding patterns are indeed different in the 2 groups. Any help or advice on this would be greatly appreciated. Thank you so much in advance. BW Marco

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substract images
by John Anderson 15 Jun '17

15 Jun '17

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Freesurfer parcelations of cortical regions in TrackVis
by Leyton Moscoso, Cristian Eduardo 15 Jun '17

15 Jun '17

Hi Freesurfer’s and TrackVis experts I am wondering if there is a way to import cortical parcelations mapped on a T1 image in TrackVis. I tried loading segmentation in TrackVis, but this does not allow me to see all parcelations in T1 as I can be done in Freeview. In TrackVis I need to upload them one by one. Thank you Cris Dr Cristian Leyton M Research Fellow in Neurology Department of Neurology Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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Freesurfer June 2017