Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Re: [Freesurfer] ERROR gtmseg
by Marina Fernández 11 Oct '19

11 Oct '19

External Email - Use Caution Dear Douglas, Thank you very much for the help. We could solve the problem with that subject but now we have a similar problem with another subject. In the previous case, we have only one problematic voxel in the skull, but now the label 75 (it shouldn't exist either) is taking a lot of voxels in the ventricles and the caudate. So, I think that we should use other solution to fix it. I know that this issue is weird. We use gtmseg command with more or less 500 subjects and we only have this type of problem with two subjects. Best regards, Marina. > Probably the easiest thing is just to edit that voxel to be one of the neighboring > segments. First, load the aseg and find that voxel. See which segment(s) are around > that voxel and get the segmentation id. Then run > mri_binarize --replaceonly 229 YourNewSegID --i aparc+aseg.mgz --o > aparc+aseg.mgz > then re-run gtmseg

2 1

Freesurfer using dof9 with preproc-sess
by Droppa, Kyle Salmon 11 Oct '19

11 Oct '19

Good evening, I am using freesurfer version 6 and I am having an issue with changing the degrees of freedom when I run preproc-sess. I ade some registrations that are 9 and 12 dof instead of the default 6, however when I try to run preproc-sess, it pulls the dof6 files instead. Is there a flag I can use that pulls the register.dof9.lta and register.dof12.lta files instead? Thank you and have a nice night! ___________________ Kyle Salmon Droppa, B.A. Clinical Research Coordinator Athinoula A. Martinos Center for Biomedical Imaging Magnetic Resonance - Physics & Instrumentation Group https://www.martinos.org/lab/mr-pig <https://www.massgeneral.org/nicc>

2 2

using dof9 or dof12 in preproc-sess
by Droppa, Kyle Salmon 11 Oct '19

11 Oct '19

Hello, I posted this earlier and wasn't able to get a response. I am using freesurfer version 6 and I am having an issue with changing the degrees of freedom when I run preproc-sess. I made some registrations that are 9 and 12 dof instead of the default 6 using bbregister, however when I try to run preproc-sess, it pulls the dof6 files instead. Is there a flag I can use that makes preproc use the register.dof9.lta and register.dof12.lta files instead? Thank you and have a nice day!

2 1

local Gyrification Index
by LOSKE, PHILIPP (PGR) 11 Oct '19

11 Oct '19

External Email - Use Caution Hello FreeSurfer Team, I am trying to compute the local Gyrification index on my subjects with recon-all -s <subj> -localGI. Running this under FS 6.0 runs without errors, with FS 5.3. I get: mesh_outer = struct with fields: vertices: [68598x3 double] faces: [137192x3 double] facesOfVertex: [68598x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (82.56 sec). ... creating path file for vertex 1 / 68598 area file for outer ROIs saved at 1 {Unable to perform assignment because the left and right sides have a different number of elements. Error in dsearchn (line 84) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); } >> ERROR: make_roi_paths did not complete successfully! Now I wonder why the computation works in version 6 but not in 5.3. My subjects are originally reconstructed with version 5.3., does the computation for local Gyrification Index differ between both versions or can I just run the command in FS6? Cheers Philipp The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

2 1

fsaverage label into functional space
by Lauri Tuominen 10 Oct '19

10 Oct '19

External Email - Use Caution Dear FreeSurfers! I would like to confirm something before I proceed with my analyses. I think I am just confused again. I am doing resting state analysis using fsfast. I am trying to use a label defined in the fsaverage space as a seed using the fcseed-config & fcseed-sess commands. Now these commands say that the label should be in fuctional space, which I gather is the space of the f.nii. So in order to move the label into functional space I say: mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01 --hemi lh --temp ${projectdir}/${sessionj}/rest/001/f.nii --fill-ribbon --reg ${projectdir}/${session}/rest/register.dof6.lta To my surprise, the voxel size here corresponds to the anatomical (orig.mgz) but not the functional space (f.nii). To test this further I did: mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01 --hemi lh --temp $SUBJECTS_DIR/$/${sessionj}/mri/orig.mgz --fill-ribbon --reg ${projectdir}/${session}/rest/register.dof6.lta And I get exactly the same ROI in the volume. So just to confirm, is this what I want for the fcseed -commands? Thank you so much again! Lauri Tuominen

