Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

mri_glmfit error (mri_reshape number of elements)
by Mcnorgan, Christopher 05 Jul '17

05 Jul '17

Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the fsaverage surfaces, rather than self surfaces. I’ve already inspected the individual contrasts, loading the fsaverage surface in tksurfer and rendering each subject’s contrast as an overlay, and would now like to compute the group-level results. I first ran isxconcat-sess, and saw no errors indicated in the program output. mri_glmfit was then called as followed, and produced the following output (same result for the rh): $ mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh --glmdir glm.wls --nii.gz Reading source surface /home/chris/LDT/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh --glmdir glm.wls --nii.gz sysname Linux hostname brocasarea machine x86_64 user chris FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz logyflag 0 usedti 0 labelmask /home/chris/LDT/fsaverage/label/lh.cortex.label maskinv 0 glmdir glm.wls IllCondOK 0 ReScaleX 1 DoFFx 0 wFile cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory glm.wls Loading y from /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz Saving design matrix to glm.wls/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 537168 Pruning voxels by thr: 0.000000 Segmentation fault (core dumped) This seems to have its root in a mismatch between the vertices in the fsaverage lh.cortex label and those in the contrast data. However, I carried out subject-level analyses in the fsaverage surface space specifically to facilitate a group-level analysis in fsaverage surface space, so I can’t see where I went wrong. The only other post I could find that was similar was related to an attempt to carry out a group analysis in native surface space, which is not the case here. Thanks for your time

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Building your own fsaverage
by Silas 05 Jul '17

05 Jul '17

Dear FreeSurfer team, I'm making a surface based group analysis of 40 multiple sclerosis subjects using FreeSurfer tools. What are the advantages of building your own fsaverage (make_average_subject) instead of using the premade fsaverage? Would you in general recommend this? What is the pro's and con's of building your own fsaverage? All the best, Silas I searched the mailing stream and found this answer: 'make_average_subject script, but as Doug implies you probably don't need to. Our warp is high-enough dimensional that you rarely need to build average subjects from your own population'

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freesurfer@nmr.mgh.harvard.edu
by 糜超 05 Jul '17

05 Jul '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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GLM fitting for the cortical volume
by Ali Radaideh 05 Jul '17

05 Jul '17

Dear FS experts, I have managed to run the *glm_fit* on the cortical thickness and area on a group of MS patients. However, i am not sure how to do this on the cortical volume. which file represents the cortical volume in subject's directory? Many thanks, -- *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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Speeding up mri_robust_register with --cost ROBENT
by Michael Waskom 05 Jul '17

05 Jul '17

Hi Freesurfers, I'm using mri_robust_register to obtain a registration between high resolution (.7mm isotropic) whole-head T1w and T2w images from the same subject. An example command line is: mri_robust_register --mov T2w.nii.gz --dst T1w.nii.gz --lta T2w_to_T1w.lta --warp T2w_reg.nii.gz --cost ROBENT --entradius 2 --entcorrection --satit --iscale This works extremely well -- much better than FLIRT. (I'm using this registration to do some preprocessing before running recon-all, so unfortunately bbregister is not an option). But, it takes *forever*. (My runtimes are about 90 minutes using OMP parallelization with 24 cores, or about 16 hours running in serial). I'm interested in playing with the various options to see if I can get a suitable registration with a faster runtime. But it's not obvious to me how I should fiddle with the knobs to get started. For example, would increasing or decreasing `entradius` be expected to make things go faster? Also, I am acquiring the images in the same session, back to back, so I can assume that the images start off with a pretty good (but not exact) registration. Is there a way to use that assumption to speed things up? Thanks, Michael

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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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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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Freesurfer June 2017