Freesurfer

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30090 discussions

Surface edits: Cortex that extends into the putamen + Missing gray matter
by Vincent Koppelmans 03 Jul '17

03 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 the attached image). 2) Cortical gray matter is missing in the medial temporal lobes (see the bottom row of the attached image). I can’t find solutions for these particular issues under https://surfer.nmr.mgh.harvard.edu/fswiki/Edits <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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Strange Discrepancy Between Activation Location on Surface vs. Volume
by Taylor, Johnmark 03 Jul '17

03 Jul '17

Hello, I am running into an odd issue. In particular, I have run a GLM analysis in *volume* space, and I am visualizing the results both on the surface using tksurfer, and on the volume using tkmedit. In both cases, I am using the register.dof6.dat file to do the registration. Oddly, when I visualize the results on the *surface*, the activation patch falls on the medial surface of the hemisphere, in the *precuneus*, whereas when I visualize the results on the *volume*, the patch is in the *intraparietal sulcus* (which is where we expect to see this particular activation). I have made a label out of the activation in both cases and viewed it in the other space just to make sure that it is in fact the same activation, and it is. Any idea what might be going on? It seems to me that it can't be an issue with the BOLD volume --> structural volume registration, since the activations look normal on tkmedit. It seems to me, then, that it must have to do with the relationship between the anatomical volume and the anatomical surface--could this be where the problem lies? Maybe an imperfect surface reconstruction? Thank you very much, JohnMark

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bad file conversion
by Michael Davies 03 Jul '17

03 Jul '17

Hello, i was wondering if you could possibly help me with a subjects file that has loaded badly. It not only loaded up-side down but looks as though there are additional deficits that need correcting. Any tips or advice would be greatly appreciated! Kind regard, Michael

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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

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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 ______________________________________________________________________

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