Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

Start a nNew thread

Removal from the mailing list
by Rollo, Patrick 15 Sep '20

15 Sep '20

External Email - Use Caution Can I be removed from the mailing list? Thanks

1 0

big ventricles in 7.1.0
by Hugh Wang 15 Sep '20

15 Sep '20

External Email - Use Caution Hi, I'm using Freesurfer 6.0 and 7.1.0 to process the same scan with big ventricles using -bigventricles option in recon-all. However 7.1.0 gave a worse result than 6.0. In the pic attached, the left image is the segmentation using 6.0, which basically got the ventricles correct except some voxels are classified as wm-hypointensity, and the right image is using 7.1.0, which classifies the left ventricle as white matter. Any suggestion is appreciated! Thanks, Hugh

1 0

Standard best practices for creating binary GM, WM and CSF masks from freesurfer recon-all output
by Stephan Heunis 15 Sep '20

15 Sep '20

External Email - Use Caution Hi there I am new to Freesurfer and I would like some help with best practices for exporting binary GM, WM and CSF masks. I have run recon-all (FS v7.1) on some T1w images. I would now like to create binary GM, WM and CSF masks from the recon-all results. I have an existing adapted script that uses AFNI’s *3dcalc* to match certain label values in *aparc+aseg.mgz* and output binary masks (I have since realized I can also use *mri_binarize* for that), see below for the exact label values that are matched and added together per tissue segmentation. However, I have also seen the output files such as *brainmask.mgz*, *ribbon.mgz*, *wm.mgz*; so I am uncertain about what the standard practices are for creating binary masks for GM, WM and CSF from freesurfer’s output. I’ve searched a bit on the mailing list and found two similar questions: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg46545.html and https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11365.html. However, these suggest different approaches (e.g. inverting WM and VCSF to get GM, vs matching several structures and adding them together), and I am unsure whether these will end up covering the same voxels. *So, my main question is:* is there a standard best practice for generating binary masks for GM, WM and CSF, i.e. which labels should be included or excluded? Or which standard outputs of freesurfer should be used? Additionally I would also like to get a binary mask of the amygdala and the Brodmann areas 4a, 4p and 6. The amygdala seems to work fine. For the motor areas, I have tried my standard route of matching the label values (404, 405, 406 respectively) in aparc+aseg.mgz, but this doesn’t seem to yield any matches, i.e. all voxels in the resulting mask image have value zero. *My second question:* can you perhaps think of a reason for this error? *And question 2, part 2:* I assume BA 4a, 4p and 6 are all bilateral, since I didn’t see them being specified as LH or RH, is there a quick way to get only the LH? Best regards, Stephan Heunis -------------------- GM, WM and CSF labels used in current script: # Grey matter: # Subcortical nuclei: # - 10: Left-Thalamus-Proper # - 11: Left-Caudate # - 12: Left-Putamen # - 49: Right-Thalamus-Proper # - 50: Right-Caudate # - 51: Right-Putamen # Cerebellum: # - 8: Left-Cerebellum-Cortex # - 47: Right-Cerebellum-Cortex # Hippocampus and amygdala # - 17: Left-Hippocampus # - 18: Left-Amygdala # - 53: Right-Hippocampus # - 54: Right-Amygdala # Cortical ribbon: # - within(a,1000,3000): ctx-lh-[all], ctx-rh-[all] # White Matter: # - 2: Left-Cerebral-White-Matter # - 7: Left-Cerebellum-White-Matter # - 41: Right-Cerebral-White-Matter # - 46: Right-Cerebellum-White-Matter # - 251: CC_Posterior # - 252: CC_Mid_Posterior # - 253: CC_Central # - 254: CC_Mid_Anterior # - 255: CC_Anterior # CSF: # - 4: Left-Lateral-Ventricle # - 14: 3rd-Ventricle # - 43: Right-Lateral-Ventricle

2 2

a question on Talairach transformation
by Yi Li 15 Sep '20

15 Sep '20

External Email - Use Caution Hi, I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software. I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template? In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)? Thank you so much for your help in advance. Best regards Yi Li --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

