[Freesurfer] mri_segstats --avgwf output question
External Email - Use Caution Hi there, I'm running mri_segstats on a collection of clusters resulting from a statistical analysis. My command line usage is as follows: mri_segstats --i lh.fwhm10.thickness.mgh --avgwf clusterAverages.txt --seg cache.th13abs.sig.ocn.mgh The results from my statistical analysis in the case of left hemisphere thickness shows 4 clusters that are significant in total, but the clusterAverages.txt contains a total of 5 mean thickness values per subject. This extra value is also reflected in other analyses in my dataset (for other hemisphere and for thickness, area and volume). Is the extra value listed per subject a global mean of some sort? If so, is it the first column of values or the last? Thank you, Lara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] LMW and missing timepoints
External Email - Use Caution Wonderful. Thanks! Lara From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Diers, Kersten /DZNE Sent: Tuesday, July 11, 2023 3:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] LMW and missing timepoints External Email - Use Caution Hello, the LME model accounts for dependencies between timepoints, but does so in a flexible way: it does not require the same number of observations for each participant, nor does it require identical intervals between observations. Also including a single timepoints for some cases is fine. In general, one can think of it as a regression problem: sometimes more data/timepoints are available to model the slopes across time, sometimes less. This probably affects the precision of the estimates, but apart from that, varying numbers of timepoints and variable intervals are not a fundamental problem for LME models. Best regards, Kersten Am 10.07.2023 um 22:11 schrieb Lara Foland-Ross mailto:lfol...@stanford.edu>>: CAUTION: This email originated from outside of DZNE. Do not click links or open attachments unless you recognize the sender and know the content is safe. ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig beim Anklicken von Links oder Öffnen von Anhängen External Email - Use Caution Hi there, We have a longitudinal structural neuroimaging dataset with anywhere between 1 and 4 timepoints collected for each participant. How does LME handle missing data when analyzing longitudinal trends? Thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1g8dJNHLTxI9M-lML0BIEY1G6x9zUwWo3khaMJCsBrwLYssSaSkEnksxLVt1lSK3fQbYv-fyR06hFzi0RCNQ3Q92UmErO7jEZCr1qiCz092kIs6IJVf2NRDqQSvf4N-2yqcq0pj8Lj5je2-EqXe0qfDz9rVNRF7vXMzpNQiRcE0J-hEWlDffkzUmGuVkqvmgQG437d5nbC4Fp5o4hpS2ujvmtPf9Q4OkCb4dL2dhp8Of24GB_yAdZe0Nigu04D67vYWlMeF5BWGtN4UmSMVo9fc30G5T7kYSALEREBTdohbAeg2BIqTvLMK7iR6FGFg1xOqtcbqu0MMwT1l8WJlMSZg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1YFT6sc5KEjTJ6SNF0Zj5pYIJjLHLEjKyN57OOschlwEAG-X_mHEnPv76kp8IgavKllXtrm6oLvJOJhkgM0wQNW2UhKxL-pYJ4wvZxH3iZlFFL8LAlytLSaM0blpicgX02qeeSVsyKOaYkiseVqz4Pdw65sKIQEJTzrMx6Gvj3bLbtxN6nFNMaAIdy5HpnFPe3dhn79cPOqW1GiJSg4xtaD-UHwa9lk5yAKs_FM-haYlyP5KPVAUyKb31JH1Fy4YpoSJyT7mExJVy6DImIVBghScv5Eo3gMc0MzSDi0CoT_AUEvxyaDA6pI8JooYiHYThVqGtJOnTM_p9fI0WrKzqdQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZsAJyR41S2_NL_DHcHcaa2pob2rngUzOt2gGZoKzPg8L6ZHFR6z3GurYnu4sDhuKstFvCMdVlqk1BckCQ0nZvG9LgA7dvnKsYIhQ0RRXCIKghHKAwtQawAbO3VTZR3J3MJhKOilnJEW_SJ_CoIh4-iTgyZ7Wut3mq37Jp5pjtZt7crSrFHfX6KddVHAEn5Ur-ewzVqJVYvP1QHCHfGBIB6oxOWDqVrJoYsQEncsw9FSrZ4E05hNo_cFKqhSWh1emzOiWsodAiPKrlIdLyE3MHcQDx5YMA5VwN-mlRz3c6l6TYt2mkDRZi9LOOOMain_mBp_MpGj1F5HL4tYgtbbedw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline<https://secure-web.cisco.com/18As-1tcAkt__g7AZ6AIuQSJbyECIdUxWskHXBLN5HautStMmfOUMs_fYThi-fFHETa1ayQuqSYNMxrxkbVGgEzJYNuhZjveUTXGXBfsUszePv25b5vkskZJRV8RbnmtKTolBmQ5NkLq-nkbYGR2vwv7r1kqyxbTIOdWY0UC90ygC4WKmlIUpEmVZRJ-xHotto0ilyQbRQsoKwmMcAPtkDKktdnY_slMqTaWfRGNE4z50cyKHpGAcko_AXpeSwENWFNGdimVCepMxMngmSmwYg2X2w8dtxKbg1O6clmmfid7ntQt1i4zPV7m511pfDyPpYuku2Bf-_DIburmjbcy9tg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> https://secure-web.cisco.com/1ZsAJyR41S2_NL_DHcHcaa2pob2rngUzOt2gGZoKzPg8L6ZHFR6z3GurYnu4sDhuKstFvCMdVlqk1BckCQ0nZvG9LgA7dvnKsYIhQ0RRXCIKghHKAwtQawAbO3VTZR3J3MJhKOilnJEW_SJ_CoIh4-iTgyZ7Wut3mq37Jp5pjtZt7crSrFHfX6KddVHAEn5Ur-ewzVqJVYvP1QHCHfGBIB6oxOWDqVrJoYsQEncsw9FSrZ4E05hNo_cFKqhSWh1emzOiWsodAiPKrlIdLyE3MHcQDx5YMA5VwN-mlRz3c6l6TYt2mkDRZi9LOOOMain_mBp_MpGj1F5HL4tYgtbbedw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline<https://secure-web.cisco.com/18As-1tcAkt__g7AZ6AIuQSJbyECIdUxWskHXBLN5HautStMmfOUMs_fYThi-fFHETa1ayQuqSYNMxrxkbVGgEzJYNuhZjveUTXGXBfsUszePv25b5vkskZJRV8RbnmtKTolBmQ5NkLq-nkbYGR2vwv7r1kqyxbTIOdWY0UC90ygC4WKmlIUpEmVZRJ-xHotto0ilyQbRQsoKwmMcAPtkDKktdnY_slMqTaWfRGNE4z50cyKHpGAcko_AXpeSwENWFNGdimVCepMxMngmSmwYg2X2w8dtxKbg1O6clmmfid7ntQt1i4z
[Freesurfer] LMW and missing timepoints
External Email - Use Caution Hi there, We have a longitudinal structural neuroimaging dataset with anywhere between 1 and 4 timepoints collected for each participant. How does LME handle missing data when analyzing longitudinal trends? Thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] how to shrink WM surface in one region
External Email - Use Caution Hi Bruce, Thanks for the quick reply. I'm unable to connect to the ftp or file drop sites outlined here: https://secure-web.cisco.com/1J6xj9uOYT0-orYt6Ug7tMaMV01I_XctGV48pcqQv9Tr9ubNryoR2olV4-GZJyFgXWIBKzChaTvUZ54ksRY3KJN7HS48GCFQHRgDcmX_C-9ExNQIhqWdtNsYPC5OXH5nhrGcAKr3-uf272_69Veym_yD9lSwnLGQPUn5WQu9064ju2XzAwLDCebCC96F4Y6omecL5RtQ1JZSrfRCQEzghed-QmdPB_hYiSPIEAr2WmeST-j61bq6MsltUPilNv1Zb3m64BXbT7ODVQNFrmgDgaw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFtpFileExchange. I can log into the ftp server, but don't have permissions access to drop files there. ...So instead, I put the image snapshots in a public google doc here: https://secure-web.cisco.com/183XTP5FLjT6Xx2SHQPem_2YqmbLW8bRZYSzfF6XOXFaE26dUdAVup5y7KygrjHrik6wX5NA-RoUFJlfQWQ1z4451Xv53-Xvt5JoaARbOpbtSWgIiJ6USMmPPiJchKK87-3qYOBDqU0FBAceHoAVuxP0igy5Wq9ElrROrkaUFodEjCvo8v7aiYduMuVx5Wp82JZbB2XkL8bAOZCJmFHibVCc0czcug4fUNasmddKRZMghDLeyqaPiWWculL5jw8L6HZ2RiZNWPoeRFvbyO3orYw/https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1HF5qcbiYRDdGZbvhoImfwVqX4xARgSnPDUnbuPKqMpY%2Fedit%3Fusp%3Dsharing Hopefully that will suffice. Thanks again, Lara From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Fischl, Bruce Sent: Wednesday, June 23, 2021 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to shrink WM surface in one region Hi Lara Can you send us some pictures? The answer depends on why the white matter surface is settling at the wrong place Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Lara Foland-Ross Sent: Wednesday, June 23, 2021 7:11 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] how to shrink WM surface in one region External Email - Use Caution Hi everyone, Very quick question - I need