3 2

Brodmann area parcellation
by sang ho shin 10 Oct '19

10 Oct '19

External Email - Use Caution Dear Freesurfer Developers, I am trying to get the seed mask of premotor and motor cortex. Because I can't get it through 'recon-all -all', I tried to find brodmann area ('recon-all -s subjid -ba-labels') But I received ERROR message. Can you tell me how to get Brodmann area through recon-all or freesurfer parcellation? And I appreciate if you can help me to solve this error message as follows, ================================================================= sinsanghoui-MBP:~ shinsangho$ export SUBJECTS_DIR=~/freesurfer_subjects sinsanghoui-MBP:~ shinsangho$ echo $SUBJECTS_DIR *sinsanghoui-MBP:~ shinsangho$ recon-all -s NOR82_PJI -i ~/DTI_analysis/nor82_pji_t1/coT1.nii -ba-labels* Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Users/shinsangho/freesurfer_subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64 /Users/shinsangho/freesurfer_subjects/NOR82_PJI \n mri_convert /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz \n mri_convert.bin /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii... TR=1670.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.000121244, -1, 0) j_ras = (-0.0235518, -2.85817e-06, 0.999723) k_ras = (0.999723, 0.000121211, 0.0235518) writing to /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz... /Users/shinsangho/freesurfer_subjects/NOR82_PJI/label #-------------------------------------------- #@# BA_exvivo Labels lh Fri Oct 4 17:43:23 BST 2019 \n mri_label2label --srcsubject fsaverage --srclabel /Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject NOR82_PJI --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n srclabel = /Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = NOR82_PJI trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/shinsangho/freesurfer_subjects FREESURFER_HOME /Applications/freesurfer Loading source label. Found 4129 points in source label. MRISread(/Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white): could not open file Starting surface-based mapping Reading source registration /Users/shinsangho/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface * /Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white* *No such file or directory* *ERROR: could not read /Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white* Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64 recon-all -s NOR82_PJI exited with ERRORS at Fri Oct 4 17:43:25 BST 2019 For more details, see the log file /Users/shinsangho/freesurfer_subjects/NOR82_PJI/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ================================================== Best wishes, Sangho ᐧ

3 6

Assign different number in FreeSurferColorLUT
by Gwang-Won Kim 10 Oct '19

10 Oct '19

2 1

Freesurfer 6 current state of submillimeter processing
by Daniel Westfall 10 Oct '19

10 Oct '19

External Email - Use Caution Hi Everyone, I just wanted to double check the current state of processing T3 submillimeter data with Freesurfer 6. We have two studies: one with 0.9 mm isotropic and the other with 0.8 mm isotropic. After doing some investigating, I found that there is either the option to run recon-all with the -hires flag ( https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon) or I found that on the release notes for Freesurfer 6 there is a patch ( https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/) I would guess that the patch method is the most recent version that I should use? Thank you for the assistance. Best, Daniel

2 1

Re: [Freesurfer] Issues with segmentHA_T1.sh command
by Iglesias Gonzalez, Juan E. 10 Oct '19

10 Oct '19

Dear Ola, This looks like a very ugly error but someone experienced something similar in the past and it turned out to be a permissions problem. https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… Can you please double check this is not your case? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Olamide Abiose <oabiose(a)stanford.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, 10 October 2019 at 14:29 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Issues with segmentHA_T1.sh command External Email - Use Caution Hello, I'm having great difficulty running the segmentHA_T1.sh command. I'm using the latest development version of Freesurfer and have downloaded Matlab R2014b. I get the following message when I try to run the command. Any advice/suggestions you can offer would be greatly appreciated! Thank you very much. #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Oct 9 17:49:49 PDT 2019 /usr/bin/time -o /dev/stdout @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01 run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 0.333333333333333333333333333333333333 /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 /opt/freesurfer-dev/bin/ 0 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client:: Error using checkRequiredMCRProducts (line 25) Java exception occurred: java.lang.NullPointerException at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56) at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108) at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67) Error in deployrc (line 9) Error in matlabrc (line 238) Command exited with non-zero status 255 @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01 @#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90 Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Wed Oct 9 17:50:15 PDT 2019

