Freesurfer

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30086 discussions

Hippocampal and amygdala subregions using earlier freesurfer version segmentations
by Keith Harenski 16 Sep '20

16 Sep '20

External Email - Use Caution Hello, I just wanted to verify that using segmentations from earlier freesurfer versions (5.3) are valid as input into the subsequent further segmentation into the hippocampal and amygdala subregions. I understand the input volumes will vary based on version. Thank you, Keith -- Keith Harenski Mobile MRI Manager / Data Analyst II Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office (Cell): 505.504.1338 | Fax: 505.272.8002 kharenski(a)mrn.org | www.mrn.org | www.lrri.org

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Freeview 7.1.1 won't start on Mac: segmentation fault
by Alex White 16 Sep '20

16 Sep '20

External Email - Use Caution Hello again dear Freesurfer experts I recently updated to v7.1.1, in order to get the latest version of Freeview. I’m using Mac OS 10.15.6. Freeview seems to start once each time I boot up my machine, but if I quite it, I can’t re-start it again (until re-booting the machine). In the terminal I get an error like this: /Applications/freesurfer/7.1.1/bin/freeview: line 2: 6667 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“ The number after “line 2” isn’t always the same. If I try to start Freeview by clicking on its icon, I get a window that says, “freeview quit unexpectedly.” I can send you the full crash report if you like. Any advice? Thanks again, Alex White

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Re: [Freesurfer] Freeview 7.1.1 won't start on Mac: segmentation fault
by fsbuild 16 Sep '20

16 Sep '20

External Email - Use Caution Hello Alex, If you want to use the Finder to directly launch the freeview *application*, then I would double click on an application bundle (named *.app or in this case Freeview.app)  which is directly under /Applications/freesurfer/7.1.1.  You can drag the application icon into your dock to run Freeview from there. The shell script under /Applications/freesurfer/7.1.1/bin is usually run from the command line by typing “freeview” in a terminal window after you have setup your shell environment (set FREESURFER_HOME and source the freesurfer setup script which sets/modifies PATH, etc.).  With everything set in the terminal window shell environment, then running the freeview script from the command line will launch the Freeview.app - see below.. - R. Open a terminal window and at the prompt type “bash”, then do, Mac:~> export FREESURFER_HOME=/Applications/freesurfer/7.1.1 Mac:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.1.1-20200726-8b40551 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.1FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjectsMNI_DIR           /Applications/freesurfer/7.1.1/mni Mac:~> which freeview/Applications/freesurfer/7.1.1/bin/freeview ....then the freeview application should launch when you type ... Mac:~> freeview … and you can run all the other commands under $FREESURFER_HOME/bin ...On Sep 16, 2020, at 03:17, Alex White <alexander.l.white@gmail..com> wrote:        External Email - Use Caution        Hello again dear Freesurfer experts I recently updated to v7.1.1, in order to get the latest version of Freeview. I’m using Mac OS 10.15..6. Freeview seems to start once each time I boot up my machine, but if I quite it, I can’t re-start it again (until re-booting the machine). In the terminal I get an error like this:  /Applications/freesurfer/7.1.1/bin/freeview: line 2:  6667 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“The number after “line 2” isn’t always the same. If I try to start Freeview by clicking on its icon, I get a window that says, “freeview quit unexpectedly.” I can send you the full crash report if you like. Any advice? Thanks again, Alex White _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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

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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

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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

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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.

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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.

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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/

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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.

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