Re: [Freesurfer] recon-all with T1 and T2 images
Hi Heidi it is easy to imagine there being a regionally specific bias between processing so you are better off doing them all the same way cheers Bruce On Wed, 25 Apr 2018, Heidi Lindroth wrote: External Email - Use Caution Hello, I have processed the majority of my T1 images using the general recon-all command. After reviewing segmentation, a number of images have the pial surface included in the gray matter. I re-ran an image with the recon-all command combining the T1 and T2 images and it greatly reduced the segmentation errors. Going forward, are there quality differences between those images processed with only recon-all versus those processed with recon-all T1 & T2? Can I still combine images processed with T1 only and those with T1 & T2 in the same analysis? Or, do I need to rerun all scans with the recon-all T1 & T2 command? Thank you, Heidi Lindroth BSN RN PhD Candidate | School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindr...@wisc.edu ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_compute_volume_fractions
External Email - Use Caution I am getting same Error with many permutations of arguments, mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader identity.nofile arg = 6 reading registration file 002_S/mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from 002_S/mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from 002_S/mri/aseg.mgz mri_compute_volume_fractions: could not load registration file from 002_S/mri/aseg.mgz Thanks, Dhivya From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 6:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions try mri_compute_volume_fractions --o test --regheader On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > Thanks Bruce! > > I even tried with --regheader > > mri_compute_volume_fractions mri/aseg.mgz --o test --regheader identity.nofile > > It gives me below error, > > arg = 6 > reading registration file mri/aseg.mgz > regio_read_register(): Success > Error reading inplaneres from mri/aseg.mgz > regio_read_register(): Success > Error reading inplaneres from mri/aseg.mgz > mri_compute_volume_fractions: could not load registration file from > mri/aseg.mgz > > Thanks, > Dhivya > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, April 25, 2018 6:01 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > oh, this must be Doug's code, not mine. Try using --regheader instead > > And also please send us the full command and all screen output from it in > the future. > cheers > Bruce > On > Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: > >>External Email - Use Caution >> >> Sorry for bothering with more questions! >> >> I am getting an error saying , >> >> mri_compute_volume_fractions: could not load registration file from >> identity.nofile >> >> And my command is, >> >> mri_compute_volume_fractions identity.nofile mri/aseg.mgz test >> >> and if I try to give in this format which the documentation says, >> >> mri_compute_volume_fractions [options] --o --reg >> >> Am I going wrong somewhere? >> >> Thanks, >> Dhivya >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, April 25, 2018 4:22 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mri_compute_volume_fractions >> >> Hi Dhivya >> >> if you are doing it in the space of the anatomicals, then use >> identity.nofile as the reg file (which is a special file name that will >> internally create an identity matrix). The output stem is whatever you >> pick - it will be prepended to the files that are written with the volume >> fractions. >> >> cheers >> Bruce >> On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >> >>>External Email - Use Caution >>> >>> Hi, >>> >>> I would like to get CSF/GM/WM segmentations from aseg.mgz or in other >>> words from labeled brain. Can I do that with mri_compute_volume_fractions ? >>> Also, I am not sure about the parameters to supply, >>> and ? >>> >>> Could Someone point me to some documentation on how should use this >>> function to get the segmentations ? >>> >>> Thanks, >>> Dhivya >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@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. >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu
Re: [Freesurfer] mri_compute_volume_fractions
just run the command as I sent it: mri_compute_volume_fractions --o test --regheader the aseg is the default name. You are putting it in the wrong place and it thinks the aseg is a registration file On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > I am getting same Error with many permutations of arguments, > > mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader > identity.nofile > > arg = 6 > reading registration file 002_S/mri/aseg.mgz > regio_read_register(): Success > Error reading inplaneres from 002_S/mri/aseg.mgz > regio_read_register(): Success > Error reading inplaneres from 002_S/mri/aseg.mgz > mri_compute_volume_fractions: could not load registration file from > 002_S/mri/aseg.mgz > > > Thanks, > Dhivya > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, April 25, 2018 6:21 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > try > > mri_compute_volume_fractions --o test --regheader > > On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: > >>External Email - Use Caution >> >> Thanks Bruce! >> >> I even tried with --regheader >> >> mri_compute_volume_fractions mri/aseg.mgz --o test --regheader >> identity.nofile >> >> It gives me below error, >> >> arg = 6 >> reading registration file mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from mri/aseg.mgz >> mri_compute_volume_fractions: could not load registration file from >> mri/aseg.mgz >> >> Thanks, >> Dhivya >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, April 25, 2018 6:01 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mri_compute_volume_fractions >> >> oh, this must be Doug's code, not mine. Try using --regheader instead >> >> And also please send us the full command and all screen output from it in >> the future. >> cheers >> Bruce >> On >> Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >> >>>External Email - Use Caution >>> >>> Sorry for bothering with more questions! >>> >>> I am getting an error saying , >>> >>> mri_compute_volume_fractions: could not load registration file from >>> identity.nofile >>> >>> And my command is, >>> >>> mri_compute_volume_fractions identity.nofile mri/aseg.mgz test >>> >>> and if I try to give in this format which the documentation says, >>> >>> mri_compute_volume_fractions [options] --o --reg >>> >>> Am I going wrong somewhere? >>> >>> Thanks, >>> Dhivya >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Wednesday, April 25, 2018 4:22 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] mri_compute_volume_fractions >>> >>> Hi Dhivya >>> >>> if you are doing it in the space of the anatomicals, then use >>> identity.nofile as the reg file (which is a special file name that will >>> internally create an identity matrix). The output stem is whatever you >>> pick - it will be prepended to the files that are written with the volume >>> fractions. >>> >>> cheers >>> Bruce >>> On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >>> External Email - Use Caution Hi, I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, I am not sure about the parameters to supply, and ? Could Someone point me to some documentation on how should use this function to get the segmentations ? Thanks, Dhivya ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> ___ >>> Freesurfer mailing list >>> Freesurfer@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. >>> >>> >>> >>> ___ >>> Freesurfer maili
Re: [Freesurfer] mri_compute_volume_fractions
External Email - Use Caution mri_compute_volume_fractions --o test --regheader unknown option --o If I am not giving any input before arguments, it is not taking them. Thanks, Dhivya From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 10:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions just run the command as I sent it: mri_compute_volume_fractions --o test --regheader the aseg is the default name. You are putting it in the wrong place and it thinks the aseg is a registration file On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > I am getting same Error with many permutations of arguments, > > mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader > identity.nofile > > arg = 6 > reading registration file 002_S/mri/aseg.mgz > regio_read_register(): Success > Error reading inplaneres from 002_S/mri/aseg.mgz > regio_read_register(): Success > Error reading inplaneres from 002_S/mri/aseg.mgz > mri_compute_volume_fractions: could not load registration file from > 002_S/mri/aseg.mgz > > > Thanks, > Dhivya > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, April 25, 2018 6:21 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > try > > mri_compute_volume_fractions --o test --regheader > > On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: > >>External Email - Use Caution >> >> Thanks Bruce! >> >> I even tried with --regheader >> >> mri_compute_volume_fractions mri/aseg.mgz --o test --regheader >> identity.nofile >> >> It gives me below error, >> >> arg = 6 >> reading registration file mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from mri/aseg.mgz >> mri_compute_volume_fractions: could not load registration file from >> mri/aseg.mgz >> >> Thanks, >> Dhivya >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, April 25, 2018 6:01 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mri_compute_volume_fractions >> >> oh, this must be Doug's code, not mine. Try using --regheader instead >> >> And also please send us the full command and all screen output from it in >> the future. >> cheers >> Bruce >> On >> Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >> >>>External Email - Use Caution >>> >>> Sorry for bothering with more questions! >>> >>> I am getting an error saying , >>> >>> mri_compute_volume_fractions: could not load registration file from >>> identity.nofile >>> >>> And my command is, >>> >>> mri_compute_volume_fractions identity.nofile mri/aseg.mgz test >>> >>> and if I try to give in this format which the documentation says, >>> >>> mri_compute_volume_fractions [options] --o --reg >>> >>> Am I going wrong somewhere? >>> >>> Thanks, >>> Dhivya >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Wednesday, April 25, 2018 4:22 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] mri_compute_volume_fractions >>> >>> Hi Dhivya >>> >>> if you are doing it in the space of the anatomicals, then use >>> identity.nofile as the reg file (which is a special file name that will >>> internally create an identity matrix). The output stem is whatever you >>> pick - it will be prepended to the files that are written with the volume >>> fractions. >>> >>> cheers >>> Bruce >>> On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >>> External Email - Use Caution Hi, I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, I am not sure about the parameters to supply, and ? Could Someone point me to some documentation on how should use this function to get the segmentations ? Thanks, Dhivya ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is i
