Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation
by Yendiki, Anastasia 26 Nov '18

26 Nov '18

In that case, it seems that the low values are introduced when transforming the skeleton from template space to individual space. If this is so, it has nothing to do with using the freesurfer segmentation per se. I would ask on the FSL list. On Nov 26, 2018 3:41 PM, "Winkelbeiner, Stephanie A" <Swinkelbei(a)northwell.edu> wrote: External Email - Use Caution So, I initially did that with the all_FA_skeletonised and got values around 0.6 for the Cc as expected. Interestingly enough though, when I do the same with the individual FA_skeletons that I obtained with the tbss_deproject command the values are around 0.1… Could you think of a reason why that is? From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Monday, November 26, 2018 1:58 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation External Email. Use Caution. You don't want to be averaging zero voxels, so masking makes sense. When you click on the voxels inside one of those segmentation regions (e.g. one of the CC regions) in freeview, are the FA values that you see high? On Nov 25, 2018 8:42 AM, "Winkelbeiner, Stephanie A" <Swinkelbei(a)northwell.edu<mailto:Swinkelbei@northwell.edu>> wrote: External Email - Use Caution Hi Anastasia, I have checked and they do align. However the freesurfer parcels naturally cover more of the brain than the FA skeletons. I was wondering if this was the problem? Therefore I added a binary mask of the FA skeletons. I also tried subtracting the parcels from the FA skeletons with fslmaths to make sure that only the area of the skeleton is read out. But that doesn't give convincing results either. Anyone having other suggestions? Thanks, Steph Sent from my Samsung Galaxy smartphone. -------- Original message -------- From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>> Date: 23/11/18 17:50 (GMT-05:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [EXTERNAL] Re: [Freesurfer] extracting FA from FA_skeletonised with freesurfer parcellation Have you checked if the registered segmentation and the FA map align correctly in freeview? On Nov 23, 2018 1:27 PM, "Winkelbeiner, Stephanie A" <Swinkelbei(a)northwell.edu<mailto:Swinkelbei@northwell.edu>> wrote: Hi, I try to extract FA values from the FSL FA skeleton using the freesurfer aparc.a2009s+aseg+2mm parcellations. I did the following: 1. Recon-all to obtain à aparc.a2009s+aseg+2mm 2. TBSS in FSL to obtain à all_FA_skeletonised 3. Tbss_deproject to split up all_FA_skeletonised into individual skeletons (native space) (*_FA_FA_all_FA_skeletonised.nii.gz) 4. Non-linear transformation of aparc.a2009s+aseg+2mm to subjects’ native space (parc2dwi.nii.gz) 5. Creating binary mask for each subjects FA skeleton to exclude 0 voxels (*_FA_skeleton_mask.nii.gz) 6. Extracting FA values using mri_segstats with the following command: cd subj1/ mri_segstats \ --seg mri/parc2dwi.nii.gz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i skeletons/SPN01_CMH_0001_01_FA_FA_all_FA_skeletonised.nii.gz \ --mask skeletons/SPN01_CMH_0001_01_FA_skeleton_mask.nii.gz \ --excludeid 0 \ --sum skeletons_FA.stats The FA values I obtain are around 0.1 which is highly unlikely, especially for regions such as the corpus callosum. Is there some obvious error in my approach? Or can someone recommend a different approach? I would be very grateful for some help! Thanks, Steph Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> Northwell Health Visit us at Northwell.edu<http://northwell.edu/> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

2 1

Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation
by Winkelbeiner, Stephanie A 26 Nov '18