3 8

Re: [Freesurfer] left-right flip?
by Douglas N. Greve 15 Sep '20

15 Sep '20

That is a fiducial. And do you know what side the fiducial was placed on? mri_info does not help. How did you convert from dicom? ps. Please make sure to post to the list and not to us personally On 9/15/2020 11:36 AM, Ellen Ji wrote: > External Email - Use Caution > Hi Doug - see the screenshot attached. I believe this is the fiducial? > > > On 9/15/2020 5:33 PM, Ellen Ji wrote: >> Oh no, then I guess we have to assume a fiducial wasn't used. Is >> there any other way to determine which is left and right? Does the >> LAS/ASR/PSR from mri_info tell us that at all? >> >> Thanks, >> >> Ellen >> >> >> On 9/15/2020 5:23 PM, Douglas N. Greve wrote: >>> How do you know which side of the subject is left and right? I don't >>> see a fiducial. >>> You do not need to convert the orientation to RAS. >>> >>> On 9/15/2020 10:29 AM, Ellen Ji wrote: >>>> External Email - Use Caution >>>> I loaded each T1 into freeview and verified that what freeview >>>> thinks is left and right, and anterior and posterior, is also what >>>> I see. Attached is a screenshot. >>>> >>>> However, when I ran "mri_info --orientation, the orientations of >>>> the subjects are either LAS or ASR and PSR (i.e. not consistent and >>>> not RAS). Is this going to affect the output of recon-all? Do I >>>> need to convert all the orientations to RAS before running recon-all? >>>> >>>> Thanks, >>>> >>>> Ellen >>>> >>>> >>>> On 9/15/2020 4:17 PM, Douglas N. Greve wrote: >>>>> How are you checking the LR orientation? >>>>> >>>>> On 9/15/2020 4:10 AM, Ellen Ji wrote: >>>>>> External Email - Use Caution >>>>>> >>>>>> Dear experts, >>>>>> >>>>>> I recently performed recon-all on a set of subjects and the >>>>>> output (aparcstats2table and asegstats2table) will be part of a >>>>>> meta-analysis of other labs' cohorts. When assessing the >>>>>> asymmetry index direction (relative size of left vs right >>>>>> hemisphere across multiple rois), our dataset shows an inversion >>>>>> of the mean asymmetry index in several structures compared to the >>>>>> other cohorts. >>>>>> >>>>>> For example, in our dataset, the lateral ventricle volume is on >>>>>> average larger in the right hemisphere >>>>>> compared to the left, while the opposite is true for all other >>>>>> cohorts. The same inversion of asymmetry is visible in other >>>>>> structures that in general are more asymmetrical. >>>>>> >>>>>> In order to check this, I went through each T1 to make sure the >>>>>> orientation was correct and indeed they are. >>>>>> >>>>>> Is there any possible way that there was a left-right inversion >>>>>> somewhere during the recon-all pipeline? I want to make sure I >>>>>> did everything correctly on our end and that the results are due >>>>>> to the biology and not a technical mistake! >>>>>> >>>>>> I found this website on Left-right reversal, and it seems >>>>>> relevant to my issue, but I'm not fully understanding what this >>>>>> means (how would bias occur during segmentation?) - >>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal >>>>>> >>>>>> Many thanks for your input, >>>>>> Ellen >>>>>> >>>>>> --- >>>>>> >>>>>> Ellen Ji, PhD >>>>>> Postdoctoral Research Fellow >>>>>> Psychiatric University Hospital >>>>>> University of Zürich >>>>>> ellen.ji(a)bli.uzh.ch >>>>>> homanlab.github.io/ellen/ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> _______________________________________________ >>>>> 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 Mass General Brigham Compliance HelpLine at >>> http://www.massgeneralbrigham.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.

