Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30067 discussions

Surface edits: Cortex that extends into the putamen + Missing gray matter
by Vincent Koppelmans 01 Jul '17

01 Jul '17

Hi all, I was wondering how to fix the following issues: 1) The cortical ribbon extends into the gray matter of the putamen (see the top row of this image: https://www.dropbox.com/s/x1euf9otl2nv6ff/Fix.png?dl=0) 2) Cortical gray matter is missing in the medial temporal lobes (see the bottom row of this image: https://www.dropbox.com/s/x1euf9otl2nv6ff/Fix.png?dl=0) I can’t find solutions for these particular issues under https://surfer.nmr.mgh.harvard.edu/fswiki/Edits How should I approach this? Suggestions are very much welcome. Thank you! - Vincent

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Using asegstats2table for gtm.stats.dat?
by Elijah Mak 01 Jul '17

01 Jul '17

Hi Unix experts, I am trying to extract the PVC-ed values from gtm.stats.dat for every subject. Is there a fast way to do this using a similar workflow with asegstats2table? Thanks. Best Wishes, Elijah

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Editing pial surface and aseg
by Lya Katarina Paas Oliveros 30 Jun '17

30 Jun '17

Dear FreeSurfer team I am correcting some structural MRI scans after the automated surface-based analysis and the automated segmentation. I would like to know if you have any information about how often the Voxel Edit is used and if it makes sense to correct the subcortical segmentation. I have identified specifically problems with the shape of the putamen and its borders, in some cases the shape of the putamen overlaps with the cortex. Additionally, if I am editing both the Pial and WM surfaces with "Recon Edit" and the subcortical segmentation with "Voxel Edit", after saving both changes can I run both analysis at the same time (recon-all -autorecon-pial -subjid AND recon-all -autorecon2-noaseg -autorecon3 -subjid)? Or do I need first to do, for example, Recon Edit, save the changes and run the analysis and then do Voxel Edit, save the changes and run the other analysis? 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Ubuntu 16.04 LTS Thank you very much in advance. Best regards, Lya Paas

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Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011
by Corinna Bauer 29 Jun '17