to shrink the white matter surface in a very specific (constrained) region. Can you please confirm that the right way to go about this is to (1) manually remove voxels from the WM volume in freeview, then (2) save edits on that WM volume, and then (3) run recon-all? Specifically, re: #3 - many brains also need control points, so I'm running " recon-all -autorecon2-cp -autorecon3" Using this command structure, I'm not seeing that any of the edits I'm making to the WM volume are influencing the white matter surface line... Only the control points. Thank you in advance, Lara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ol1Q11CaB9oKoj5iyxZnro7EGji1hj3xI4MFL1Hsy2IZrVINTJPmbPvZcM-KbzaSLERzuSaNvz-zO_GCUTwEG16g0DFEo4CDD6J34ArWooG7jtaD7QNeY4aL6fQf_uScApuPZB2prcI4tL4GnBthy74-WdVyT4PNgXOQ0jF6yNj83nGzNRCvgJMk8bYTYH-NIQALK_-K_3iT6RIdIQREAdwGWSNMtPKiUV831dKp0vWIw4F77ef35ftwu64z2Ke4X7xaU5na1TPQndcS5GCAjg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ol1Q11CaB9oKoj5iyxZnro7EGji1hj3xI4MFL1Hsy2IZrVINTJPmbPvZcM-KbzaSLERzuSaNvz-zO_GCUTwEG16g0DFEo4CDD6J34ArWooG7jtaD7QNeY4aL6fQf_uScApuPZB2prcI4tL4GnBthy74-WdVyT4PNgXOQ0jF6yNj83nGzNRCvgJMk8bYTYH-NIQALK_-K_3iT6RIdIQREAdwGWSNMtPKiUV831dKp0vWIw4F77ef35ftwu64z2Ke4X7xaU5na1TPQndcS5GCAjg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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://secure-web.cisco.com/1fzTQRYqmAV-6Yr9bfT3PR24391lt59doFpNwJpSwP1GhxfjWtTnxI6DTMZ66OOJw3lWjK2LAaSA2-MvNEb2-ZvkLDwUEDpf3bZ4d_nQ0iZPcZZ4f8EyY1EAhKTtyBQwHRIMMFMyxovr3mvsabMMS9QLgMgvMvoC1-auPiEGYuBwXKndZ7TYOL0E0JFWN64KYodiT183Z82J-kRdQq1Yko3k7APRzmKIOcol5rBovzffe5MvABb5IehdA2FkjoqhYCrFpt8QkXzIb4EZtCFfnUQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to shrink WM surface in one region
External Email - Use Caution Hi everyone, Very quick question - I need to shrink the white matter surface in a very specific (constrained) region. Can you please confirm that the right way to go about this is to (1) manually remove voxels from the WM volume in freeview, then (2) save edits on that WM volume, and then (3) run recon-all? Specifically, re: #3 - many brains also need control points, so I'm running " recon-all -autorecon2-cp -autorecon3" Using this command structure, I'm not seeing that any of the edits I'm making to the WM volume are influencing the white matter surface line... Only the control points. Thank you in advance, Lara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker
External Email - Use Caution
Hello,
I am using Freesurfer7.1.1 ("docker pull freesurfer/freesurfer:7.1.1").
The docker command I'm using is:
docker run -it --platform linux/amd64 freesurfer_gui
Thanks,
Lara
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Paul Wighton
Sent: Tuesday, May 11, 2021 8:13 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker
External Email - Use Caution
Hi Lara,
What container are you using? Is it `freesurfer/freesurfer:7.1.1`? Can you
share the docker run command you're using?
-Paul
On Mon, May 10, 2021 at 10:00 PM Lara Foland-Ross
mailto:lfol...@stanford.edu>> wrote:
External Email - Use Caution
Sure. Here's the output:
sh-4.2# mri_info mri/rawavg.mgz
Volume information for mri/rawavg.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.00, 1.00, 1.00
type: FLOAT (3)
fov: 256.000
dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.00
ras xform present
xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 5.3997
: x_a = 0., y_a = 0., z_a = 1., c_a =18.
: x_s = 0., y_s = -1., z_s = 0., c_s = 0.
talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1. 0. 0. 133.3997
0. 0. 1. -110.
0. -1. 0. 128.
0. 0. 0. 1.
voxel-to-ras determinant -1
ras to voxel transform:
-1. -0. -0. 133.3997
-0. -0. -1. 128.
-0. 1. -0. 110.
-0. -0. -0. 1.
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
Sent: Monday, May 10, 2021 12:25 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker
Can you run
mri_info /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz
On 5/10/2021 1:00 PM, Lara Foland-Ross wrote:
External Email - Use Caution
Hello,
I'm trying to run Freesurfer7.1 on docker. I have a macbook air with an apple
chip with BigSur as the OSX.
To test out the installation, I ran recon-all on bert:
recon-all -all -s bert
The command quits with this error:
"ERROR: cannot determine file type for
/usr/local/freesurfer/subjects/bert/mri/rawavg.mgz
Linux 8c70180fb77b 5.10.25-linuxkit #1 SMP PREEMPT Tue Mar 23 09:24:45 UTC 2021
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Mon May 10 16:50:51 UTC 2021"
I'm attaching the recon-all.log file.
Could you please advise on how to troubleshoot?
Many thanks,
Lara
Lara Foland-Ross, Ph.D.
Senior Research Associate and Imaging Lab Manager
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
https://secure-web.cisco.com/1yiv8vlZ3k9XL8VmPsKSFGBhQpV_d1CqNGmb1zm8XRsvfT3IM0DINYYDRQOyhKnWxV2zYkTvRevpEDkpJSUPX2UIz_g6YWkF_5uDZqIxO0NuMONwMlRd8wdVNYIRNnNRxtCWGvMh0n7SeQiWp0bu1sExRCHzBrEyAYzUVQ30xiiUf4pnngkeuPNRqljMcMN-TgCWP33MJ6S9haztQJSuz6lOFDdvsQMWEzx4Xa4u-VtjPyl9xMlkgmH1eV5B8Q5w1gpPoMScnypjrvc8bex67KA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1vIG1ZdnORPNRjlNyEUTpSJVMFgbMgXIajEG3mdnQjMUs0ou9_oAMIFh1YZQ_F0m3xV7cChPU83_yX5EaY_OeU77qDYjjgesjwVlsa9j9NqAjvmZz4HrnXIeWalHN6RjTSQkE6nFVxqnRBb543YZC867W9r9fMzI1nxkY_VBfPMRt7JGLK6QFFUaVwQGMz0WJXPGw7EsREGFrWq-hrwMFU1Jlod5-3hg02A5cCUnLSmnIfo28F9nd53tWeHR3tvlC1onFtqd9jQBKtyow4CuhYQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ff
Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker
External Email - Use Caution Sure. Here's the output: sh-4.2# mri_info mri/rawavg.mgz Volume information for mri/rawavg.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.00, 1.00, 1.00 type: FLOAT (3) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.00 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 5.3997 : x_a = 0., y_a = 0., z_a = 1., c_a =18. : x_s = 0., y_s = -1., z_s = 0., c_s = 0. talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 133.3997 0. 0. 1. -110. 0. -1. 0. 128. 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 133.3997 -0. -0. -1. 128. -0. 1. -0. 110. -0. -0. -0. 1. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, May 10, 2021 12:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails in Freesurfer7.1 on docker Can you run mri_info /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz On 5/10/2021 1:00 PM, Lara Foland-Ross wrote: External Email - Use Caution Hello, I'm trying to run Freesurfer7.1 on docker. I have a macbook air with an apple chip with BigSur as the OSX. To test out the installation, I ran recon-all on bert: recon-all -all -s bert The command quits with this error: "ERROR: cannot determine file type for /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz Linux 8c70180fb77b 5.10.25-linuxkit #1 SMP PREEMPT Tue Mar 23 09:24:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon May 10 16:50:51 UTC 2021" I'm attaching the recon-all.log file. Could you please advise on how to troubleshoot? Many thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1yiv8vlZ3k9XL8VmPsKSFGBhQpV_d1CqNGmb1zm8XRsvfT3IM0DINYYDRQOyhKnWxV2zYkTvRevpEDkpJSUPX2UIz_g6YWkF_5uDZqIxO0NuMONwMlRd8wdVNYIRNnNRxtCWGvMh0n7SeQiWp0bu1sExRCHzBrEyAYzUVQ30xiiUf4pnngkeuPNRqljMcMN-TgCWP33MJ6S9haztQJSuz6lOFDdvsQMWEzx4Xa4u-VtjPyl9xMlkgmH1eV5B8Q5w1gpPoMScnypjrvc8bex67KA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] editing surfaces in two different Freesurfer versions
External Email - Use Caution Hi there, We are making the switch to Freesurfer v7.1 and wondering - can we continue editing surfaces in 7.1 that had previously undergone editing in versions 5.3 or 6.0? Thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer
External Email - Use Caution Hi there, Reposting this message (below). Would appreciate any guidance you can provide. Thanks, Lara From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lara Foland-Ross Sent: Friday, February 7, 2020 12:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer External Email - Use Caution Hello, I'm analyzing a large dataset using an LME model to examine longitudinal changes in brain structure that vary as a function of group (patients vs controls). Because some participants were scanned several years apart in early childhood, the intra-subject registration failed in the longitudinal processing stream. For this reason, my data were not initially processed using the longitudinal processing stream within Freesurfer. However, per this thread - https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55847.html - I still plan to use the LME model. As I understand it, this model assumes that the longitudinal processing stream was conducted. Therefore, I have the following questions: 1. would the "base" (aka within-subject template) for each subject be = time point 1? 2. would the "long run" for each subject be = each subject's individual time points? 3. assuming #1 and 2 are correct, would I need to set my directory structure to match that used in the longitudinal processing stream? For example, if I have 2 time points for subject 1234, and they are initially labeled "1234.time1" and "1234.time2", then in order to run the LME model, I would create a copy of "1234.time1" and rename the copy as "1234" to indicate to the software that this should be used as the base. And, I would also need to rename "1234.time1" and "1234.time2" as "1234.time1.long.1234" and "1234.time2.long.1234" to indicate that these folders should be used as the longitudinal time points. Does this seem appropriate? Thanks in advance for your help, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ 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] converting mgh to gii
External Email - Use Caution Hello Freesurfer experts, I'd like to convert my subjects' thickness mgh files to gii format for use in an analysis with a separate software package. Could you please confirm whether the following command is appropriate? Will this provide thickness maps that are in alignment? mris_convert -c lh.thickness.fwhm15.fsaverage.mgh fsaverage/surf/lh.white lh.thickness.fwhm15.fsaverage.gii Many thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer
External Email - Use Caution Hello, I'm analyzing a large dataset using an LME model to examine longitudinal changes in brain structure that vary as a function of group (patients vs controls). Because some participants were scanned several years apart in early childhood, the intra-subject registration failed in the longitudinal processing stream. For this reason, my data were not initially processed using the longitudinal processing stream within Freesurfer. However, per this thread - https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55847.html - I still plan to use the LME model. As I understand it, this model assumes that the longitudinal processing stream was conducted. Therefore, I have the following questions: 1. would the "base" (aka within-subject template) for each subject be = time point 1? 2. would the "long run" for each subject be = each subject's individual time points? 3. assuming #1 and 2 are correct, would I need to set my directory structure to match that used in the longitudinal processing stream? For example, if I have 2 time points for subject 1234, and they are initially labeled "1234.time1" and "1234.time2", then in order to run the LME model, I would create a copy of "1234.time1" and rename the copy as "1234" to indicate to the software that this should be used as the base. And, I would also need to rename "1234.time1" and "1234.time2" as "1234.time1.long.1234" and "1234.time2.long.1234" to indicate that these folders should be used as the longitudinal time points. Does this seem appropriate? Thanks in advance for your help, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] QDEC cluster output
External Email - Use Caution Hi Freesurfer experts, I’m running a simple qdec analysis to examine group differences in surface measures between a patient and control group, controlling for age and TBV. I noticed that when I run Monte Carlo Simulations (threshold=1.3, sign=abs), I get the following output in my terminal window: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWPCWPLow CWPHi NVtxs Annot 17.365 125481 2114.03-34.44.11.6 0.01660 0.01500 0.01820 4933 insula 23.851 73048 1830.45 -8.4 30.1 29.4 0.03440 0.03210 0.03670 3210 superiorfrontal 3 -3.248 128137 4923.73 -8.1 -64.05.8 0.00010 0.0 0.00020 7680 lingual Simulation complete. However, when I click on “Find clusters and go to max”, the output in my terminal window changes to be as follows: Generating cluster stats using min threshold of 1.3... Found 3 clusters Contrast: 'lh-Diff-Control-Klinefelter-Intercept-volume', 20fwhm, DOF: 35 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation - --- -- - - -- 1 -4. 334923.73 -12.0 -67.1 34.7 7680 precuneus 21.7799 92114.03 -26.3 23.8 -6.0 4933 lateralorbitofrontal 31.4634 211830.45-6.6 33.8 49.8 3210 superiorfrontal Lastly, I see that the x/y/z coordinates of the peak coordinates listed above are on the very edge of the corrected cluster. Yet, visual inspection of the peaks from uncorrected significance maps suggest that the peaks it is quite far from the “hottest” parts of the uncorrected significance maps. My questions are: 1. Why are these values different, and what values should I report? 2. Are the peaks listed above the center of gravity? Or highest p value of the cluster? Curious as to why the heatmap values are so different from the values above. Many thanks, Lara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hippocampus subfields and manual editing
External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's hippocampus. Final volumes of manually edited hippocampi were submitted to a repeated measures ANOVA which showed a significant main effect of diagnosis on the overall size of this structure (controlling for age and TBV). We recently submitted this paper and just received a request from a reviewer that asked that we run a subfield analysis on these data to better understand the regions driving this overall effect. What I'd like to know is: would the subfield approach *not* be recommended on this dataset considering that artifacts necessitated a good deal of manual intervention for the entire region? Second, if it a subfield approach *is* okay to run on these data, how can I feed in my manually edited volumes to ensure that the corrected segmentations of the entire hippocampus is used during subfield creation? thanks very much in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ 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] feeding data not processed with longitudinal pipeline into Linear Mixed Effects (LME) model
Hello Freesurfer experts, I have two longitudinal datasets. In each dataset, some participants have only a single timepoint. For this reason, I aim to run the Linear Mixed Effects (LME) Model described at https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels. I understand that it is recommended that before running LME, I process my data using the longitudinal stream (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing). However: 1. in one dataset, some participants were scanned several years apart in early childhood, which caused the intra-subject registration to fail in the longitudinal processing stream and 2. in the second dataset, editing of longitudinal timepoints was time prohibitive - several hours of edits were spent per brain at the cross-sectional level due to the use of an older sub-optimal pulse sequence. And, several more hours are required for the editing of each base or longitudinal timepoint. Given each of these circumstances, is it feasible/appropriate to run LME using data that was not initially processed using the longitudinal processing stream within Freesurfer? Thanks in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ 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] hippocampus subfields in longitudinal dataset
Thank you! A quick followup question:
I'm interested in running the new devel version (e.g., segmentHA_T1_long.sh
from
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala)
on my data which was originally processed using the longitudinal pipeline in
version 5.3.
Can you please confirm that this is appropriate?
Thanks,
Lara
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez,
Eugenio <e.igles...@ucl.ac.uk>
Sent: Thursday, September 14, 2017 12:12 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampus subfields in longitudinal dataset
Dear Lara,
The sh script implements a longitudinal segmentation algorithm that segments
both time points simultaneously using a subject specific atlas, improving the
reliability of the segmentation. You can read the details here
http://www.sciencedirect.com/science/article/pii/S1053811916303275
Cheers
Eugenio
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lara Foland-Ross
<lfol...@stanford.edu>
Sent: Thursday, September 14, 2017 2:38:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] hippocampus subfields in longitudinal dataset
Hello Freesurfer experts,
I have a longitudinal data set already processed in the longitudinal pipeline
of v5.3. I'd now like to use the hippocampus subfield commands available in 6.0.
I'm wondering whether I will arrive at the same result using either of the
following two approaches:
1. run "recon-all -s ${subjTp} -hippocampal-subfields-T1" separately on the
time1 and time 2 longitudinal scans
2. run longHippoSubfieldsT1.sh
Thanks in advance,
Lara
___
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] hippocampus subfields in longitudinal dataset
Hello Freesurfer experts,
I have a longitudinal data set already processed in the longitudinal pipeline
of v5.3. I'd now like to use the hippocampus subfield commands available in 6.0.
I'm wondering whether I will arrive at the same result using either of the
following two approaches:
1. run "recon-all -s ${subjTp} -hippocampal-subfields-T1" separately on the
time1 and time 2 longitudinal scans
2. run longHippoSubfieldsT1.sh
Thanks in advance,
Lara
___
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] problems with segmentHA_T1_long.sh
Hello, I ran a longitudinal analysis cortical structure in Freesurfer version 5.3. I'd now like to compute hippocampus subfields using the new beta version of the "Segmentation of hippocampal subfields and nuclei of the amygdala" tool (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala). I'm running into several errors when running segmentHA_T1_long.sh. Upon closer inspection of the script, it's not clear to me whether this tool is compatible with scans processed in the 5.3 version of the longitudinal pipeline. Can you please confirm? Thanks, Lara ___ 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] hippocampal subfield analysis - registered two scans prior to analysis
My apologies - there was a typo in my last message. The error reads that the program could not find mri/001.mgz: cibsr-i27-410:inProgress6.0b kel32$ pwd /Volumes/Xspace/Freesurfer/inProgress6.0b cibsr-i27-410:inProgress6.0b kel32$ ls 18512_T1_v5.3_hipp_v6.0 18512_hipp fsaverage cibsr-i27-410:inProgress6.0b kel32$ recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2 /Volumes/Xspace/Freesurfer/Liraglutide6.0b/rawdata/18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm T2hipp_in_long INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-OSX-dev-20160326 INFO: SUBJECTS_DIR is /Volumes/Xspace/Freesurfer/inProgress6.0b Actual FREESURFER_HOME /Volumes/ToolsMac/freesurfer6.0b -rw-rw-r-- 1 kel32 staff 1368492 Apr 26 08:33 /Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/scripts/recon-all.log Darwin cibsr-i27-410.stanford.edu 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Volumes/ToolsMac/freesurfer6.0b Previous: /Volumes/ToolsMac/freesurfer5.3 # #@# MotionCor Tue Apr 26 08:41:07 PDT 2016 ERROR: no run data found in /Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/mri. Make sure to have a volume called 001.mgz in /Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Darwin cibsr-i27-410.stanford.edu 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 recon-all -s 18512_T1_v5.3_hipp_v6.0 exited with ERRORS at Tue Apr 26 08:41:08 PDT 2016 For more details, see the log file /Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Can you please advise on how best to proceed? May thanks! Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Martin Reuter <mreu...@nmr.mgh.harvard.edu> Sent: Tuesday, April 26, 2016 6:06 AM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Hi Lara, mri/orig.mgz should be there also in the longitudinal directories. If it is missing, more might be wrong. I would recommend rerunning those long runs from scratch. Best, Martin On 04/25/2016 07:07 PM, Lara Foland-Ross wrote: > Thank you Eugenio! This worked like a charm. > > Wondering now if you could help me troubleshoot running this command on 2 > scans from a single subject (time 1 and time 2) that were processed using the > longitudinal pipeline in version 5.3. > > I ran the following: > > recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2 > 18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm > T2hipp > > and got the error that Freesurfer could not find mri/orig file... It is > indeed not there, presumably because it isn't produced after the creation and > editing of the long.base timepoints. I read elsewhere on the list that the > hippocampal subfield analysis could be run on the individual longitudinal > timepoints but can't seem to get this to work. Can you advise? > > Many thanks in advance for your continued help! > Lara > > > Lara Foland-Ross, Ph.D. > Research Associate > Center for Interdisciplinary Brain Sciences Research > Stanford University School of Medicine > 401 Quarry Road, Room 1356 > Stanford, CA 94305-5795 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias > <e.igles...@bcbl.eu> > Sent: Tuesday, April 5, 2016 3:59 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two > scans prior to analysis > > Almost correct! > recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 > subj1_hipp/I0001.dcm T2hipp > Also, this is assuming that you have defined the environment variable > SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd . > Cheers, > /Eugenio > > > Juan Eugenio
Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Thank you Eugenio! This worked like a charm. Wondering now if you could help me troubleshoot running this command on 2 scans from a single subject (time 1 and time 2) that were processed using the longitudinal pipeline in version 5.3. I ran the following: recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2 18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm T2hipp and got the error that Freesurfer could not find mri/orig file... It is indeed not there, presumably because it isn't produced after the creation and editing of the long.base timepoints. I read elsewhere on the list that the hippocampal subfield analysis could be run on the individual longitudinal timepoints but can't seem to get this to work. Can you advise? Many thanks in advance for your continued help! Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.igles...@bcbl.eu> Sent: Tuesday, April 5, 2016 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Almost correct! recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp/I0001.dcm T2hipp Also, this is assuming that you have defined the environment variable SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd . Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Lara Foland-Ross" <lfol...@stanford.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, April 6, 2016 12:29:09 AM Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Hi Eugenio, Thank you so much for the quick and helpful reply. I checked the images in Freeview and they actually line up quite nicely! Can you provide further guidance on how to run recon-all once with both the -all and the hippocampal-subfields-T1T2 flags? For example, in my rawdata directory, I have two folders: subj1_T1 and subj1_hipp. I cd'd into the rawdata folder and ran the following with no success: recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp T2hipp Is this directory setup correct? And can you please point out the errors in the above recon-all command? Many thanks again for your help! Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.igles...@bcbl.eu> Sent: Tuesday, April 5, 2016 2:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview? 3. If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags. Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Lara Foland-Ross" <lfol...@stanford.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Hello, I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain. My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I m
Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis
Hi Eugenio, Thank you so much for the quick and helpful reply. I checked the images in Freeview and they actually line up quite nicely! Can you provide further guidance on how to run recon-all once with both the -all and the hippocampal-subfields-T1T2 flags? For example, in my rawdata directory, I have two folders: subj1_T1 and subj1_hipp. I cd'd into the rawdata folder and ran the following with no success: recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 subj1_hipp T2hipp Is this directory setup correct? And can you please point out the errors in the above recon-all command? Many thanks again for your help! Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.igles...@bcbl.eu> Sent: Tuesday, April 5, 2016 2:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Dear Lara, Two things: 1. You don't need to recon the T2 scan. The recon-all stream only works for T1 data anyway. 2. The registration between the T1 and T2 scans happens internally (with a mri_register command similar to the one you wrote) during the hippocampal subfield segmentation. You only need to coarsely align the T1 and T2 scans manually if the initial alignment between the two is terrible. What happens when you open them both in Freeview? 3. If the alignment is decent, just run recon-all once, with both the -all and the -hippocampal-subfields-T1T2 flags. Feel free to send me the T1 and T2 scans if you are not sure whether they are sufficiently well aligned or not. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Lara Foland-Ross" <lfol...@stanford.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, April 5, 2016 11:14:39 PM Subject: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis Hello, I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain. My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned. I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands: mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV. Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss. Many thanks in advance, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ 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] hippocampal subfield analysis - registered two scans prior to analysis
Hello, I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain. My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned. I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands: mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV. Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss. Many thanks in advance, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ 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] initial processing in devel 6.0 version and final stats processing in stable version 6.0?
Hi Freesurfer experts, We'd like to begin a cortical thickness and hippocampal subfield analysis in the most recent devel version of FS. Can you please confirm that we will we be able to run the analysis of these data in the final stable release of 6.0? Thanks, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ 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] registration errors in longitudinal analysis
Dear Freesurfer experts, I am working on a longitudinal analysis of cortical structure and am experiencing some errors with registration. I have 3 timepoints for each participant: time 1: age 2 time 2: age 5 time 3: age 10 Time 1 and 2 are from a 1.5T scanner. Time 3 is from a 3T scanner. Despite the age range and scanner difference, the registrations in the longitudinal pipeline (I'm using version 5.3) are performing relatively well. However, in comparing the LONG outputs slice by slice, it appears that in a majority of my subjects, there are some minor mismatches in brain anatomy. An example is attached here (minor_reg_error.jpg). In other instances, there are more substantial registration errors. Again, example attached here (major_reg_error.jpg). My question is how much mismatch is acceptable? And how can I go about fixing poor registrations in subjects who have significant errors in alignment? Many thanks in advance, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 ___ 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] matlab script to convert array back to thickness file format?
Hi there, We're using load_mgh.m to load several individual (single subject) cortical thickness maps (each 1X163842) that we'll use to compute a group-level statistic in matlab. We're not changing the dimensionality or order of the information loaded and we would like to know if there is a matlab script we might use to convert our resulting (1X163842) array of statistical values back into a .mgh file that can be read on FreeSurfer. Thanks! Lara -- Lara Foland-Ross Postdoctoral Fellow Stanford Mood and Anxiety Disorders Laboratory Department of Psychology Stanford University 450 Serra Mall, Stanford, CA 94305 Jordan Hall, Building 420, Room 142 ___ 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.