Re: [Freesurfer] mri_compute_volume_fractions
hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I run: mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname sulc.nmr.mgh.harvard.edu machine x86_64 user fischl setenv SUBJECTS_DIR /homes/4/fischl/links/subjects cd /autofs/space/tiamat_003/users/subjects mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz . . . On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > mri_compute_volume_fractions --o test --regheader > unknown option --o > > If I am not giving any input before arguments, it is not taking them. > > Thanks, > Dhivya > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, April 26, 2018 10:52 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > just run the command as I sent it: > > mri_compute_volume_fractions --o test --regheader > > the aseg is the default name. You are putting it in the wrong place and it > thinks the aseg is a registration file > > On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: > >>External Email - Use Caution >> >> I am getting same Error with many permutations of arguments, >> >> mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader >> identity.nofile >> >> arg = 6 >> reading registration file 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> mri_compute_volume_fractions: could not load registration file from >> 002_S/mri/aseg.mgz >> >> >> Thanks, >> Dhivya >> >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, April 25, 2018 6:21 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mri_compute_volume_fractions >> >> try >> >> mri_compute_volume_fractions --o test --regheader >> >> On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >> >>>External Email - Use Caution >>> >>> Thanks Bruce! >>> >>> I even tried with --regheader >>> >>> mri_compute_volume_fractions mri/aseg.mgz --o test --regheader >>> identity.nofile >>> >>> It gives me below error, >>> >>> arg = 6 >>> reading registration file mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> mri_compute_volume_fractions: could not load registration file from >>> mri/aseg.mgz >>> >>> Thanks, >>> Dhivya >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Wednesday, April 25, 2018 6:01 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] mri_compute_volume_fractions >>> >>> oh, this must be Doug's code, not mine. Try using --regheader instead >>> >>> And also please send us the full command and all screen output from it in >>> the future. >>> cheers >>> Bruce >>> On >>> Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >>> External Email - Use Caution Sorry for bothering with more questions! I am getting an error saying , mri_compute_volume_fractions: could not load registration file from identity.nofile And my command is, mri_compute_volume_fractions identity.nofile mri/aseg.mgz test and if I try to give in this format which the documentation says, mri_compute_volume_fractions [options] --o --reg Am I going wrong somewhere? Thanks, Dhivya From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 4:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions Hi Dhivya if you are doing it in the space of the anatomicals, then use identity.nofile as the reg file (which is a special file name that will internally create an identity matrix). The output stem is whatever you pick - it will be prepended to the files that are written with the
[Freesurfer] aparcstats2table for white surface total area
External Email - Use Caution Hello, Forgive me, I'm new to FreeSurfer. I wish to collate values of white surface total area from all my subjects into a single table, so that I can control for this in my analyses. I understand this value is in the aparc.stats files for each participant and hemisphere, so I have tried: aparcstats2table -subjectfile sublist -hemi lh -meas WhiteSurfArea -tablefile aparc_stats_lh.wsa.table but WhiteSurfArea isn't an option for -meas. Please let me know if you can help, Many thanks, Emma Davies PhD Student Department of Psychiatry University of Cambridge Douglas House 18b Trumpington Road Cambridge CB2 8AH ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] aparcstats2table for white surface total area
If you just run aparcstats2table it should be in the table. I don't think there is a way to only get that value On 04/26/2018 11:20 AM, Sian Emma Davies wrote: > > External Email - Use Caution > > Hello, > > Forgive me, I’m new to FreeSurfer. I wish to collate values of white > surface total area from all my subjects into a single table, so that I > can control for this in my analyses. I understand this value is in the > aparc.stats files for each participant and hemisphere, so I have tried: > > aparcstats2table –subjectfile sublist –hemi lh –meas WhiteSurfArea > –tablefile aparc_stats_lh.wsa.table > > but WhiteSurfArea isn’t an option for –meas. Please let me know if you > can help, > > Many thanks, > > Emma Davies > > PhD Student > > Department of Psychiatry > > University of Cambridge > > Douglas House > > 18b Trumpington Road > > Cambridge > > CB2 8AH > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_compute_volume_fractions