26 Nov '18

External Email - Use Caution Hi Anastasia, I have checked and they do align. However the freesurfer parcels naturally cover more of the brain than the FA skeletons. I was wondering if this was the problem? Therefore I added a binary mask of the FA skeletons. I also tried subtracting the parcels from the FA skeletons with fslmaths to make sure that only the area of the skeleton is read out. But that doesn't give convincing results either. Anyone having other suggestions? Thanks, Steph Sent from my Samsung Galaxy smartphone. -------- Original message -------- From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu> Date: 23/11/18 17:50 (GMT-05:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] extracting FA from FA_skeletonised with freesurfer parcellation Have you checked if the registered segmentation and the FA map align correctly in freeview? On Nov 23, 2018 1:27 PM, "Winkelbeiner, Stephanie A" <Swinkelbei(a)northwell.edu> wrote: Hi, I try to extract FA values from the FSL FA skeleton using the freesurfer aparc.a2009s+aseg+2mm parcellations. I did the following: 1. Recon-all to obtain --> aparc.a2009s+aseg+2mm 2. TBSS in FSL to obtain --> all_FA_skeletonised 3. Tbss_deproject to split up all_FA_skeletonised into individual skeletons (native space) (*_FA_FA_all_FA_skeletonised.nii.gz) 4. Non-linear transformation of aparc.a2009s+aseg+2mm to subjects’ native space (parc2dwi.nii.gz) 5. Creating binary mask for each subjects FA skeleton to exclude 0 voxels (*_FA_skeleton_mask.nii.gz) 6. Extracting FA values using mri_segstats with the following command: cd subj1/ mri_segstats \ --seg mri/parc2dwi.nii.gz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i skeletons/SPN01_CMH_0001_01_FA_FA_all_FA_skeletonised.nii.gz \ --mask skeletons/SPN01_CMH_0001_01_FA_skeleton_mask.nii.gz \ --excludeid 0 \ --sum skeletons_FA.stats The FA values I obtain are around 0.1 which is highly unlikely, especially for regions such as the corpus callosum. Is there some obvious error in my approach? Or can someone recommend a different approach? I would be very grateful for some help! Thanks, Steph Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> Northwell Health Visit us at Northwell.edu<http://northwell.edu/> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

3 3

Bar/scatter plots for Interaction effects
by Azeez, Azeezat 26 Nov '18

26 Nov '18

External Email - Use Caution Hello, I used FSGD option to run statistical test on 3 fixed factors each with 2 contrast levels. (DEVELOPMENT : old vs young, SEX: male vs female, DIAGNOSE: Control Vs disease ) I report significant interaction effects of DEVxSEXxDIA at a spefic cluster. How can I plot groups to observe trends (ie: young male control). Which output file can I potentially export into Excel/SPSS to make this figure? Thank You, -- Azeezat Azeez

2 4

aseg.stats calculations
by Song, Da-Yea 26 Nov '18

26 Nov '18

External Email - Use Caution Hello, I had a question regarding the aseg.stats and was hoping to get some help. 1. How is the TotalGray calculated? On the wiki page it mentioned that it is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried calculating this based on the formula but got different results. a. TotalGray (from the aseg.stats) = 751765.612392 b. 298534.487540 (lhCortex) + 287682.124852 (rhCortex) + 58860.000000 (SubCortGray) + 49.3682 (L_cerebellum-cortex) + 50.1232 (R_cerebellum-cortex) = 645176.103792 2. We have subjects that were processed in v4.0.4 and v6.0.0. Since the TotalGray measure did not exist in the v.4.0.4, what could we use to calculate the volume? Thank you so much in advance for your help! Best, Da-Yea ---------------------------------------------------------------------- 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.

2 3

myelin analysis with cortical thickness pvr
by Damien MARIE 26 Nov '18

26 Nov '18

External Email - Use Caution Hi, I would like to replicate an analysis I did with qdec but regressing out thickness at the vertex level. It’s a myelin group difference with age and left average myelin as nuisance factors. I used the mri_glmfit command line generated during that qdec analysis and added the pvr flag but I got that error message: ERROR: dimension mismatch between X and contrast /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat X has 7 cols, C has 6 cols I understood I had to change the contrast.mat and added a 0 at the end for the pvr: +1.00000 -1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 Can you please tell me if it is correct??? I would like to be sure. I see more or less the same results than before except that some clusters are a bit degraded let say, as if I was working with a lower level of smoothing. Damien

