Freesurfer

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30132 discussions

Cortical thickness information
by Rashmi Singh 18 Jan '12

18 Jan '12

Hey Bruce, Thank you for the informations. May I ask you few additional questions? A) In your answer to my first question you wrote "you can also just look at the map itself without averaging over an ROI". What does this mean in reference to calculation of the cortical thickness. B) For my question B in my previous e mail, may be I was not clear, I am actually asking you about the information present in the ?.aparc .stats file that is not in the table. As I understand the table represents the different ROI and has information of the mean (average) thickness within each ROI of the cortical parcellation ( 35 different regions). But there are some additional information present before the table begins. And it says # Measure Cortex,NumVert,Number of Vertices, 143103, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 94823.1, mm^2 # Measure Cortex, MeanThickness,Mean Thickness, 2.62665, mm My question is about this measurement. What does this Cortical measure mean thickness is representing? C) Can you please explain me a little bit in detain how would I run the mris_anatomical_stats, I mean can you help me with the command line or suggest me a tutorial where I can find the information? D) I don't know what is qdec? Please advise. E) If I want to know the total cortical surface area do I add up the surface area measurements for each ROI given in the table for each hemisphere and then I add the two individual hemisphere measurements for getting the total cortical surface area? Looking forward for your response, Thanks, Rashmi. " On 1/18/12 9:18 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> wrote: On Wed, 18 Jan 2012, Rashmi Singh wrote: Hello, This is Rashmi. I am very new to neurobiology and computing and my very first project involves measuring cortical thickness from the reconstructed surfaces generated by FreeSurfer. I have recently started to self teach myself FreeSurfer, but with a background in immunology and almost no background in neurobiology I know I have a long way to go and need a lot of help. I have learnt to run FreeSurfer and am currently using Version 5.1.0. I am also referring the FreeSurfer Lectures and Tutorial available online for free to learn usage of Tktools. Despite that I don't have access to your tutorial data, I have found this tutorial helpful in learning how to use Tktools to view volumes and surfaces. At present I have few basic (naïve) questions that I need your help with, excuse me if you find my question ignorant. A)My first question is about the cortical parcellation stats files. After running the recon all on my MPRAGE data, I did get the ?.aparc.stats file in the stats folder. I also see ?.aparc.a2009S.stats files. I read and kind of understood the difference between these two files in how differently they calculate the gray matter. My question is which of these two files should be considered for measurement as generated by the automated calculation of the cortical thickness. the thickness is a map over the whole cortex. The aparc and aparc.a2009S are different regions of interest (ROIs) that follow different anatomical conventions. You can use either to obtain the average thickness in the ROIs contained in each, but you can also just look at the map itself without averaging over an ROI. B) Besides the cortical thickness parameters the ?.aparc file has information on the white surface area and the mean thickness. Is the mean thickens represents the average cortical thickness of the respective hemisphere? If not what does it represents and how can I calculate the hemisphere based cortical thickness? the mean thickness is the mean within each ROI. mris_anatomical_stats will compute the mean thickness over the hemi if you want. C) How would I calculate the average cortical thickness of the whole brain? average the two hemi thicknesses. That will be close enough D) In research articles related to measurement of cortical thickness, authors have reported mapping of the thickness measured on the inflated or semi-inflated surface . How is it done and what is the significance of doing it. this is for visualization. Just bring up the inflated surface in tksurfer and load the lh or rh thickness. E)Once I have the measure of all the cortical thickness how do I compare all the Subjects measurements participating in my study? qdec is probably the easiest way to do this. F) Do you in your tutorial have some reference images for labelled subcortical regions that are generated in aseg.mgz files. yes, we use an atlas that we compiled from manually labeled subjects here at MGH. Thanks for your response in advance. Hope to hear from you soon. Regards, Rashm. _________________________________________________________________________ ___ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. 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. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