29 Jun '17

Dear Dr. Yeo, Our research group is currently trying to segment the Yeo atlas into separate labels, but just came across this thread which indicates that you have already done this. Would you be willing to re-share the link to your previously extracted individual labels from your 7 and 17 networks? Thank you! Corinna On Thu, May 14, 2015 at 4:54 AM, Thomas Yeo <ythomas(a)csail.mit.edu> wrote: > Hi Annie, > > I have previously extracted individual regions from the 7 and 17 > networks. You can download them here > (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_ > JNeurophysiol11_SplitLabels.zip?dl=0). > Please see the README in the folder for more explanations. There > should be a precuneus DMN region. > > The 17 networks consist of 114 regions that have been previously published: > > 1) Krienen et al., Reconfigurable state-dependent functional coupling > modes cluster around a core functional architecture. Philosophical > Transactions of the Royal Society B, 369:20130526, 2014 > > 2) Yeo et al., Functional connectivity during rested wakefulness > predicts vulnerability to sleep deprivation. Neuroimage 111:147-158, > 2015 > > Hope this helps. > > Cheers, > Thomas > > On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 <poohann1122(a)gmail.com> wrote: > > Hello Dr. Yeo, > > > > Thank you for your previous help and reply. We've worked out the way to > > switch the resolution of parcellation and successfully extracted the > > anatomical information using your mask derived from iFC work. > > > > However, we came across a new problem to apply the cortical mask and need > > your kind help again. We aim to conduct a seed-based analysis to > investigate > > structural covariance based on the network defined by iFC, and find your > > work of cortical parcellation conceptually perfectly suit our research > > question. Based on the current approach, however, it seemed that we could > > only extract the anatomical information from the whole well-defined > network, > > but not the specific hub within the network (e.g., the anatomical > > information of the precuneus from the DMN). We wonder if you have any > > suggestion to resolve our problem, ie, to be specific, is there any way > to > > only extract the discrete hub information rather than the whole network? > > > > We really appreciate your generous help. Thank you very much. > > > > p.s. This email would also forward to my senior colleague, Dr. > Hsiang-Yuan > > Lin, who is a child and adolescent psychiatrist doing imaging research in > > Taiwan. > > > > > > 2015-05-13 19:15 GMT+08:00 陳昱潔 <poohann1122(a)gmail.com>: > >> > >> Hi Professor Yeo : > >> > >> Thank you for helping us so much! > >> After mris_anatomical_stat I tried aparcstats2table to extract the > table. > >> But I failed with generating the table. > >> > >> > >> Best wishes, > >> Annie > >> > >> 2015-05-12 8:29 GMT-04:00 Thomas Yeo <ythomas(a)csail.mit.edu>: > >> > >>> Hi Annie, > >>> > >>> I assume this means 5202 is your subject ID? Maybe you should check if > >>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_ > 7Networks_N1000.annot > >>> exist? > >>> > >>> If so, you can run mris_anatomical_stats to generate statistics for > >>> the parcellation. > >>> > >>> Cheers, > >>> Thomas > >>> > >>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 <poohann1122(a)gmail.com> wrote: > >>> > Hi Professor Yeo : > >>> > After I rechecked the directory and run again mri_surf2surf > >>> > I got the result: > >>> > "Saving target data > >>> > Converting to target annot > >>> > Saving to target annot > >>> > > >>> > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_ > 7Networks_N1000.annot" > >>> > The file of 5202/label didn't come out with > >>> > lh.Yeo2011_7Networks_N1000.annot > >>> > But it seems succeed, right? > >>> > How can I get the stat of this parcellation ? > >>> > > >>> > Thank you very much! > >>> > > >>> > Best wishes, > >>> > Annie > >>> > > >>> > 2015-05-12 6:06 GMT-04:00 Thomas Yeo <ythomas(a)csail.mit.edu>: > >>> > > >>> >> Hi Annie, > >>> >> > >>> >> mri_surf2surf is complaining that it cannot write out the > annotation. > >>> >> > >>> >> Just to clarify, is your subject called test_run_allindex? In other > >>> >> words, is the variable s equal to test_run_allindex? > >>> >> > >>> >> Does the directory "/home/annie/test_run_allindex/label/" exist? If > >>> >> not, then you first need to create the directory first, and then > >>> >> mri_surf2surf can write the resulting annotation file into the > >>> >> directory. > >>> >> > >>> >> Cheers, > >>> >> Thomas > >>> >> > >>> >> On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 <poohann1122(a)gmail.com> wrote: > >>> >> > Hi Professor Yeo : > >>> >> > > >>> >> > We tried the code > >>> >> >>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh > >>> >> >>> --sval-annot > >>> >> >>> > >>> >> >>> > >>> >> >>> > >>> >> >>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_ > 7Networks_N1000.annot > >>> >> >>> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot > >>> >> > However there came an error of "could not write annot file > >>> >> > /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_ > N1000.annot > >>> >> > No such file or directory" > >>> >> > And we checked our individual subject's label there isn't > >>> >> > lh.Yeo2011_7Networks_N1000.annot > >>> >> > Should we generate/import the lh.Yeo2011_7Networks_N1000.annot > into > >>> >> > our > >>> >> > subjects/label first? > >>> >> > What can we do ? > >>> >> > Thank you very much! > >>> >> > > >>> >> > Best wishes, > >>> >> > Annie > >>> >> > > >>> >> > > >>> >> > 2015-05-05 8:36 GMT-04:00 Thomas Yeo <ythomas(a)csail.mit.edu>: > >>> >> > > >>> >> >> Hi Annie, > >>> >> >> > >>> >> >> Please cc the freesurfer list when you reply because there might > be > >>> >> >> other people more qualified to answer your question. > >>> >> >> > >>> >> >> Based on what you are saying, I think you can first use > >>> >> >> mri_surf2surf > >>> >> >> (with the "sval-annot" flag) to transform the 2011 functional > >>> >> >> networks > >>> >> >> .annot file from fsaverage space to the subject's native surface > >>> >> >> space. Type "mri_surf2surf --help" to see examples. > >>> >> >> > >>> >> >> You can then use mris_anatomical_stats to compute thickness > >>> >> >> statistics. > >>> >> >> > >>> >> >> Cheers, > >>> >> >> Thomas > >>> >> >> > >>> >> >> On Tue, May 5, 2015 at 3:21 PM, 陳昱潔 <poohann1122(a)gmail.com> > wrote: > >>> >> >> > Dear Pro. Yeo: > >>> >> >> > > >>> >> >> > Very appreciate for your reply ! > >>> >> >> > > >>> >> >> > We are trying to use your definition of the functional network > >>> >> >> > regions > >>> >> >> > to > >>> >> >> > re-parcellate our images > >>> >> >> > and get the regions of volume or cortical thickness for our > study > >>> >> >> > interest > >>> >> >> > of structural network. > >>> >> >> > However, we did not want to re-run the first recon-all again > due > >>> >> >> > to > >>> >> >> > it's > >>> >> >> > spending to much time. > >>> >> >> > And we are still can't find the way to solve this problem. > >>> >> >> > Thank you very much for helping us! > >>> >> >> > > >>> >> >> > Best wishes, > >>> >> >> > Annie Chen > >>> >> >> > > >>> >> >> > 2015-05-02 8:25 GMT+08:00 Thomas Yeo <ythomas(a)csail.mit.edu>: > >>> >> >> >> > >>> >> >> >> Hi Yu-Chieh, > >>> >> >> >> > >>> >> >> >> I am cc-ing the freesurfer list who may help you with your > >>> >> >> >> issues. > >>> >> >> >> > >>> >> >> >> Can you explain what exactly you are trying do? The > parcellation > >>> >> >> >> is > >>> >> >> >> released in different resolutions including fsaverage5. Why > >>> >> >> >> can't > >>> >> >> >> you > >>> >> >> >> just use the fsaverage5 parcellation? > >>> >> >> >> > >>> >> >> >> Cheers, > >>> >> >> >> Thomas > >>> >> >> >> > >>> >> >> >> On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 <poohann1122(a)gmail.com> > >>> >> >> >> wrote: > >>> >> >> >> > Dear professor Yeo : > >>> >> >> >> > > >>> >> >> >> > My name is Yu-chieh Chen , I am a graduated student from > >>> >> >> >> > National > >>> >> >> >> > Taiwan > >>> >> >> >> > University of medical school, and my supervisor is professor > >>> >> >> >> > Susan > >>> >> >> >> > Shur-Fen > >>> >> >> >> > Gau from department of psychiatry, National Taiwan > University > >>> >> >> >> > Hospital & > >>> >> >> >> > College of Medicine. We are very interesting about your > paper > >>> >> >> >> > published > >>> >> >> >> > in > >>> >> >> >> > 2011 which using resting MRI to separate brain regions to > >>> >> >> >> > functional > >>> >> >> >> > networks. We'd like to use your percellation to re-separate > >>> >> >> >> > the > >>> >> >> >> > brain > >>> >> >> >> > regions based on your released data in Freesurfer( > >>> >> >> >> > > >>> >> >> >> > > >>> >> >> >> > http://ftp.nmr.mgh.harvard.edu/fswiki/ > CorticalParcellation_Yeo2011). > >>> >> >> >> > And > >>> >> >> >> > use > >>> >> >> >> > these volume of brain regions for our study, however, there > >>> >> >> >> > comes > >>> >> >> >> > the > >>> >> >> >> > problem that we assumed that we can change the fsaverage > into > >>> >> >> >> > fsaverage5, > >>> >> >> >> > thus we may get the new volume of the parcellation_Yeo. But > it > >>> >> >> >> > is > >>> >> >> >> > not > >>> >> >> >> > work. > >>> >> >> >> > So I send this email for help. Last , I am very appreciate > >>> >> >> >> > your > >>> >> >> >> > kindness > >>> >> >> >> > and > >>> >> >> >> > very sorry for my inappropriate and rough. > >>> >> >> >> > Thank you very much for read this email and sorry for > occupied > >>> >> >> >> > your > >>> >> >> >> > time. > >>> >> >> >> > > >>> >> >> >> > Best wishes, > >>> >> >> >> > Yu-chieh Chen > >>> >> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> > > >>> >> > > >>> > > >>> > > >> > >> > > > > _______________________________________________ > 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. >

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FS ignoring wm.mgz edits
by KALEY E ELLIS 29 Jun '17

29 Jun '17

Dear FreeSurfer Developers, We are attempting to make manual white matter edits to our subjects. The edits are saving; however, after running with recon-all, the WM surface does not appear to be taking into account our edits made to wm.mgz. Below is additional information, and I have attached our recon-all.log. We are only editing the cross because our dataset is comprised of single timepoints. We are using FreeSurfer v5.3 and our operating system is OS X El Capitan version 10.11.6. Command to open and edit WM: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red Command to submit edits: recon-all -autorecon2-wm -autorecon3 -subjid Recon-all log (see attached) Thank you, Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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CT DIOCMs
by John Anderson 29 Jun '17

29 Jun '17

Dear Freesurfer experts, I have T1 images acquired using CT scan not MRI. I have the following questions please: 1. "mri_convert" failed to convert the dicoms to nifti, so I used "dcm2nii" part of mricron to convert the dicoms to nifti. I am wondering if there are any tools in Freesurfer to convert CT scan dicoms to nii or mgz formats 2. Can this type of images be processed in Freesufrer using the traditional pipeline for surfaces reconstruction. I mean using "recon-all" Thank you for your guidance Jon

2 1

mri_normalize problem normalization2
by Chris Adamson 28 Jun '17

28 Jun '17

Hello, For one subject I'm getting a weird error on mri_normalize in normalization2. When it goes into the "3d normalization pass 1 of 2" I get an error HISTOalloc(-2147383648): could not allocate histogram The image that is produced by MRI3dGentleNormalize line 874 of mri_normalize/mri_normalize.c has a block of pixels with HUGE negative values. They are in the background and nowhere near the brain. The data comes from a public dataset so I can send it for debugging if required. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.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 ______________________________________________________________________

2 2

Qdec input fields
by Rockers, Elijah D. 28 Jun '17

28 Jun '17

Hi, We like using Qdec to display cortical thickness results. The only drawback is that we are unable to manually input values into the boxes for threshold values, FDR rate, etc.. We are running Centos7. We thought the graphics drivers were the problem, but even after buying a whole new GFX card with different drivers, the same problem persists. Even stranger, our colleague can SSH in from a Mac using X forwarding, and she does not experience that problem. I know this may not strictly be a Freesurfer problem, but I was hoping someone else may have run into this problem before, and has some insight that could help us. Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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ERROR: bits = 0 not supported
by 糜超 28 Jun '17

28 Jun '17

Hi, I am preprocessing my fMRI data acquired with Philips. when I using the command 'dcmunpack -src . -targ sess01 -run 101 bold nii f.nii .....' The error occurred likes below: Found 31 total files. Found 12 unique series: 0 101 301 401 501 601 701 801 901 1001 1101 1201 Subject xxx Date xxx Time 110223 Institution xxxxx. 0 Survey unknown unknown unknown unknown unknown unknown ./PS_0002 101 Survey unknown unknown unknown unknown unknown 140 ./XX_0003 301 T1W_3D_TFE_ref unknown unknown unknown unknown unknown 190 ./IM_0004 401 FE_EPI unknown unknown unknown unknown unknown 2835 ./XX_0007 501 FE_EPI_EX1 unknown unknown unknown unknown unknown 2835 ./IM_0008 601 FE_EPI_EX2 unknown unknown unknown unknown unknown 2835 ./IM_0011 701 FE_EPI_EX3 unknown unknown unknown unknown unknown 2835 ./IM_0013 801 FE_EPI_EX4 unknown unknown unknown unknown unknown 2835 ./XX_0016 901 FE_EPI_EX5 unknown unknown unknown unknown unknown 2835 ./XX_0018 1001 FE_EPI_EX6 unknown unknown unknown unknown unknown 2835 ./IM_0019 1101 FE_EPI_EX7 unknown unknown unknown unknown unknown 2835 ./XX_0022 1201 FE_EPI_EX8 unknown unknown unknown unknown unknown 2835 ./XX_0024 mri_convert ./XX_0003 ./bold/101/f.nii --nskip 0 --ndrop 0 nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./XX_0003... Starting DICOMRead2() dcmfile = ./XX_0003 dcmdir = . WARNING: tag image orientation not found in ./XX_0003 Ref Series No = 101 ERROR: bits = 0 not supported. My os is Linux 16.04 and the Freesurfer's version is 5.3.

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QDEC Error in Analysis
by AYUSHI SHUKLA 28 Jun '17

28 Jun '17

Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s <subjid> -qcache" on my data and it says that this has run successfully without any errors. But when I hit analyze on the qdec GUI, I get the following error- "Error in Analyze: Couldn't open /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file." I went through the old questions with the same issue, however I could not figure a solution for my problem as when I check in the directory, the file is present. I have tried to re-run recon-all and recon-all -s as well, but it is still giving the same error. I was wondering if someone could help me with this issue. Warm Regards Ayushi Shukla

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