External Email - Use Caution Yep , I am using "o" . I am running it on Ubuntu 16.04 and my freesurfer version is , freesurfer/5.3.0/bin/freesurfer mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz still I am getting , unknown option --o Trying to give as per documentation, which is --o outstem --regheader subject I am really sorry to bother you with so many questions. Is it something to do with version of freesurfer? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 11:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I run: mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname sulc.nmr.mgh.harvard.edu machine x86_64 user fischl setenv SUBJECTS_DIR /homes/4/fischl/links/subjects cd /autofs/space/tiamat_003/users/subjects mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz . . . On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > mri_compute_volume_fractions --o test --regheader > unknown option --o > > If I am not giving any input before arguments, it is not taking them. > > Thanks, > Dhivya > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, April 26, 2018 10:52 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > just run the command as I sent it: > > mri_compute_volume_fractions --o test --regheader > > the aseg is the default name. You are putting it in the wrong place and it > thinks the aseg is a registration file > > On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: > >>External Email - Use Caution >> >> I am getting same Error with many permutations of arguments, >> >> mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader >> identity.nofile >> >> arg = 6 >> reading registration file 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> mri_compute_volume_fractions: could not load registration file from >> 002_S/mri/aseg.mgz >> >> >> Thanks, >> Dhivya >> >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, April 25, 2018 6:21 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mri_compute_volume_fractions >> >> try >> >> mri_compute_volume_fractions --o test --regheader >> >> On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >> >>>External Email - Use Caution >>> >>> Thanks Bruce! >>> >>> I even tried with --regheader >>> >>> mri_compute_volume_fractions mri/aseg.mgz --o test --regheader >>> identity.nofile >>> >>> It gives me below error, >>> >>> arg = 6 >>> reading registration file mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> mri_compute_volume_fractions: could not load registration file from >>> mri/aseg.mgz >>> >>> Thanks, >>> Dhivya >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Wednesday, April 25, 2018 6:01 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] mri_compute_volume_fractions >>> >>> oh, this must be Doug's code, not mine. Try using --regheader instead >>> >>> And also please send us the full command and all screen output from it in >>> the future. >>> cheers >>> Bruce >>> On >>> Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >>> External Email - Use Caution Sorry for bothering with more questions! I am getting an error saying , mri_compute_volume_fractions: could not load registration file from identity.nofile And my command is, mri_compute_volume_fractions identity.nofile mri/aseg.mgz test and if I try to give in this format which the documentation says, >>
Re: [Freesurfer] mri_compute_volume_fractions
External Email - Use Caution Dhivya, this syntax works for me with version 6. With version 5.3.0 I am getting the same error mesage. I do not know how the correct syntax is with version 5.3.0. Antonin Skoch Yep , I am using "o" .I am running it on Ubuntu 16.04 and my freesurfer version is , freesurfer/5.3.0/bin/freesurfer mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz still I am getting , unknown option --o Trying to give as per documentation, which is --o outstem --regheader subject I am really sorry to bother you with so many questions. Is it something to do with version of freesurfer? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 11:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I run: mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname sulc.nmr.mgh.harvard.edu machine x86_64 user fischl setenv SUBJECTS_DIR /homes/4/fischl/links/subjects cd /autofs/space/tiamat_003/users/subjects mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz . . . On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > mri_compute_volume_fractions --o test --regheader > unknown option --o > > If I am not giving any input before arguments, it is not taking them. > > Thanks, > Dhivya > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, April 26, 2018 10:52 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > just run the command as I sent it: > > mri_compute_volume_fractions --o test --regheader > > the aseg is the default name. You are putting it in the wrong place and it > thinks the aseg is a registration file > > On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: > >>External Email - Use Caution >> >> I am getting same Error with many permutations of arguments, >> >> mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader >> identity.nofile >> >> arg = 6 >> reading registration file 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> mri_compute_volume_fractions: could not load registration file from >> 002_S/mri/aseg.mgz >> >> >> Thanks, >> Dhivya >> >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, April 25, 2018 6:21 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mri_compute_volume_fractions >> >> try >> >> mri_compute_volume_fractions --o test --regheader >> >> On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >> >>>External Email - Use Caution >>> >>> Thanks Bruce! >>> >>> I even tried with --regheader >>> >>> mri_compute_volume_fractions mri/aseg.mgz --o test --regheader >>> identity.nofile >>> >>> It gives me below error, >>> >>> arg = 6 >>> reading registration file mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> mri_compute_volume_fractions: could not load registration file from >>> mri/aseg.mgz >>> >>> Thanks, >>> Dhivya >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Wednesday, April 25, 2018 6:01 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] mri_compute_volume_fractions >>> >>> oh, this must be Doug's code, not mine. Try using --regheader instead >>> >>> And also please send us the full command and all screen output from it in >>> the future. >>> cheers >>> Bruce >>> On >>> Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >>> External Email - Use Caution Sorry for bothering with more questions! I am getting an error saying , mri_compute_volume_fractions: could not load registration file from identity.nofile >>
[Freesurfer] Comparison between T1 only recon-all and T1 + FLAIR recon-all
External Email - Use Caution Hello, In the past we have only used the T1 image as input for recon-all. However, we are now also acquiring a FLAIR image and were thinking of using both for new studies. Does anyone have any data on the differences/advantages of using FLAIR images with the FLAIRpial command? Any input would be greatly appreciated. Thanks! Andrew O'Shea, MSc. Clinical Research Coordinator II Woods Lab Center for Cognitive Aging and Memory McKnight Brain Institute Department of Clinical and Health Psychology College of Public Health and Health Professions University of Florida Phone (Office): (352) 294-5827 Phone (Cell): (586) 899-2771 Email: aos...@phhp.ufl.edu ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Using mprage flag.
External Email - Use Caution Hello FreeSurfers When should I use the MPRAGE flag for recon-all? Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Using mprage flag.
if you have an mprage it usually helps a bit cheers Bruce On Thu, 26 Apr 2018, Aaron Tanenbaum wrote: External Email - Use Caution Hello FreeSurfers When should I use the MPRAGE flag for recon-all? Aaron Tanenbaum ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_compute_volume_fractions
External Email - Use Caution Thanks Antonin, I will probably try with version 6. Thanks, Dhivya From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Antonin Skoch [a...@ikem.cz] Sent: Thursday, April 26, 2018 1:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_compute_volume_fractions External Email - Use Caution Dhivya, this syntax works for me with version 6. With version 5.3.0 I am getting the same error mesage. I do not know how the correct syntax is with version 5.3.0. Antonin Skoch Yep , I am using "o" . I am running it on Ubuntu 16.04 and my freesurfer version is , freesurfer/5.3.0/bin/freesurfer mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz still I am getting , unknown option --o Trying to give as per documentation, which is --o outstem --regheader subject I am really sorry to bother you with so many questions. Is it something to do with version of freesurfer? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 11:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I run: mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname sulc.nmr.mgh.harvard.edu machine x86_64 user fischl setenv SUBJECTS_DIR /homes/4/fischl/links/subjects cd /autofs/space/tiamat_003/users/subjects mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz . . . On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > mri_compute_volume_fractions --o test --regheader > unknown option --o > > If I am not giving any input before arguments, it is not taking them. > > Thanks, > Dhivya > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, April 26, 2018 10:52 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > just run the command as I sent it: > > mri_compute_volume_fractions --o test --regheader > > the aseg is the default name. You are putting it in the wrong place and it > thinks the aseg is a registration file > > On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: > >>External Email - Use Caution >> >> I am getting same Error with many permutations of arguments, >> >> mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader >> identity.nofile >> >> arg = 6 >> reading registration file 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> mri_compute_volume_fractions: could not load registration file from >> 002_S/mri/aseg.mgz >> >> >> Thanks, >> Dhivya >> >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, April 25, 2018 6:21 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mri_compute_volume_fractions >> >> try >> >> mri_compute_volume_fractions --o test --regheader >> >> On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >> >>>External Email - Use Caution >>> >>> Thanks Bruce! >>> >>> I even tried with --regheader >>> >>> mri_compute_volume_fractions mri/aseg.mgz --o test --regheader >>> identity.nofile >>> >>> It gives me below error, >>> >>> arg = 6 >>> reading registration file mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> mri_compute_volume_fractions: could not load registration file from >>> mri/aseg.mgz >>> >>> Thanks, >>> Dhivya >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Wednesday, April 25, 2018 6:01 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] mri_compute_volume_fractions >>> >>> oh, this must be Doug's code, not mine. Try using --regheader instead >>> >>> And also please