1 0

Freesurfer flips brains?
by Léoné, F.T.M. (Frank) 18 Jan '12

18 Jan '12

Dear all, I must be missing something really obvious, but it seems my brains are flipped. What I do: - I have a highres structural scan, nii file format - I convert it to a surface using recon-all - Coregister the highres structural to the functional scan, so it is in the voxel size and orientation as the functional scans - I try to bbregister the coregistered and resliced T1 with the surface But then: hey, it doesn't fit, my low-res T1 is flipped compared to my y surface, hence to my original T1. So is it indeed true that my T1 might have been flipped? If so, does it make a wrong assumption on neurological vs radiological convention, or what is going on? Thanks in advance, best, Frank

2 1

Re: [Freesurfer] rendering problem
by Gabriel Gonzalez Escamilla 18 Jan '12

18 Jan '12

3 2

Cortical thickness question
by Rashmi Singh 18 Jan '12

18 Jan '12

Hello, This is Rashmi. I am very new to neurobiology and computing and my very first project involves measuring cortical thickness from the reconstructed surfaces generated by FreeSurfer. I have recently started to self teach myself FreeSurfer, but with a background in immunology and almost no background in neurobiology I know I have a long way to go and need a lot of help. I have learnt to run FreeSurfer and am currently using Version 5.1.0. I am also referring the FreeSurfer Lectures and Tutorial available online for free to learn usage of Tktools. Despite that I don't have access to your tutorial data, I have found this tutorial helpful in learning how to use Tktools to view volumes and surfaces. At present I have few basic (naïve) questions that I need your help with, excuse me if you find my question ignorant. A)My first question is about the cortical parcellation stats files. After running the recon all on my MPRAGE data, I did get the ?.aparc.stats file in the stats folder. I also see ?.aparc.a2009S.stats files. I read and kind of understood the difference between these two files in how differently they calculate the gray matter. My question is which of these two files should be considered for measurement as generated by the automated calculation of the cortical thickness. B) Besides the cortical thickness parameters the ?.aparc file has information on the white surface area and the mean thickness. Is the mean thickens represents the average cortical thickness of the respective hemisphere? If not what does it represents and how can I calculate the hemisphere based cortical thickness? C) How would I calculate the average cortical thickness of the whole brain? D) In research articles related to measurement of cortical thickness, authors have reported mapping of the thickness measured on the inflated or semi-inflated surface . How is it done and what is the significance of doing it. E)Once I have the measure of all the cortical thickness how do I compare all the Subjects measurements participating in my study? F) Do you in your tutorial have some reference images for labelled subcortical regions that are generated in aseg.mgz files. Thanks for your response in advance. Hope to hear from you soon. Regards, Rashm. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