1 0

left-right flip?
by Ellen Ji 15 Sep '20

15 Sep '20

External Email - Use Caution Dear experts, I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts. For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical. In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are. Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake! I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal Many thanks for your input, Ellen --- Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji(a)bli.uzh.ch homanlab.github.io/ellen/

3 2

Re: [Freesurfer] left-right flip?
by Douglas N. Greve 15 Sep '20

15 Sep '20

If you don't have a fiducial, then there is no way to know for sure; mri_info just gets the same info that freeview gets, which comes from the header. How did you convert the file from dicom? On 9/15/2020 11:33 AM, Ellen Ji wrote: > External Email - Use Caution > Oh no, then I guess we have to assume a fiducial wasn't used. Is there > any other way to determine which is left and right? Does the > LAS/ASR/PSR from mri_info tell us that at all? > > Thanks, > > Ellen > > > On 9/15/2020 5:23 PM, Douglas N. Greve wrote: >> How do you know which side of the subject is left and right? I don't >> see a fiducial. >> You do not need to convert the orientation to RAS. >> >> On 9/15/2020 10:29 AM, Ellen Ji wrote: >>> External Email - Use Caution >>> I loaded each T1 into freeview and verified that what freeview >>> thinks is left and right, and anterior and posterior, is also what I >>> see. Attached is a screenshot. >>> >>> However, when I ran "mri_info --orientation, the orientations of the >>> subjects are either LAS or ASR and PSR (i.e. not consistent and not >>> RAS). Is this going to affect the output of recon-all? Do I need to >>> convert all the orientations to RAS before running recon-all? >>> >>> Thanks, >>> >>> Ellen >>> >>> >>> On 9/15/2020 4:17 PM, Douglas N. Greve wrote: >>>> How are you checking the LR orientation? >>>> >>>> On 9/15/2020 4:10 AM, Ellen Ji wrote: >>>>> External Email - Use Caution >>>>> >>>>> Dear experts, >>>>> >>>>> I recently performed recon-all on a set of subjects and the output >>>>> (aparcstats2table and asegstats2table) will be part of a >>>>> meta-analysis of other labs' cohorts. When assessing the asymmetry >>>>> index direction (relative size of left vs right hemisphere across >>>>> multiple rois), our dataset shows an inversion of the mean >>>>> asymmetry index in several structures compared to the other cohorts. >>>>> >>>>> For example, in our dataset, the lateral ventricle volume is on >>>>> average larger in the right hemisphere >>>>> compared to the left, while the opposite is true for all other >>>>> cohorts. The same inversion of asymmetry is visible in other >>>>> structures that in general are more asymmetrical. >>>>> >>>>> In order to check this, I went through each T1 to make sure the >>>>> orientation was correct and indeed they are. >>>>> >>>>> Is there any possible way that there was a left-right inversion >>>>> somewhere during the recon-all pipeline? I want to make sure I did >>>>> everything correctly on our end and that the results are due to >>>>> the biology and not a technical mistake! >>>>> >>>>> I found this website on Left-right reversal, and it seems relevant >>>>> to my issue, but I'm not fully understanding what this means (how >>>>> would bias occur during segmentation?) - >>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal >>>>> >>>>> Many thanks for your input, >>>>> Ellen >>>>> >>>>> --- >>>>> >>>>> Ellen Ji, PhD >>>>> Postdoctoral Research Fellow >>>>> Psychiatric University Hospital >>>>> University of Zürich >>>>> ellen.ji(a)bli.uzh.ch >>>>> homanlab.github.io/ellen/ >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> 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 >> Mass General Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.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.

1 0

custom lut for surface overlay in freeview
by Sebastien Proulx 15 Sep '20

15 Sep '20

External Email - Use Caution Hello, Is it possible to use my own lookup table for surface overlays in Freeview? I could not find it from the GUI and in terminal using :overlay=someOverlay.mgh:colormap=someCustomLUT.txt did not work (the :colormap argument is not recognized). The goal, using my own lut with an alpha channel to more finely control transparency. If Freeview cannot do that, does tksurfer can? Linux 16.04 Freesurfer version: linux_centos7_x86_64-7.0.0 Thanks a lot for your help! Sebastien

2 1

recon-all -s BIO-ALS-701-043 exited with ERRORS
by Zaninotto, Ana Luiza Costa 15 Sep '20