4 4

Re: [Freesurfer] Contents of Freesurfer digest...
by David Kamson 10 Oct '19

10 Oct '19

External Email - Use Caution Martin, thank you for these comments. These are extremely valuable! Although my patients had tumors, these are cured (this is why I have so few of them…) and have no residual mass effect/deformity beyond biopsy tracks / small resection cavities. Thus far, I was able to get pretty accurate looking segmentations of deep nuclei on aseg. Segmentation issues were associated with the surface structures (e.g. dura/falx being misclassified as gray or brain tissue adjacent to resection cavities are correctly classified as brain but GM/WM often misclassified). I’m OK restricting the analysis to ventricular and deep GM volume, since what I’m trying to measure is marked atrophy of these structure after chemotherapy which I guess is in the range of 1-5%/year. The changes are mostly marked enough to enable a visual qualitative analysis, however, quantitative data would be clinically more helpful to clarify when, and how much change to expect after treatment. Do you think increasing the number of time points analyzed (I have 4-6 scans per year for each patient) could eliminate the noise from head positioning/slicing as long as the volumetric trends remain consistent? Again, the data would be normalized per individual and I would not use absolute volume for any comparative analysis. Thank you again. This message board is of incredible value! Best regards, David ---------------------------------------------------------------------- Message: 1 Date: Wed, 09 Oct 2019 10:48:48 +0200 From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Questions re slice thickness, aseg and longitudinal analysis To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <7a4d059cb5cb42f390e03f523677a3362d17cb81.camel(a)nmr.mgh.harvard.edu<mailto:7a4d059cb5cb42f390e03f523677a3362d17cb81.camel@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="UTF-8" Hi David, I am not very optimistic: 5mm is too thick for FreeSurfer (recommendation is 1 up to 1.5). You will certainly get something, but it can be very unreliable and completely wrong. Especially longitudinally these thick slices will induce large variance due to different head positioning (and different slice angulations) in the scanner. Furthermore, FreeSurfer does not take Gad-Enhanced images. Also it will not work if tumor lesions are present. About your questions: 1. Surfaces update the aseg, but if you are only interested in the volumes, you can skip this expensive step (potentially at the cost of slightly higher noise levels in your measurements). 2. I think not (see above). 5mm is too low. 3. Theoretically yes, but I have never tested if the scripts will do it. You could run up to the aseg in the cross, then create base (up to aseg) and then run the longs up to aseg. Not even sure you really need the base aseg. You might be able to just run the initial base registration step, obtain the transformations and median norm.mgz image, could be sufficient for the long runs. 4. No. Gad images won't work. Best, Martin External Email - Use Caution Freesurfers, First of all, I'd like to express my gratitude to the community for the support that keeps researchers like myself afloat! I have a unique set of oncology patients that I want to evaluate for brain atrophy in a retrospective longitudinal analysis. I was thinking about using Aseg.auto results to assess longitudinal volume changes, but before I invest all the time I wanted to check with the community whether this makes any sense at all: The dataset that looks like this: - 22 patients (no control dataset [yet]) - 10-25 MRIs per patient acquired over 2-8 years in relatively uniform intervals - Patients had most of their scans on the same scanner, but scanners differed widely between patients - All patients have axial T1 post gadolinium scans of 1x1x5mm resolution (3D acquisition available in <10%) - About 80% of scans have an axial pre-contrast T1 sequence - All scans are skullstripped (third party algorithm) I'm looking for crude changes, no subtleties; volumes of interest are: - Whole brain volume - White matter volume - Ventricular volume (mainly lateral ventricle) - Subcortical gray matter volume (whole thalamus most importantly) I ran a few test analyses and to my surprise I was able to generate pretty acceptable surfaces, however, topology fixing took about 24H per scan, and I feel aseg.auto contained all the volumetric data I was really interested in. My concrete questions are: 1) Does the full autorecon pipeline affect Aseg.auto? If there is no benefit, I could reduce the per scan analysis time from 28 hours to 1-2 h. 2) Would this low-resolution dataset be accepted by reviewers if used for Aseg? Should I do any quantitative validation beyond a visual quality analysis of Aseg? 3) Can I perform a longitudinal analysis only for the Aseg results? 4) Is it OK to use T1-gad images for the analysis? I'd appreciate any input! Best regards, David O. Kamson, MD PhD Neuro-oncology fellow Johns Hopkins Hospital & National Institutes of Health _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer