[Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash
External Email - Use Caution Hi there, I am a Master's student who is looking to segment the hippocampus and analyze diffusion data of the segments. I am trying to utilize the segmentation function with this command: segmentHA_T1.sh subj01 But I am met with this error saying that Matlab has crashed. The crash log is attached to this email. I have freesurfer version 7.1.1, running on MacOs 11.7.10. I have followed your website instructions to download Matlab R2014b. Following the installation process of Matlab, I was met with this message: Installing Product: MATLAB Compiler Runtime - Core 8.4 (Oct 08, 2023 11:29:15) Installing Product: MATLAB Compiler Runtime - GPU 8.4 (Oct 08, 2023 11:29:21) Notes: On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable: /var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/bin/maci64: (Oct 08, 2023 11:29:21) Exiting with status 0 (Oct 08, 2023 11:29:21) End - Successful. Finished R2014b installed successfully in /Applications/freesurfer/7.1.1/MCRv84 And so I have appended the path using this code into my bashrc profile: export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.aMmBemHB/install-target/v84/bin/maci64 I am wondering if I can get some help with running the hippocampus segmentation protocol . Thank you so much for your time, I greatly appreciate your support. matlab_crash_dump.28607-2 Description: Binary data ___ 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] Freesurfer crash when loading "volume" surf
External Email - Use Caution Hi there, yes, I can open an MRI volume just fine, using the code $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz But when it comes to surface files, it opens some of the surface files while crashing with other ones. Do you happen to know anything about this? Thank you, M On Fri, Oct 27, 2023 at 7:44 AM Wang, Ruopeng wrote: > Can you load a MRI volume? From the crash report, it seems to be a system > related issue that triggered the crash. > > Ruopeng > > On Oct 26, 2023, at 8:42 PM, Mirsol Choi wrote: > > External Email - Use Caution > > Hi there, > > I have processed a t1 image using recon-all function, and when I try to > open the surface file "lh.volume" or "rh.volume", freesurfer crashes > everytime. This crash also occurs for other surface files as well, such as > "lh.area.pial". > > Attached is the error message, do you know how I can go about this? > > For your reference I am using a macOS, running freesurfer 7.4.1. > > Thank you, I look forward to hearing from you. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1J_rhra9wCe2cs4-qMCeYstu-FJFahUJnaobujngFGI_fJqG5_Y6iMZqK1NfFboSuMnYCQ-78qG9095rtcEZTU9DLSgHmbgcweDDgH6Wiu3XN1dF2RNoZEG_10q0OvrK7TOGYXNLqbcvuL7LsL0CsOQH1fm3SZsC7220NlxLxaUE_uTSH1XRLRy9aR8HrGYFMnbvyRKxNYcKjRxnLhBpLiwfzjgKR2ILEV6WNgkpwulgdMPMXvnfD1M0zBrkFdqLrCxLDQWtBPX-FOoVnsKjwTMF2Vr0o8eoe7xGbyMpc4U1TBEfdqxEKBUPAcqRvvQaWeUG9hWipIlcpJS7eVR1zrw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1J_rhra9wCe2cs4-qMCeYstu-FJFahUJnaobujngFGI_fJqG5_Y6iMZqK1NfFboSuMnYCQ-78qG9095rtcEZTU9DLSgHmbgcweDDgH6Wiu3XN1dF2RNoZEG_10q0OvrK7TOGYXNLqbcvuL7LsL0CsOQH1fm3SZsC7220NlxLxaUE_uTSH1XRLRy9aR8HrGYFMnbvyRKxNYcKjRxnLhBpLiwfzjgKR2ILEV6WNgkpwulgdMPMXvnfD1M0zBrkFdqLrCxLDQWtBPX-FOoVnsKjwTMF2Vr0o8eoe7xGbyMpc4U1TBEfdqxEKBUPAcqRvvQaWeUG9hWipIlcpJS7eVR1zrw/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 > https://secure-web.cisco.com/10iSJWJYst_Gdjpc8RTflQz9sqOepwJXdj7Hjyz9266K6o91-6kOruj1CYtr6BxL2xhyFxXEIoL0XxRNmRVCpllG-g9qc8V04V5_cIuf1RmgqfhVbeEFbrTqU6LYIxgV9UVp5LtXE1wkbp-V5SyCs_CCva0pGIe0uDFvWjneTcnaZvzEi7MFgeR99SeVnZCpMhaSKqMbk767u18giwSJzOBCwZcVglsr8MNH5xBIQZuK6oX6Qu0CTGFs4BsZqcmyZ_Y0BlgNKDh04iB-w3dXaYRhD9l9FByNg3XG0ATOR0yL9f6Ut1LZyYp3c3dqTLWUIBd8nzGdd_uNVnWoF6tsIsw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/10iSJWJYst_Gdjpc8RTflQz9sqOepwJXdj7Hjyz9266K6o91-6kOruj1CYtr6BxL2xhyFxXEIoL0XxRNmRVCpllG-g9qc8V04V5_cIuf1RmgqfhVbeEFbrTqU6LYIxgV9UVp5LtXE1wkbp-V5SyCs_CCva0pGIe0uDFvWjneTcnaZvzEi7MFgeR99SeVnZCpMhaSKqMbk767u18giwSJzOBCwZcVglsr8MNH5xBIQZuK6oX6Qu0CTGFs4BsZqcmyZ_Y0BlgNKDh04iB-w3dXaYRhD9l9FByNg3XG0ATOR0yL9f6Ut1LZyYp3c3dqTLWUIBd8nzGdd_uNVnWoF6tsIsw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > 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 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] dt_recon question
External Email - Use Caution Hi there, I am currently going through the dt_recon tutorial on your website and I just have a quick question regarding the recon-all and dt_recon commands on freesurfer. For me to process dt_recon, my understanding is that I must process recon-all first. But where my confusion lies is: - do I perform recon-all on the actual dwi.nii.gz image, then dt_recon with the same dti files (including the bval and bvec of the same dwi.nii.gz file) OR - should I have two separate sets of data, one T1 and one DTI, and perform recon-all on T1 images and take DWI images from the same subject to perform dt_recon? My understanding was that the second bullet is the right way to go since the dt_recon uses the outputs from T1 recon-all to register properly. Please let me know which one is correct, and if I am missing something. Thank you so much for your help, I really appreciate your time. M ___ 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.
[Freesurfer] Finding Intracranial volume
External Email - Use Caution Hi fellow freesurfers! I am a Masters student currently working with diffusion images. I would like to ask you experts how I can obtain ICV from my T1/T2 or diffusion images. Is there a certain output from recon-all that produces intracranial volume? Or is there a different command I must use? Thank you all so much for your time. I look forward to hearing from you. Peter ___ 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] Finding Intracranial volume
External Email - Use Caution Thank you Paul! On Wed, Nov 1, 2023 at 3:33 PM Wighton, Paul wrote: > Hi Peter, > > recon-all produces an estimate of ICV. In aseg.stats there is a line > that looks like: > > # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total > Intracranial Volume, 1696008.240403, mm^3 > > You can read more about how it is computed at > https://secure-web.cisco.com/1jljg6dkUgcWIVn7pjegiZm1C7K-LPzZxj3WP5JbiWaMqmbEdmAN3LEIHV65Yh-u6aVwJU3HxO34dyC0NzPsI2_KBOm8LgjyIOhK8fu5Xd-Svi9wPALxpmh_kvsXcbO365N6zYbK509nkCZF58iv7-yueDf7bRlFlVaa7vFBR_gWX6_rUVqZJjogo0Oj0WWfogxVckKBBb7ilATdRDyy638SXB8IUlaNTvPhPRyF135ckIUSpOUHwEtJ6VbKmZ-IeL3DYwC8Z7ncgO996v5ZZvCzJwoldXgcHBk5e42Ykchma6hd8PGQlWFc-JnHggT7vjT2Y6PMVHhOi-U4h71Fo6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FeTIV > > -Paul > > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mirsol Choi < > mir...@ualberta.ca> > Sent: Wednesday, November 1, 2023 5:23 PM > To: Freesurfer support list > Subject: [Freesurfer] Finding Intracranial volume > > External Email - Use Caution > > Hi fellow freesurfers! > > I am a Masters student currently working with diffusion images. > > I would like to ask you experts how I can obtain ICV from my T1/T2 or > diffusion images. > > Is there a certain output from recon-all that produces intracranial > volume? Or is there a different command I must use? > > Thank you all so much for your time. I look forward to hearing from you. > > Peter > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/13XlueYafVGyOGGN2B7Vq-bIYnYpHPG5ChpLQCW2JmPWRq1doEFJd2zHwqscgSE72GLMMMCt3yd4D8qUXhg1cGWOQnY6O08ouIXU8kQqF2rO38Z8zKvdrF7dkifO4A5QU2xlkIUgkQi2TsI6BbIQq6URiDqayC5ym056muZjeR03vXzmDEzDP950c5f51xcsQhMqWytjFcCfRWDD9MUUK0gxwFRq2byk_0iGDLj-78b1guw0bQENMID69F5pnAiav7FqMxjhbqKZ6s_T2cDNwvU-DukTdSzT4oBDWPwV5sYeizfHhh0lJoJMoiel_J8wcnC6IbLxT3SnS50vv20qttQ/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 > https://secure-web.cisco.com/1cjuEDTh5NQZgidaXBFrj88NoNAUF9LkKpBC51JnH6-FrwgVeG1BgH7IqRqE45eiDznYThjxfLpPPsZPCb4a35BByCMkuyaZeq74BzPgBqOxkba7T3c834e-pYfBrZN7NRaPi93fsQa-xJz7f_NRsyn5jQJv922YL5KiIPjRlvngCzvZfPW9FJ2P4ZQ2rv-XvbevI-YtXIXd0hI4ckulF91Sha3vIgRy7_grLBAISgct81CBuzcjVfq8bQz9dv1D3w5CjJ-xw3BaFCXb6rwouoGj5JTTf19vu-6hz-NXN7iH4njI_DTBQ-8O9EDxYvm6xRyatYrQMwOemySdhbiO-_A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1cjuEDTh5NQZgidaXBFrj88NoNAUF9LkKpBC51JnH6-FrwgVeG1BgH7IqRqE45eiDznYThjxfLpPPsZPCb4a35BByCMkuyaZeq74BzPgBqOxkba7T3c834e-pYfBrZN7NRaPi93fsQa-xJz7f_NRsyn5jQJv922YL5KiIPjRlvngCzvZfPW9FJ2P4ZQ2rv-XvbevI-YtXIXd0hI4ckulF91Sha3vIgRy7_grLBAISgct81CBuzcjVfq8bQz9dv1D3w5CjJ-xw3BaFCXb6rwouoGj5JTTf19vu-6hz-NXN7iH4njI_DTBQ-8O9EDxYvm6xRyatYrQMwOemySdhbiO-_A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > 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 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] Mapping input volume (fa.nii) to hippocampus segmentation volume
External Email - Use Caution Hello Freesurfers, I am trying to segment the hippocampus into its subfields and take the FA values from each subfield area. I am able to segment the hippocampus using the command (segmentHA_T1.sh) and I was also able to perform the dt-recon function on dwi data. I am trying to map the fa.nii file from dt-recon into the hippocampus subfield volume rh.hippoAmygLabels-T1.v22.HBT.mgz, however when I run the code that is provided by vol2subfield -help: vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --outreg outreg.lta or vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --o fa.rh.hbt.mgz I am met with a message stating "set: Variable name must contain alphanumeric characters." How can I fix this "variable name must contain alphanumeric characters" issue and run this command? Thank you all for your time, help and expertise. M ___ 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.
[Freesurfer] vol2subfield troubleshoot
External Email - Use Caution Hello Freesurfers, My name is Mirsol and I am currently trying to obtain FA values from particular hippocampus subfields by registering our fractional anisotropy map (FA.nii.gz) from dt_recon command and our hippocampus segmentations from the command segmentHA_T1.sh. I have followed the protocol on the website "Segmentation of hippocampal subfields and nuclei of the amygdala" to perform the segmentation, and at the bottom of the website, it mentions: "6. Multimodal integration To extract values within the subfields from another modality (eg, DTI or fMRI), use vol2subfield. Run with --help for examples." Upon using vol2subfield --help on UNIX (macOS), I was shown these scripts: 1. To get a registration between an input volume and a subfield volume vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v22.HBT.mgz --outreg outreg.lta 2. To map the input volume into the subfield volume space vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v22.HBT.mgz --o fa.rh.hbt.mgz 3. To compute segmentation statistics of the input volume vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v22.HBT.mgz \ --o fa.rh.hbt.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol avgwfvol.mgz I have tried all three codes presented here, but I am met with this message when I do. "set: Variable name must contain alphanumeric characters." I am quite unsure what to do from here and have not been able to troubleshoot this issue. If someone out there could offer some advice or support, I will be forever grateful. Thank you so much for your time, Mirsol ___ 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.
[Freesurfer] Cannot locate reg.lta
External Email - Use Caution
Hi there,
I am currently trying to run vol2subfield command that allows us to get a
registration between an input volume (ie. FA map) to a subfield volume
(hippocampus segmentation).
Upon tying vol2subfield --help, this was the message provided:
"vol2subfield (run with --help to get more info)
Required inputs
--i input volume
--sf subfield volume : full path or relative to subject/mri
--reg reg.lta : registration that maps input volume to conformed
Outputs
--o output volume
--outreg outreg.lta : registration between invol and subfield
--stats stats.dat : run mri_segstats with --sum stats.dat output
--avgwf avgwf.dat : run mri_segstats with --avgwf avgwf.dat output
--avgwfvol avgwfvol : run mri_segstats with --avgwfvol avgwfvol output
Other options
--ctab ctab : color table to use with mri_segstats. Default is
/home/masterslab/freesurfer/FreeSurferColorLUT.txt
--nearest : use nearest neighbor interpolation (default)
--trilin : use triliear interpolation
--cubic : use cubic interpolation
--tmp tmpdir : for debugging
These are meant to make it easy to interface with the various subfield
segs produced by FS
--lh.hippoamyg : set subfield to lh.hippoAmygLabels-T1.v21.mgz
--rh.hippoamyg : set subfield to rh.hippoAmygLabels-T1.v21.mgz
--lh.hbt : set subfield to lh.hippoAmygLabels-T1.v21.HBT.mgz
--rh.hbt : set subfield to rh.hippoAmygLabels-T1.v21.HBT.mgz
--thalamus : set subfield to ThalamicNuclei.v10.T1.mgz
--brainstem: set subfield to brainstemSsLabels.v12.mgz
vol2subfield 7.4.1
vol2subfield provides routines that make it easier to integrate
arbitrary volumes with volumes that share a RAS space ("header
registration") with the orig volume in the FreeSurfer mri folder.
This script was written to manage "subfield" segmentations (eg,
hippocampal, amygdalar, thalamic, and brainstem), but it can be used
much more generally.
The input registration is the LTA registration between the input
volume and the orig.mgz (eg, computed with bbregister or
mri_coreg). IF THIS REGISTRATION IS INACCURATE THEN THE OUTPUT OF THIS
SCRIPT WILL BE WRONG!! To check the input registration run
tkregisterfv --mov invol --reg reg.lta --surfs
This script can have three types of outputs:
1. To get a registration between an input volume and a subfield volume
vol2subfield --i fa.nii.gz --reg reg.lta --sf
rh.hippoAmygLabels-T1.v21.HBT.mgz --outreg outreg.lta
outreg.lta will map fa.nii.gz to
rh.hippoAmygLabels-T1.v21.HBT.mgz. Note that the "subfield" volume can
be anything that shares a RAS space with the orig.mgz (eg,
orig/001.mgz). It does not need to be a segmentation volume.
2. To map the input volume into the subfield volume space
vol2subfield --i fa.nii.gz --reg reg.lta --sf
rh.hippoAmygLabels-T1.v21.HBT.mgz --o fa.rh.hbt.mgz
fa.rh.hbt.mgz will be the fa.nii.gz sampled into the space of
rh.hippoAmygLabels-T1.v21.HBT.mgz (ie, it will be in voxel-for-voxel
registration). Again, the "subfield" volume can be anything that
shares a RAS space with the orig.mgz (eg, orig/001.mgz). It does not
need to be a segmentation volume. This volume is appropriate for running
mri_segstats. Note that there is not an output registration, but, if you
want to save it, just use --outreg as above.
3. To compute segmentation statistics of the input volume
vol2subfield --i fa.nii.gz --reg reg.lta --sf
rh.hippoAmygLabels-T1.v21.HBT.mgz \
--o fa.rh.hbt.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol
avgwfvol.mgz
This will create three files (but you do not need to specify all of
them) using mri_segstats (and excluding the 0 segmentation). See
mri_segstats --help for what each of these outputs mean. Note that
there is not an output registration, but, if you want to save it, just
use --outreg as above.
For information about the subfields created by FS, see
https://secure-web.cisco.com/17XF0ZnFdoeIqVKRGWwoBOtca4h4jeD6xXfzmAx0GK1TEHc6ku1GhIkdFBzbn36o1rcif4KRHO87IKXpdHGLZw1k-nZDyHz7Vu8uGwXT44KJEFVNXejSueSj1edsZc0D_huZabn0k0PREK7HsGlbw_JJp6YTehNNfStifBUn3N_zQAdgimUKnTIoZfx2y4VFLImcdmDMbUEFvkRKbMxPjcFDvSodvokrUNK-MvWRCpAyGS791OuFmDb1bKLcPrGDl5l1YMPd9-C_jIGJCHthGXRzd_AbIKNJbTeSISn5f_gtDVP5TOmez29S2bKF_QC1sWpcpYbHYx96jWplaNKSkjw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala
http://secure-web.cisco.com/1r9hdzClzfpb9wkcYJZzj-5x_1dXL8bvIXvPjcusisxNujtH5dYbdeMeOZI3hVO5OH-AJhxNvDP3jOSU2eMfIJ14UqSsl3htId6fnUaNMEe2yGFUve4qPdpc6cQuVpiRO5_VGD2WYb0-jKtf1iKI752MKosvbNWWL1SE0IZPABCzhKd-k-id0WN6O07i7BSy0JHF8Vx_-c7Te0SKbxEP9BS-KDDZ-7NcGDUVujRtWQwz0_-SoVaVmOAd1Y_rakZ2OvVahfuVFrZHYJxFBIPHnMaKRcfuNMwX_lZ7KxS5J1lGSkOcV92izLtUFFxpFgQCc2sEU3B_JvOCrMPFDXXLCNA/http%3A%2F%2Ffreesurfer.net%2Ffswiki%2FThalamicNuclei
https://secure-web.cisco.com/1zX2UZrV6ZpJQDeBcxFrsoi9bFd1JnN4YH4d0ttvaTwhHgn1HjqbunM0jDue4eUdn1YlXPQ361LMxCIeJFLbz0gcdJRYogkD_F3-br9S9jYnVdyU0zhc8tH0X4lshFbn84uCJmaueA-65PEIoEm-e1nTelyt7syg_uBH5_b
Re: [Freesurfer] Cannot locate reg.lta
External Email - Use Caution
Thank you for your prompt response!
On Tue, Nov 28, 2023 at 5:07 PM Douglas N. Greve
wrote:
> You have to create your own registration. Eg, try bbregister
>
> On 11/28/2023 6:42 PM, Mirsol Choi wrote:
>
> External Email - Use Caution
>
> Hi there,
>
> I am currently trying to run vol2subfield command that allows us to get a
> registration between an input volume (ie. FA map) to a subfield volume
> (hippocampus segmentation).
>
> Upon tying vol2subfield --help, this was the message provided:
>
> "vol2subfield (run with --help to get more info)
>
> Required inputs
> --i input volume
> --sf subfield volume : full path or relative to subject/mri
> --reg reg.lta : registration that maps input volume to conformed
>
> Outputs
> --o output volume
> --outreg outreg.lta : registration between invol and subfield
> --stats stats.dat : run mri_segstats with --sum stats.dat output
> --avgwf avgwf.dat : run mri_segstats with --avgwf avgwf.dat output
> --avgwfvol avgwfvol : run mri_segstats with --avgwfvol avgwfvol output
>
> Other options
> --ctab ctab : color table to use with mri_segstats. Default is
> /home/masterslab/freesurfer/FreeSurferColorLUT.txt
> --nearest : use nearest neighbor interpolation (default)
> --trilin : use triliear interpolation
> --cubic : use cubic interpolation
> --tmp tmpdir : for debugging
>
> These are meant to make it easy to interface with the various subfield
> segs produced by FS
>--lh.hippoamyg : set subfield to lh.hippoAmygLabels-T1.v21.mgz
>--rh.hippoamyg : set subfield to rh.hippoAmygLabels-T1.v21.mgz
>--lh.hbt : set subfield to lh.hippoAmygLabels-T1.v21.HBT.mgz
>--rh.hbt : set subfield to rh.hippoAmygLabels-T1.v21.HBT.mgz
>--thalamus : set subfield to ThalamicNuclei.v10.T1.mgz
>--brainstem: set subfield to brainstemSsLabels.v12.mgz
>
> vol2subfield 7.4.1
>
> vol2subfield provides routines that make it easier to integrate
> arbitrary volumes with volumes that share a RAS space ("header
> registration") with the orig volume in the FreeSurfer mri folder.
> This script was written to manage "subfield" segmentations (eg,
> hippocampal, amygdalar, thalamic, and brainstem), but it can be used
> much more generally.
>
> The input registration is the LTA registration between the input
> volume and the orig.mgz (eg, computed with bbregister or
> mri_coreg). IF THIS REGISTRATION IS INACCURATE THEN THE OUTPUT OF THIS
> SCRIPT WILL BE WRONG!! To check the input registration run
> tkregisterfv --mov invol --reg reg.lta --surfs
>
> This script can have three types of outputs:
>
> 1. To get a registration between an input volume and a subfield volume
>
> vol2subfield --i fa.nii.gz --reg reg.lta --sf
> rh.hippoAmygLabels-T1.v21.HBT.mgz --outreg outreg.lta
>
> outreg.lta will map fa.nii.gz to
> rh.hippoAmygLabels-T1.v21.HBT.mgz. Note that the "subfield" volume can
> be anything that shares a RAS space with the orig.mgz (eg,
> orig/001.mgz). It does not need to be a segmentation volume.
>
> 2. To map the input volume into the subfield volume space
>
> vol2subfield --i fa.nii.gz --reg reg.lta --sf
> rh.hippoAmygLabels-T1.v21.HBT.mgz --o fa.rh.hbt.mgz
>
> fa.rh.hbt.mgz will be the fa.nii.gz sampled into the space of
> rh.hippoAmygLabels-T1.v21.HBT.mgz (ie, it will be in voxel-for-voxel
> registration). Again, the "subfield" volume can be anything that
> shares a RAS space with the orig.mgz (eg, orig/001.mgz). It does not
> need to be a segmentation volume. This volume is appropriate for running
> mri_segstats. Note that there is not an output registration, but, if you
> want to save it, just use --outreg as above.
>
> 3. To compute segmentation statistics of the input volume
>
> vol2subfield --i fa.nii.gz --reg reg.lta --sf
> rh.hippoAmygLabels-T1.v21.HBT.mgz \
> --o fa.rh.hbt.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol
> avgwfvol.mgz
>
> This will create three files (but you do not need to specify all of
> them) using mri_segstats (and excluding the 0 segmentation). See
> mri_segstats --help for what each of these outputs mean. Note that
> there is not an output registration, but, if you want to save it, just
> use --outreg as above.
>
>
> For information about the subfields created by FS, see
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1Bcw_SYnH0V5_rsKV3Q9Pgyyj6vH2LSJ7eFqgpEQHoLHncVU-vwWLrjcV2BEp7H3xFf3EU-fKagwk-93cZDdhg6qbdBNDNzk35vy
[Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution Hello there, I am wondering if there is a way to convert register.dat file produced from dt_recon to reg.lta. I need a reg.lta file that contains registration between the DTI data and processed (recon-all) T1 data. I have tried to perform bbregister, but the alignment is completely off. Thank you so much for your time! Mirsol ___ 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] Converting register.dat file to reg.lta
External Email - Use Caution Hi Yujing, I really appreciate your quick response. The following is the error I get when I try to perform this: Mirsols-MacBook-Pro:dtrecon mirsolchoi$ lta_convert --inreg register.dat --outreg reg.lta 7.4.1 --inreg: register.dat input TK REG transform. --outreg: reg.lta output reg.dat matrix. INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. error: corRead(): can't open file /Users/mirsolchoi/Desktop/subjects/sub-001/dtrecon/COR-.info ERROR readREG: cannot read src MRI Mirsols-MacBook-Pro:dtrecon mirsolchoi$ Is there an additional file I need to complete this process? Thank you so much for your time. Mirsol On Wed, Nov 29, 2023 at 3:24 PM Huang, Yujing wrote: > You can try lta_convert. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Mirsol Choi > *Sent:* Wednesday, November 29, 2023 5:19 PM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Converting register.dat file to reg.lta > > > > *External Email - Use Caution* > > Hello there, > > > I am wondering if there is a way to convert register.dat file produced > from dt_recon to reg.lta. I need a reg.lta file that contains registration > between the DTI data and processed (recon-all) T1 data. > > > > I have tried to perform bbregister, but the alignment is completely off. > > > > Thank you so much for your time! > > Mirsol > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1zzlvYJc5T32vCjS1K8v8ZlPN6eeYADrFDIstXIETzUM6rPNfZCqlx1FynjTqlfu6S34aqEatZuKRZs2wr1dsd3zdLiZfXiS--s-au26O8n4vYtdS6hTZXPRmbMwsKgPOUyBhzwRzfmpj2e504WULnnxGgg2aDR4zWxspSKN1E3FoVpyfnSr3vL_SJonRCVW-ENaJOrNlbAFTvjQ5VkSP3Wx_xCte0P8BNZT6d5mOtTFCF20ckxPDDWTPfvGIfXWvBIZnJ2HE8790vLymblOd5h7fRMDT8ZnEuBN5vEZscSF_RB1_xVNelSTyepz1mdP6dWClmntOFYOTkvfQtFdwxw/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 > https://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHCCpLiRnY_Xic-gf_i0YJPObJDRTQy6wChMCTy7W9NR25M_2UGsme7eE5kwuSaQwM2WbJNMkn4uYnqSsdOTobOs34hJAk79batugUcDbe7gs6n5HF31hmCL7Lqa6JnYln4t78ARKckYX4lNNkwXn8caqLbeK6WvbDRVB7YetDWOU3xvOSW_XOQkM5yLxYEqhICyCww49G7TU6p-C2WlPC3Wglx5UfSubuH-paPdDHSGJIdGm0KZP1_rINtN533acwj9ByOk7q9cWjJ1HAEbtCSHdYga6HXQgxd3-egmn2g/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHCCpLiRnY_Xic-gf_i0YJPObJDRTQy6wChMCTy7W9NR25M_2UGsme7eE5kwuSaQwM2WbJNMkn4uYnqSsdOTobOs34hJAk79batugUcDbe7gs6n5HF31hmCL7Lqa6JnYln4t78ARKckYX4lNNkwXn8caqLbeK6WvbDRVB7YetDWOU3xvOSW_XOQkM5yLxYEqhICyCww49G7TU6p-C2WlPC3Wglx5UfSubuH-paPdDHSGJIdGm0KZP1_rINtN533acwj9ByOk7q9cWjJ1HAEbtCSHdYga6HXQgxd3-egmn2g/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > 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 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] Converting register.dat file to reg.lta
External Email - Use Caution Hi Yujing, Thanks again for your quick response. For src image, do you mean the file that I used to generate the original register.dat file? For instance, the register.dat file was produced by running dt_recon (using input of dti.nii.gz). Is this dti.nii.gz for file I should use for correct conversion to reg.lta? Thank you! M On Wed, Nov 29, 2023 at 3:40 PM Huang, Yujing wrote: > Try to specify –src <> and –trg <> > > --src > > specify src image geometry (mov volume for TKREG/register.dat) > > --trg > > specify trg image geometry > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Mirsol Choi > *Sent:* Wednesday, November 29, 2023 5:32 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Converting register.dat file to reg.lta > > > > *External Email - Use Caution* > > Hi Yujing, > > > > I really appreciate your quick response. > > > > The following is the error I get when I try to perform this: > > > > Mirsols-MacBook-Pro:dtrecon mirsolchoi$ lta_convert --inreg register.dat > --outreg reg.lta > > 7.4.1 > > > > --inreg: register.dat input TK REG transform. > > --outreg: reg.lta output reg.dat matrix. > > INFO: This REGISTER_DAT transform is valid only for volumes between COR > types with c_(r,a,s) = 0. > > error: corRead(): can't open file > /Users/mirsolchoi/Desktop/subjects/sub-001/dtrecon/COR-.info > > ERROR readREG: cannot read src MRI > > Mirsols-MacBook-Pro:dtrecon mirsolchoi$ > > > > > > Is there an additional file I need to complete this process? > > > > Thank you so much for your time. > > > > Mirsol > > > > On Wed, Nov 29, 2023 at 3:24 PM Huang, Yujing > wrote: > > You can try lta_convert. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Mirsol Choi > *Sent:* Wednesday, November 29, 2023 5:19 PM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Converting register.dat file to reg.lta > > > > *External Email - Use Caution* > > Hello there, > > > I am wondering if there is a way to convert register.dat file produced > from dt_recon to reg.lta. I need a reg.lta file that contains registration > between the DTI data and processed (recon-all) T1 data. > > > > I have tried to perform bbregister, but the alignment is completely off. > > > > Thank you so much for your time! > > Mirsol > > ___ > Freesurfer mailing list > 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/1U-iwgipV7SsqgXQL-zgbDVJqpHaIRbL1c5gz95C4fRVuka0rsunsvYt2KoHaCG5xq1Hi6KbPg_YSoLa2Gdv2-DUTzu9Si4-sUc3yz-TweNnQRxLFXu0vm63pibsdEw47MpGcaovRvNmbbkyKOJipAzapnG3Is4KTesdKl1_walbzONSO6UigAk-p0YDWu-zSilovg93MdDynR0a_3J6sP3-_j4-SnEsW4VBgkQLuLF6LKdmpCBrsbjlyUrQnJKUcuUEszQj06diMwzUIwVQ-qFGvSwWX8jF5qDrvAgkYGziOmmvqsPPVsTNEAwandQvo1axsJSXvJN9mki8T8CObyQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/1zzlvYJc5T32vCjS1K8v8ZlPN6eeYADrFDIstXIETzUM6rPNfZCqlx1FynjTqlfu6S34aqEatZuKRZs2wr1dsd3zdLiZfXiS--s-au26O8n4vYtdS6hTZXPRmbMwsKgPOUyBhzwRzfmpj2e504WULnnxGgg2aDR4zWxspSKN1E3FoVpyfnSr3vL_SJonRCVW-ENaJOrNlbAFTvjQ5VkSP3Wx_xCte0P8BNZT6d5mOtTFCF20ckxPDDWTPfvGIfXWvBIZnJ2HE8790vLymblOd5h7fRMDT8ZnEuBN5vEZscSF_RB1_xVNelSTyepz1mdP6dWClmntOFYOTkvfQtFdwxw/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/13WPJxA1Btfx5KYlK6mbOcr9MFjhpgowxsgpuxyLvgs7eDvKbO8QRZgviHc7u4e0Mu5W-H4zbLFbMz3B_h8SAt-lBaRwj6ZyWPwrX0lk29puXLjXSqdIvXJPpD53lICrzMP5cToNZUJCmSjMMPWv--wT24mZRMAZJDqYVSC4x6C7riY-OTIk531j1up2GuKFcBh8WJkI6gQfH46k9be2wm0IlQ3TEhb1hUB6NtzCxwsUJ-GlrQll_uZqLpp6KzhG3xZJ4eJ3e9UpsLITqt9PyOoT_n-KOUNkZdaNFh6D1qoNiNq-6UqyNOo_zFJrMtztjgnExmfHOhwOO2OGXYeNgqQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > <https://secure-web.cisco.com/1KDLe0BrweQumIP7IIMo9k-XySUJ1EoMjn8leVWlxuJziHCCpLiRnY_Xic-gf_i0YJPObJDRTQy6wChMCTy7W
[Freesurfer] Sample registration question
External Email - Use Caution Hi there Freesurfer, I am currently using freesurfer to take DTI metrics (FA, MD) from hippocampal subfields. At this point of my exploration with freesurfer, I am able to correctly register the hippocampal subfields and diffusion data, and obtain my FA values from the subfields. However, this is at the individual subject level. I will eventually need to register all of my samples in the same space for me to do a group analysis. However I am unsure what the order of registration should be for this process to be feasible. Does this order seem feasible for accurate analysis? 1) recon-all all of my subjects 2) dt_recon all of my subjects (one of the outputs is a registration file, which has registered the DTI data to outputs of recon-all) 3) run the hippocampus segmentation command on all subjects (segmentHA_T1.sh) to obtain hippocampal subfield segmentation 4) register the segmentation file to the FA maps (output of dt_recon) using vol2subfield command 5) After creating a subfield-FA map for each subject, spatial normalize the samples onto the same space using *mri_vol2vol* Thank you so much for taking the time reading my question. If there is a different method to spatially normalizing my datasets, or if there is a more optimal order of registration, I'd be happy to hear from you. Thank you, M ___ 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] Sample registration question
External Email - Use Caution Hi there, Is there a way to successfully obtain FA/MD values from the hippocampus subfields? Thank you, M On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve wrote: > I'm not sure what you mean. The subfields are an ROI-based analysis. Are > you saying you want to do a voxel-based analysis (without reference to > ROIs)? > > On 1/9/2024 12:05 PM, Mirsol Choi wrote: > > External Email - Use Caution > > Hi there Freesurfer, > > I am currently using freesurfer to take DTI metrics (FA, MD) from > hippocampal subfields. > At this point of my exploration with freesurfer, I am able to correctly > register the hippocampal subfields and diffusion data, and obtain my FA > values from the subfields. However, this is at the individual subject > level. > > I will eventually need to register all of my samples in the same space for > me to do a group analysis. However I am unsure what the order of > registration should be for this process to be feasible. > > Does this order seem feasible for accurate analysis? > > 1) recon-all all of my subjects > 2) dt_recon all of my subjects (one of the outputs is a registration file, > which has registered the DTI data to outputs of recon-all) > 3) run the hippocampus segmentation command on all subjects > (segmentHA_T1.sh) to obtain hippocampal subfield segmentation > 4) register the segmentation file to the FA maps (output of dt_recon) > using vol2subfield command > 5) After creating a subfield-FA map for each subject, spatial normalize > the samples onto the same space using *mri_vol2vol* > > Thank you so much for taking the time reading my question. If there is a > different method to spatially normalizing my datasets, or if there is a > more optimal order of registration, I'd be happy to hear from you. > > Thank you, > M > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1KU4jXJB1CrsIlaMiid17Ht9H8dz8aaMrgEllh75BASm41YPJpFvV9YGaQw-aq9ywLjQPjU-JEFjbZiQWZfEndP8uhI_K8iXBEN-wwTFN6ZjK7syWmvB8P5YpyqjFXSJToS93Qqgg1MSw6C82X7rFFhq057nFheAfGqu-gv0nkPsP_vD2_WtDhJFdeGBAQf7P03R9ZJw5Z70vUKbgy1lxUxP5RW6aBx9zSLvaWhcZleoNAU0n_Tp1Cx4jzMOFGjTSwDdjr6FdJnAehsOeF6nsAFwgWILwSDahrWq6e0Yo6kjc--71AFBb0tbcs27_rlaFkEkcvbXrcxUQn2g31PjLRQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 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] Sample registration question
External Email - Use Caution Hi there, Following the first registration step, should I also run another registration command to put all fa-in-subfields.mgz for each subject onto the same space for inter subject analysis of FA values? Thanks again, M On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve wrote: > Map the diffusion data to the subfield space, eg, > mri_vol2vol --mov fa.nii.gz --reg register.lta --targ subfields.mgz --o > fa-in-subfields.mgz > Then run mri_segstats > mri_segstats --ctab-default --i fa-in-subfields.mgz --seg subfields.mgz > --sum fa-in-subfields.dat > > > > On 1/12/2024 4:53 PM, Mirsol Choi wrote: > > External Email - Use Caution > Hi there, > > Is there a way to successfully obtain FA/MD values from the hippocampus > subfields? > > Thank you, > M > > > On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve > wrote: > > I'm not sure what you mean. The subfields are an ROI-based analysis. Are >> you saying you want to do a voxel-based analysis (without reference to >> ROIs)? >> >> On 1/9/2024 12:05 PM, Mirsol Choi wrote: >> >> External Email - Use Caution >> >> Hi there Freesurfer, >> >> I am currently using freesurfer to take DTI metrics (FA, MD) from >> hippocampal subfields. >> At this point of my exploration with freesurfer, I am able to correctly >> register the hippocampal subfields and diffusion data, and obtain my FA >> values from the subfields. However, this is at the individual subject >> level. >> >> I will eventually need to register all of my samples in the same space >> for me to do a group analysis. However I am unsure what the order of >> registration should be for this process to be feasible. >> >> Does this order seem feasible for accurate analysis? >> >> 1) recon-all all of my subjects >> 2) dt_recon all of my subjects (one of the outputs is a registration >> file, which has registered the DTI data to outputs of recon-all) >> 3) run the hippocampus segmentation command on all subjects >> (segmentHA_T1.sh) to obtain hippocampal subfield segmentation >> 4) register the segmentation file to the FA maps (output of dt_recon) >> using vol2subfield command >> 5) After creating a subfield-FA map for each subject, spatial normalize >> the samples onto the same space using *mri_vol2vol* >> >> Thank you so much for taking the time reading my question. If there is a >> different method to spatially normalizing my datasets, or if there is a >> more optimal order of registration, I'd be happy to hear from you. >> >> Thank you, >> M >> >> ___ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu >> >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1gRnpzcC-wyIJZvEJgw-_KtxFSVcGDUAjDIii5hXhZydgdmbsIZ13fBK1cF53oOVbi_xlaNUxv3v6fD5ZK6o_Q9tBX2IphATpwX7-CyY6WtZf41ytPjCorPIjrp-5twBXh6S6w5YXjoejKW4IMD53SnZ2YcKx4jhsZrrpPicbV1zHn2SGwFIFcTm0nU8k-noU-WGSgrI6sarabvG3slm6YBi0EqF0Z1d0rVJRzkrU-93RRODsmr8exkG6EOkf5H0-3Gwabq-25S8LLybrqZwQz8H6qngECf6O_O8Trk4tLrWlUOvw6nKVQY4zJAfSoRkFB00k0X05TFU5a4rKy7mg5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1KU4jXJB1CrsIlaMiid17Ht9H8dz8aaMrgEllh75BASm41YPJpFvV9YGaQw-aq9ywLjQPjU-JEFjbZiQWZfEndP8uhI_K8iXBEN-wwTFN6ZjK7syWmvB8P5YpyqjFXSJToS93Qqgg1MSw6C82X7rFFhq057nFheAfGqu-gv0nkPsP_vD2_WtDhJFdeGBAQf7P03R9ZJw5Z70vUKbgy1lxUxP5RW6aBx9zSLvaWhcZleoNAU0n_Tp1Cx4jzMOFGjTSwDdjr6FdJnAehsOeF6nsAFwgWILwSDahrWq6e0Yo6kjc--71AFBb0tbcs27_rlaFkEkcvbXrcxUQn2g31PjLRQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> ___ >> Freesurfer mailing list >> 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/1gRnpzcC-wyIJZvEJgw-_KtxFSVcGDUAjDIii5hXhZydgdmbsIZ13fBK1cF53oOVbi_xlaNUxv3v6fD5ZK6o_Q9tBX2IphATpwX7-CyY6WtZf41ytPjCorPIjrp-5twBXh6S6w5YXjoejKW4IMD53SnZ2YcKx4jhsZrrpPicbV1zHn2SGwFIFcTm0nU8k-noU-WGSgrI6sarabvG3slm6YBi0EqF0Z1d0rVJRzkrU-93RRODsmr8exkG6EOkf5H0-3Gwabq-25S8LLybrqZwQz8H6qngECf6O_O8Trk4tLrWlUOvw6nKVQY4zJAfSoRkFB00k0X05TFU5a4rKy7mg5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1KU4jXJB1CrsIlaMiid17Ht9H8dz8aaMrgEllh75BASm41YPJpFvV9YGaQw-aq9ywLjQPjU-JEFjbZiQWZfEndP8uhI_K8iXBEN-wwTFN6ZjK7syWmvB8P5YpyqjFXSJToS93Qqgg1MSw6C82X7rFFhq057nFheAfGqu-gv0nkPsP_vD2_WtDhJF