15 Sep '20

Dear Freesurfer Developers, I am working remotely from my Windows notebook through the NoMachine Linux. I have been trying to recon-all without success. Please see below the scripts. Thank you! epimetheus:alz14[994] recon-all -i /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355976815813134 -subject BIO-ALS-701-043-post -all -brainstem-structures Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /autofs/cluster/atassigp/ALSspeech/FS/Subjects Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Linux epimetheus.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all' -> '/autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post/scripts/recon-all.local-copy' /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post mri_convert /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355976815813134 /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post/mri/orig/001.mgz mri_convert.bin /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355976815813134 /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355976815813134... Getting Series No INFO: Found 216 files in /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004 INFO: Scanning for Series Number 4 Scanning Directory INFO: found 209 files in series INFO: loading series header info. RunNo = 3 WARNING: Run 1 appears to be truncated Files Found: 209, Files Expected (lRep+1): 1 FileName /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2015072216183223733750182 Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName HUP_PBR03_ALS701-043_150722 Date and time StudyDate 20150722 StudyTime 161523.709000 SeriesTime 161832.316000 AcqTime 161824.385000 Acquisition parameters PulseSeq epfid2d1_64 Protocol ge_fun_WholeBrain_64_1 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 30 InversionTime -1 RepetitionTime 2000 PhEncFOV 200 ReadoutFOV 200 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 448 NImageCols 448 NFrames 209 SliceArraylSize 37 IsMosaic 1 ImgPos 828.1392 504.4394 162.4422 VolRes 3.1250 3.1250 3.6000 VolDim 64 64 37 Vc -0.9480 0.0638 0.3118 Vr -0.2544 -0.7403 -0.6223 Vs 0.1911 -0.6693 0.7180 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. WARNING: files are not found to be different and cannot be sorted File1: /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2015072216183223733750182 File2: /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355233033411124 INFO: ( 64 64 37), nframes = 209, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 2000, TR = 2000 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.98571 0.04965 -0.16097 -1.09341; -0.02565 0.98867 0.14788 15.43880; 0.16649 -0.14164 0.97582 -11.39330; 0.00000 0.00000 0.00000 1.00000; FileName /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2015072216183223733750182 Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName HUP_PBR03_ALS701-043_150722 Date and time StudyDate 20150722 StudyTime 161523.709000 SeriesTime 161832.316000 AcqTime 161824.385000 Acquisition parameters PulseSeq epfid2d1_64 Protocol ge_fun_WholeBrain_64_1 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 30 InversionTime -1 RepetitionTime 2000 PhEncFOV 200 ReadoutFOV 200 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 448 NImageCols 448 NFrames 209 SliceArraylSize 37 IsMosaic 1 ImgPos 106.6647 98.5294 -23.8684 VolRes 3.1250 3.1250 3.6000 VolDim 64 64 37 Vc -0.9480 0.0638 0.3118 Vr -0.2544 -0.7403 -0.6223 Vs 0.1911 -0.6693 0.7180 VolCenter -0.8517 -13.6964 -7.1010 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 ERROR: VolSS2MosSS: number of columns in the mosaic (280) is not an integer multiple of the number of columns in the image (64) Linux epimetheus.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BIO-ALS-701-043-post exited with ERRORS at Mon Sep 14 14:43:43 EDT 2020 For more details, see the log file /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Ana Luiza Zaninotto, B.A, MSc, Ph.D. Speech and Feeding Disorders Lab MGH Institute of Health Professions - MGHIHP +1 (617) 724-6347<https://www.google.com/search?q=speech+and+feeding+disorders+lab&rlz=1C1GCE…>, +1(857)294-2080 [cid:4de4da5b-f7a4-4390-807a-af47efc8af46]

2 1

mergecontrasts-sess command not found
by Paula Maldonado 15 Sep '20

15 Sep '20

External Email - Use Caution Hi Freesurfers, I’m trying to use mergecontrasts-sess to merge two contrasts of an analysis, but I get this: mergecontrasts-sess: Command not found. I tried with other Fs-Fast commands and they work. I am running on a Ubuntu 18.04, 64 bit. I downloaded the 6.0.0. Freesurfer version from the official page. Could you help me? Thanks a lot Paula

2 1

← Newer
1
...
6
7
8
9
10
11
12
...
17
Older →

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 September 2020