2 1

FSGD-File
by Larissa Bechtle 26 Nov '18

26 Nov '18

2 1

freeview showing results in a strange manner
by 姜时泽 26 Nov '18

26 Nov '18

External Email - Use Caution | | Dear freesurfer experts, I am using freesurfer to analyze my PET data according to the tutorial online. It works pretty well and I write the values of the results of each region to the template with Matlab (file attached here entitled "lh.subj1.mgz"). However, when I try to open it with freeview, the image looks quite strange ('Picture_1') but it works with tksurfer (Picture_2). Does any one know what is wrong with this? Did I plot the result in a wrong way? Thanks very much Shize -- Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13(a)fudan.edu.cn | | | |

2 1

Paired Analysis Contrasts
by srishti goel 26 Nov '18

26 Nov '18

External Email - Use Caution Hello, I am trying to perform a paired analysis for a data set that has subjects' who belong to either group1 or group2 and have data at time point1 (tp1) and time point2 (tp2). I am following all the steps on the wiki but I want to clarify if the contrasts I plan to use for my analyses are appropriate. For my analyses, I only have two groups and no covariates. I am interested to know if the decrease in cortical thickness of subjects in group 1 across tp1 and tp2 is more than the decrease in cortical thickness of subjects in group 2 across tp1 and tp2. The contrast I think should be used for this is: 1 -1. Is that correct? I am also interested to know if the cortical thickness decreased for subjects regardless of the groups so should I use the contrast: 1 for that? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig(a)email.unc.edu skype: srishti.goel12

2 4

recon-all after n4 correction
by Kathryn Fitzgerald 26 Nov '18

26 Nov '18

External Email - Use Caution Dear FS experts, I was wondering if it is possible to run recon-all (e.g. autorecon2, autorecon3) on skull-stripped images which have gone through N4 correction. Would it be okay to run? recon-all -i sub1.nii.gz -subjid s1 -autorecon1 -sd . -noskullstrip I saw the work around for already skull-stripped images, but I wasn't sure if this would be appropriate for images which have also been corrected by N4. Or is there another way I should approach this? Thank you for the help in advance! Kind regards, Katie

2 2

Re: [Freesurfer] error while loading shared libraries, FSLVm7_64
by fsbuild 26 Nov '18

26 Nov '18

External Email - Use Caution Hello Karin, If you take a look at this page, https://surfer.nmr.mgh..harvard.edu/fswiki/CMake  you should see there is a link to a file makefile.wiki which you can download.   Besides trying to run the cmake command for you to help with building Freesurfer, there are some notes in the makefile about what packages to install with “sudo yum install <package>” for CentOS/Redhat linux.  So you could try installing those packages, and then also try using that makefile to run cmake and build freesurfer..- R. On Nov 25, 2018, at 17:00, Karin Markenroth Bloch <karin.markenroth_bloch(a)med.lu.se> wrote:        External Email - Use Caution        Dear all,I’m afraid this is a very basic Linux question, but I am not that familiar with it.  I downloaded and installed FSLVm7_64 on a Windows7 host. Installation went well, and if I type fsl in the terminal window, a GUI (a menu list) pops up.My first attempt was to click “BET”, select an input image and Run standard brain extraction using bet. Then I get the messages (see below):“ error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory” The libopenblas.so is in my /home/flsuser/Data directory. I tried installing it sudo yum install libopenblas.so, but get the reply “No package libopenblas.so available.” (see below) I have set the $FSLDIR variable : [fsluser@localhost Data]$ echo $FSLDIR /usr/local/fsl What can I do?   Very grateful for help!  YoursKarin ------------[fsluser@localhost ~]$ fsl/usr/local/fsl/bin/bet /home/fsluser/Data/s20181112-0601-00006-000001-01 /home/fsluser/Data/s20181112-0601-00006-000001-01_brain  -f 0.5 -g 0/usr/local/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directoryFinished /home/fsluser[fsluser@localhost ~]$ cd Data/ [fsluser@localhost Data]$ lslibopenblas.so  s20181112-0601-00006-000001-01.nii [fsluser@localhost Data]$ sudo yum install libopenblas.so[sudo] password for fsluser: Loaded plugins: fastestmirror, langpacksLoading mirror speeds from cached hostfile* base: mirror.hh.se* extras: mirror.hh.se* updates: mirror.hh.seNo package libopenblas.so available.Error: Nothing to do [fsluser@localhost Data]$ flirt /vflirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

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