Re: [Freesurfer] Sample registration question
External Email - Use Caution Hello, Sorry I should have clarified. Yes, I would like to perform voxelwise analysis of FA and MD values of hippocampal subfield between subjects. Is this possible with free surfer? Thank you again for your time. M On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve wrote: > oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise > analysis? > > On 1/12/2024 5:46 PM, Mirsol Choi wrote: > > External Email - Use Caution > Hi there, > > > Following the first registration step, should I also run another > registration command to put all fa-in-subfields.mgz for each subject onto > the same space for inter subject analysis of FA values? > > Thanks again, > M > > On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve > wrote: > >> Map the diffusion data to the subfield space, eg, >> mri_vol2vol --mov fa.nii.gz --reg register.lta --targ subfields.mgz --o >> fa-in-subfields.mgz >> Then run mri_segstats >> mri_segstats --ctab-default --i fa-in-subfields.mgz --seg subfields.mgz >> --sum fa-in-subfields.dat >> >> >> >> On 1/12/2024 4:53 PM, Mirsol Choi wrote: >> >> External Email - Use Caution >> Hi there, >> >> Is there a way to successfully obtain FA/MD values from the hippocampus >> subfields? >> >> Thank you, >> M >> >> >> On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve >> wrote: >> >> I'm not sure what you mean. The subfields are an ROI-based analysis. Are >>> you saying you want to do a voxel-based analysis (without reference to >>> ROIs)? >>> >>> On 1/9/2024 12:05 PM, Mirsol Choi wrote: >>> >>> External Email - Use Caution >>> >>> Hi there Freesurfer, >>> >>> I am currently using freesurfer to take DTI metrics (FA, MD) from >>> hippocampal subfields. >>> At this point of my exploration with freesurfer, I am able to correctly >>> register the hippocampal subfields and diffusion data, and obtain my FA >>> values from the subfields. However, this is at the individual subject >>> level. >>> >>> I will eventually need to register all of my samples in the same space >>> for me to do a group analysis. However I am unsure what the order of >>> registration should be for this process to be feasible. >>> >>> Does this order seem feasible for accurate analysis? >>> >>> 1) recon-all all of my subjects >>> 2) dt_recon all of my subjects (one of the outputs is a registration >>> file, which has registered the DTI data to outputs of recon-all) >>> 3) run the hippocampus segmentation command on all subjects >>> (segmentHA_T1.sh) to obtain hippocampal subfield segmentation >>> 4) register the segmentation file to the FA maps (output of dt_recon) >>> using vol2subfield command >>> 5) After creating a subfield-FA map for each subject, spatial normalize >>> the samples onto the same space using *mri_vol2vol* >>> >>> Thank you so much for taking the time reading my question. If there is a >>> different method to spatially normalizing my datasets, or if there is a >>> more optimal order of registration, I'd be happy to hear from you. >>> >>> Thank you, >>> M >>> >>> ___ >>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu >>> >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/1v6TlAXVkTURRbMgaTbvOwCu5DC2s1X-aForrBtXff5-2rgcsq2hXslcqOQhmf7q7NHUTETS0neQ0liC3nNuDjfyaKLnbiV-NTdVsXdLZzPHhD07vQd_Aq8KlWoHjaEti6To0JUT7C8RBfN1ephtC35haijaNJWPZ0fb651iI6n-EYSpJfYLFmKR2OLD1JFEvRfUhG7AQKamRTjSBlyZsXJNRHx-5T7RQ-IFngaPLo4n7pOFRyBY8J68GLZpchyPHPITZP8lK6ep9JfvH3AAvjZ5NKynzBYgLkzvoakF6WFiWHtHV5nHRdrJjLMAGFXwkmM4N85yZ1n7B-KwbttDukQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <https://secure-web.cisco.com/1KU4jXJB1CrsIlaMiid17Ht9H8dz8aaMrgEllh75BASm41YPJpFvV9YGaQw-aq9ywLjQPjU-JEFjbZiQWZfEndP8uhI_K8iXBEN-wwTFN6ZjK7syWmvB8P5YpyqjFXSJToS93Qqgg1MSw6C82X7rFFhq057nFheAfGqu-gv0nkPsP_vD2_WtDhJFdeGBAQf7P03R9ZJw5Z70vUKbgy1lxUxP5RW6aBx9zSLvaWhcZleoNAU0n_Tp1Cx4jzMOFGjTSwDdjr6FdJnAehsOeF6nsAFwgWILwSDahrWq6e0Yo6kjc--71AFBb0tbcs27_rlaFkEkcvbXrcxUQn2g31PjLRQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> >>> ___ >>> Freesurfer mailing list &
Re: [Freesurfer] Sample registration question
External Email - Use Caution Hello, My goal is to compare the FA and MD values of hippocampal subfields (only inside the hippocampus) between cognitively normal, MCI, and AD subjects. I am unsure if this would require a voxel wise analysis or an ROI analysis… to my understanding this is more of a ROI analysis between subjects - is this assumption incorrect? Thank you, Peter On Sat, Jan 13, 2024 at 10:44 AM Douglas N. Greve wrote: > So this is where I get confused on your intentions because you say that > you want to do a voxel-wise analysis of an ROI. Do you mean you want to do > a voxelwise analysis but only inside, eg, whole hippocampus? > > On 1/12/2024 6:07 PM, Mirsol Choi wrote: > > External Email - Use Caution > Hello, > > Sorry I should have clarified. Yes, I would like to perform voxelwise > analysis of FA and MD values of hippocampal subfield between subjects. Is > this possible with free surfer? > > Thank you again for your time. > > M > > On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve > wrote: > >> oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise >> analysis? >> >> On 1/12/2024 5:46 PM, Mirsol Choi wrote: >> >> External Email - Use Caution >> Hi there, >> >> >> Following the first registration step, should I also run another >> registration command to put all fa-in-subfields.mgz for each subject onto >> the same space for inter subject analysis of FA values? >> >> Thanks again, >> M >> >> On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve >> wrote: >> >>> Map the diffusion data to the subfield space, eg, >>> mri_vol2vol --mov fa.nii.gz --reg register.lta --targ subfields.mgz --o >>> fa-in-subfields.mgz >>> Then run mri_segstats >>> mri_segstats --ctab-default --i fa-in-subfields.mgz --seg subfields.mgz >>> --sum fa-in-subfields.dat >>> >>> >>> >>> On 1/12/2024 4:53 PM, Mirsol Choi wrote: >>> >>> External Email - Use Caution >>> Hi there, >>> >>> Is there a way to successfully obtain FA/MD values from the hippocampus >>> subfields? >>> >>> Thank you, >>> M >>> >>> >>> On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve >>> wrote: >>> >>> I'm not sure what you mean. The subfields are an ROI-based analysis. Are >>>> you saying you want to do a voxel-based analysis (without reference to >>>> ROIs)? >>>> >>>> On 1/9/2024 12:05 PM, Mirsol Choi wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hi there Freesurfer, >>>> >>>> I am currently using freesurfer to take DTI metrics (FA, MD) from >>>> hippocampal subfields. >>>> At this point of my exploration with freesurfer, I am able to correctly >>>> register the hippocampal subfields and diffusion data, and obtain my FA >>>> values from the subfields. However, this is at the individual subject >>>> level. >>>> >>>> I will eventually need to register all of my samples in the same space >>>> for me to do a group analysis. However I am unsure what the order of >>>> registration should be for this process to be feasible. >>>> >>>> Does this order seem feasible for accurate analysis? >>>> >>>> 1) recon-all all of my subjects >>>> 2) dt_recon all of my subjects (one of the outputs is a registration >>>> file, which has registered the DTI data to outputs of recon-all) >>>> 3) run the hippocampus segmentation command on all subjects >>>> (segmentHA_T1.sh) to obtain hippocampal subfield segmentation >>>> 4) register the segmentation file to the FA maps (output of dt_recon) >>>> using vol2subfield command >>>> 5) After creating a subfield-FA map for each subject, spatial normalize >>>> the samples onto the same space using *mri_vol2vol* >>>> >>>> Thank you so much for taking the time reading my question. If there is >>>> a different method to spatially normalizing my datasets, or if there is a >>>> more optimal order of registration, I'd be happy to hear from you. >>>> >>>> Thank you, >>>> M >>>> >>>> ___ >>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu >>>> >>>> *MailScanner has detected a possible fraud attempt f
Re: [Freesurfer] Sample registration question
External Email - Use Caution Thank you for taking the time to respond on a weekend. On Sat, Jan 13, 2024 at 11:00 AM Mirsol Choi wrote: > Hello, > > My goal is to compare the FA and MD values of hippocampal subfields (only > inside the hippocampus) between cognitively normal, MCI, and AD subjects. I > am unsure if this would require a voxel wise analysis or an ROI analysis… > to my understanding this is more of a ROI analysis between subjects - is > this assumption incorrect? > > Thank you, > Peter > > On Sat, Jan 13, 2024 at 10:44 AM Douglas N. Greve > wrote: > >> So this is where I get confused on your intentions because you say that >> you want to do a voxel-wise analysis of an ROI. Do you mean you want to do >> a voxelwise analysis but only inside, eg, whole hippocampus? >> >> On 1/12/2024 6:07 PM, Mirsol Choi wrote: >> >> External Email - Use Caution >> Hello, >> >> Sorry I should have clarified. Yes, I would like to perform voxelwise >> analysis of FA and MD values of hippocampal subfield between subjects. Is >> this possible with free surfer? >> >> Thank you again for your time. >> >> M >> >> On Fri, Jan 12, 2024 at 4:05 PM Douglas N. Greve >> wrote: >> >>> oh, I thought you wanted to do an ROI analysis. You mean for a voxelwise >>> analysis? >>> >>> On 1/12/2024 5:46 PM, Mirsol Choi wrote: >>> >>> External Email - Use Caution >>> Hi there, >>> >>> >>> Following the first registration step, should I also run another >>> registration command to put all fa-in-subfields.mgz for each subject onto >>> the same space for inter subject analysis of FA values? >>> >>> Thanks again, >>> M >>> >>> On Fri, Jan 12, 2024 at 3:00 PM Douglas N. Greve >>> wrote: >>> >>>> Map the diffusion data to the subfield space, eg, >>>> mri_vol2vol --mov fa.nii.gz --reg register.lta --targ subfields.mgz --o >>>> fa-in-subfields.mgz >>>> Then run mri_segstats >>>> mri_segstats --ctab-default --i fa-in-subfields.mgz --seg >>>> subfields.mgz --sum fa-in-subfields.dat >>>> >>>> >>>> >>>> On 1/12/2024 4:53 PM, Mirsol Choi wrote: >>>> >>>> External Email - Use Caution >>>> Hi there, >>>> >>>> Is there a way to successfully obtain FA/MD values from the hippocampus >>>> subfields? >>>> >>>> Thank you, >>>> M >>>> >>>> >>>> On Fri, Jan 12, 2024 at 2:23 PM Douglas N. Greve < >>>> dgr...@mgh.harvard.edu> wrote: >>>> >>>> I'm not sure what you mean. The subfields are an ROI-based analysis. >>>>> Are you saying you want to do a voxel-based analysis (without reference to >>>>> ROIs)? >>>>> >>>>> On 1/9/2024 12:05 PM, Mirsol Choi wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> Hi there Freesurfer, >>>>> >>>>> I am currently using freesurfer to take DTI metrics (FA, MD) from >>>>> hippocampal subfields. >>>>> At this point of my exploration with freesurfer, I am able to >>>>> correctly register the hippocampal subfields and diffusion data, and >>>>> obtain >>>>> my FA values from the subfields. However, this is at the individual >>>>> subject >>>>> level. >>>>> >>>>> I will eventually need to register all of my samples in the same space >>>>> for me to do a group analysis. However I am unsure what the order of >>>>> registration should be for this process to be feasible. >>>>> >>>>> Does this order seem feasible for accurate analysis? >>>>> >>>>> 1) recon-all all of my subjects >>>>> 2) dt_recon all of my subjects (one of the outputs is a registration >>>>> file, which has registered the DTI data to outputs of recon-all) >>>>> 3) run the hippocampus segmentation command on all subjects >>>>> (segmentHA_T1.sh) to obtain hippocampal subfield segmentation >>>>> 4) register the segmentation file to the FA maps (output of dt_recon) >>>>> using vol2subfield command >>>>> 5) After creating a subfield-FA map for each subject, spatial >>>>> normalize the sample