2 1

rendering problem
by Gabriel Gonzalez Escamilla 18 Jan '12

18 Jan '12

2 1

Re: [Freesurfer] selxavg3-sess issue in FSFAST
by Ivan Alvarez 18 Jan '12

18 Jan '12

Hello Doug, Ah! this was the root of the problem. A conflict was generated with the Stanford Vistasoft toolbox, which also contains a 'basename.m' file. Once removed from the Matlab path list, selxavg3-sess behaves normally. Thank you for the help! Kind Regards, Ivan Alvarez PhD Student Imaging and Biophysics Unit UCL Institute of Child Health 30 Guildford Street, London, WC1N 1EH On 17/01/12 17:48, Douglas N Greve wrote: > Hi Ivan, I can't pin down what the problem is. This is very strange. > There are a couple of things that you can try. First, start matlab and > run the command > which basename > This should return /home/ivan/freesurfer/fsfast/toolbox/basename.m > If it returns something else or multiple functions, then this is the > problem. > > doug > > > Ivan Alvarez wrote: >> Hello Doug, >> >> Please find attached the verbgen.sm5.lh/analysis.info file. >> >> Kind Regards, >> Ivan Alvarez >> >> PhD Student >> Imaging and Biophysics Unit >> UCL Institute of Child Health >> 30 Guildford Street, London, WC1N 1EH >> >> >> On 13/01/12 19:20, Douglas N Greve wrote: >>> Hi Ivan, can you send me verbgen.sm5.lh/analysis.info? >>> doug >>> >>> Ivan Alvarez wrote: >>>> Dear Freesurfers, >>>> >>>> I recently attempted my first FSFAST analysis following the >>>> tutorial on http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt >>>> <http://nmr.mgh.harvard.edu/%7Egreve/fsfast.intro.ppt> while using >>>> my own data. >>>> >>>> I stumbled across an error in selxavg3-sess which I can't decipher. >>>> The problem seems to arise when running the Matlab script >>>> fast_selxavg3.m andra returns: >>>> >>>> outtop = /media/data/analysis/FREESURFER_TEST/Project >>>> >>>> Extension format = nii.gz >>>> >>>> Error using basename >>>> >>>> Too many input arguments. >>>> >>>> >>>> Error in fast_ldanaflac (line 423) >>>> >>>> nuisregevname = basename(nuisreg,'dat'); % remove .dat >>>> >>>> >>>> Error in fast_selxavg3 (line 53) >>>> >>>> flac0 = fast_ldanaflac(analysis); >>>> >>>> >>>> >>>> I have looked through the Freesurfer documentation and mailing list >>>> but couldn't spot anyone with this issue. I am attaching the full >>>> log below, any insights would be greatly appreciated! >>>> >>>> >>>> >>>> >>>> ivan@sirsa:/media/data/analysis/FREESURFER_TEST/Project$ >>>> selxavg3-sess -sf sessid -analysis verbgen.sm5.lh >>>> >>>> Surface data fsaverage lh >>>> >>>> -------------------------------------------------------------- >>>> >>>> selxavg3-sess logfile is >>>> /media/data/analysis/FREESURFER_TEST/Project/log/selxavg3-sess-bold-verbgen.sm5.lh-120112125113.log >>>> >>>> >>>> -------------------------------------------------------------- >>>> >>>> preproc-sess -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -a verbgen.sm5.lh -nolog >>>> >>>> -------------------------------------------------------------- >>>> >>>> preproc-sess logfile is /dev/null >>>> >>>> -------------------------------------------------------------- >>>> >>>> $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ >>>> >>>> ivan >>>> >>>> setenv FREESURFER_HOME /home/ivan/freesurfer >>>> >>>> setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects >>>> >>>> Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 >>>> UTC 2011 x86_64 GNU/Linux >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project >>>> >>>> /home/ivan/freesurfer/fsfast/bin/preproc-sess >>>> >>>> -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -a >>>> verbgen.sm5.lh -nolog >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> instem f >>>> >>>> mc 1 f fmcpr >>>> >>>> stc 0 fmcpr >>>> >>>> sm 0 >>>> mask 1 brain >>>> >>>> Sess01 Template ----------------------------- >>>> >>>> mktemplate-sess -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -nolog -update >>>> >>>> >>>> >>>> Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> ---------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Detected input format at nii >>>> >>>> Sess01 Update not needed >>>> >>>> Run: 001 ---------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Sess01 001 Update not needed >>>> >>>> Run: 002 ---------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Sess01 002 Update not needed >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> mktemplate-sess completed >>>> >>>> Sess01 Mask ------------------------ >>>> >>>> mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -nolog -update >>>> >>>> ------------------------------------------------ >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Sess01 Update not needed for session-level mask >>>> >>>> Sess01 Update not needed for run 001 mask >>>> >>>> Sess01 Update not needed for run 001 meanval >>>> >>>> Sess01 Update not needed for run 002 mask >>>> >>>> Sess01 Update not needed for run 002 meanval >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> mkbrainmask-sess done >>>> >>>> Sess01 Registration ----------------------------- >>>> >>>> register-sess -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 >>>> -per-run -nolog -update >>>> >>>> -------------------------------------------------------------- >>>> >>>> register-sess logfile is /dev/null >>>> >>>> -------------------------------------------------------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> >>>> setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects >>>> >>>> cd /media/data/analysis/FREESURFER_TEST/Project >>>> >>>> /home/ivan/freesurfer/fsfast/bin/register-sess -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 >>>> -per-run -nolog -update >>>> >>>> >>>> freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >>>> >>>> Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 >>>> UTC 2011 x86_64 GNU/Linux >>>> >>>> >>>> >>>> Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> ---------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Run: 001 ---------------- >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> Update not needed >>>> >>>> Run: 002 ---------------- >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> Update not needed >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> register-sess completed >>>> >>>> Sess01 MC ----------------------------- >>>> >>>> mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -per-run >>>> -nolog -update >>>> >>>> Logfile is /dev/null >>>> >>>> ------------------------------------------- >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> >>>> RunList: 001 002 >>>> >>>> Sess01 001 Update not needed >>>> >>>> Sess01 002 Update not needed >>>> >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> mc-sess completed SUCCESSFULLY >>>> >>>> Sess01 To Surface ----------------------------- >>>> >>>> rawfunc2surf-sess -fwhm 5 -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -hemi lh >>>> -nolog -update >>>> >>>> instem fmcpr >>>> >>>> outstem fmcpr.sm5.fsaverage.hemi >>>> >>>> ------------------------------ >>>> >>>> 1/1 Sess01 >>>> >>>> 1/1 Sess01 001 lh --------- >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> Sess01 001 Update not needed >>>> >>>> 1/1 Sess01 002 lh --------- >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> Sess01 002 Update not needed >>>> >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> rawfunc2surf-sess completed >>>> >>>> ---------------------------------------- >>>> >>>> Started at Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Ended at Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> preproc-sess done >>>> >>>> ------------------------------------------- >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> anadir = >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01/bold/verbgen.sm5.lh >>>> >>>> >>>> DoGLMFit = 1 >>>> >>>> DoContrasts = 1 >>>> >>>> UpdateNeeded = 1 >>>> >>>> ------------------------------------------ >>>> >>>> ------- matlab output -------------------- >>>> >>>> Warning: Unable to open display 'iconic'. You will not be able to >>>> display graphics on the screen. >>>> >>>> >>>> < M A T L A B (R) > >>>> >>>> Copyright 1984-2011 The MathWorks, Inc. >>>> >>>> R2011b (7.13.0.564) 64-bit (glnxa64) >>>> >>>> August 13, 2011 >>>> >>>> >>>> Warning: Duplicate directory name: /home/ivan/matlab. >>>> >>>> >>>> >>>> To get started, type one of these: helpwin, helpdesk, or demo. >>>> >>>> For product information, visit www.mathworks.com. >>>> >>>> >>>> >>>> >> >> >> >> >> >> >> >>>> /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>> >>>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>>> >>>> >>>> #@# Sess01 ############################### >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> >>>> ------------------------- >>>> >>>> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >>>> >>>> /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>> >>>> /home/ivan/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>> >>>> /home/ivan/freesurfer/matlab/MRIread.m >>>> >>>> ------------------------- >>>> >>>> outtop = /media/data/analysis/FREESURFER_TEST/Project >>>> >>>> Extension format = nii.gz >>>> >>>> Error using basename >>>> >>>> Too many input arguments. >>>> >>>> >>>> Error in fast_ldanaflac (line 423) >>>> >>>> nuisregevname = basename(nuisreg,'dat'); % remove .dat >>>> >>>> >>>> Error in fast_selxavg3 (line 53) >>>> >>>> flac0 = fast_ldanaflac(analysis); >>>> >>>> >>>> >>>> >> ------------------------------------------ >>>> >>>> ERROR: fast_selxavg3() failed\n >>>> >>>> >>>> -- >>>> Kind Regards, >>>> Ivan Alvarez >>>> >>>> PhD Student >>>> Imaging and Biophysics Unit >>>> UCL Institute of Child Health >>>> 30 Guildford Street, London, WC1N 1EH >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >

1 0

Re: [Freesurfer] control points
by Alana Shepherd 17 Jan '12

17 Jan '12

On the brainmask the intensity within the STG wm is either slightly lower than 110 or slightly higher, though at the exact location of the control points it is 110. Similarly on the wm.mgz the intensities range around 110. I am not sure what the intensity was at these points before the cp's were added and reprocessed. On 17/01/2012, at 1:36 PM, Bruce Fischl wrote: > Can you cc the list so others can answer? Is the wm in the brain.mgz in those regions darker than 110? Does putting control points there increase the intensity? It looks like a topological defect, but control points should help > > > > On Jan 16, 2012, at 9:34 PM, Alana Shepherd <alana.shepherd(a)unsw.edu.au> wrote: > >> Hi Bruce, >> Thanks for your fast reply. Sorry - I realise I may have been unclear in my explanation. The sections are not missing from the brainmask mgz file - as if they had been cut out during skull stripping - they are actually missing from the surfs and aseg definitions (see attached screen shot). >> Regarding skull stripping - I have been changing the skull strip parameters on an 'as-need' basis - so some of the subjects have a lowered ws thresh, others I have needed to use gcut to remove excess dura, and some have been fine with the default ws thresh. >> I hope this clarifies the issue, >> Cheers >> Alana >> >> <cp fail Screen shot 2012-01-17.png> >> >> >> >> On 17/01/2012, at 1:17 PM, Bruce Fischl wrote: >> >>> Hi Alana >>> >>> Have you tried changing the skull strip parameters? >>> >>> Cheers >>> Bruce >>> >>> >>> >>> On Jan 16, 2012, at 6:33 PM, Alana Shepherd <alana.shepherd(a)unsw.edu.au> wrote: >>> >>>> Hello, >>>> I am running version 5.0, and am finding in a few cases that some areas (most commonly STG) are missing from the original brainmask - after adding control points and re-running the pipeline, these regions are still not being picked up in the surfs or in the aseg. >>>> Can you suggest any other way of remedying this? >>>> Many thanks >>>> Alana Shepherd >>>> _______________________________________________ >>>> 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. >>> >>

2 3

Pial extension into cerebellum
by Mahinda Yogarajah 17 Jan '12

17 Jan '12

Dear Freesurfer Experts, I have read the advice on the wiki regarding what to do when pial surfaces extend into the cerebellum. I had a few questions to clairfy things: 1) If I have made other (non-cerebellar) edits to the brainmask.mgz, and added control points can I simply do cp brainmask.mgz brain.finalsurfs.manedit.mgz edit the cerebellum voxels out on the brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name Will this then apply non-cerebellar and cerebellar edits (as well as control points) and give appropriate segmentations ? OR Do I have to make non-cerbellar edits to brainmask.mgz cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz make cerebellar edits to brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name Thanks. Mahinda

1 0

FSFAST v 5.1 group level volume analysis
by tapsya＠nmr.mgh.harvard.edu 17 Jan '12

17 Jan '12

Hi Doug, http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes states that "FSFAST - now masks the volume-based analysis to include only subcortical areas" and indeed, it looks like our group level volume results are in subcortical space only. We always use volume (native space full brain) analysis especially for sanity checks. At the group level, looking at analysis results in full volume (default brain mask) is essential for quality control and getting a feel of what is going on with the data. Is there a way to set up the volume analysis so that it is run for the whole brain (brain mask) at group level? Thank you! Best regards, Tapsya

2 1

how to convert the *.annot to *.gii
by Zhang, Yuning 17 Jan '12

17 Jan '12

Hi, dear experts, In freesurfer , is there a way to convert the" *h.aparc.annot" file to Gifti file format so that caret can recognize it. thanks yuning

1 0

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