External Email - Use Caution
Hi Freesurfer/Tracula experts,
I would like to use my own diffusivity and anisotropy maps (FA, MD, etc) with Tracula as opposed to the maps generated by dtifit during the course of trac-all -prep. I see that there is a -notensor option to stop dtifit from producing metric maps; however I am wondering if there's any way to get Tracula to recognize alternative metric maps that I supply to it.
My main goal is to sub in my own metric maps for the purposes of having Tracula generate tract profiles (pathstats.byvoxel.txt) with metric maps I generated via an alternative fitting method to dtifit. Is there any way to do this?
Additionally, is there any way to have Tracula perform these same types of analyses with kurtosis maps or other types of dMRI data?
I've been working mainly with Tracula 6.0 as I have received an as yet unresolved mri_binarize error with Tracula 7.2. However, I am curious if the above is possible with either or both versions.
Thank you!
Kayti Thorn (she/her) Database Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425
Hi Kayti - Yes, there is a way to get stats from other maps, in 7.2. We just haven't had a chance to document it yet 🙂
If you look in your trac-all.log or trac-all.cmd file, you'll find the dmri_pathstats command lines that produce the stats. You can use a modified version of those commands to indicate the path to the map you want to get stats from, and the name that you want it to have in the output stats tables.
For example, let's say you have mean kurtosis (mk) maps that you saved in every subject's dmri/ directory, and you want to get both overall and along-the-tract stats on the SLF1:
dmri_pathstats --intrc subject1/dpath/rh.slf1_avg16_syn_bbr --meas subject1/dmri/dkifit_mk.nii.gz --measname mk --path rh.slf1 --subj subject1 --out subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.overall.txt --outvox subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.byvoxel.txt
Let us know if this works! Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Thorn, Kathryn keithka@musc.edu Sent: Tuesday, March 15, 2022 4:36 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Freesurfer/Tracula experts,
I would like to use my own diffusivity and anisotropy maps (FA, MD, etc) with Tracula as opposed to the maps generated by dtifit during the course of trac-all –prep. I see that there is a –notensor option to stop dtifit from producing metric maps; however I am wondering if there’s any way to get Tracula to recognize alternative metric maps that I supply to it.
My main goal is to sub in my own metric maps for the purposes of having Tracula generate tract profiles (pathstats.byvoxel.txt) with metric maps I generated via an alternative fitting method to dtifit. Is there any way to do this?
Additionally, is there any way to have Tracula perform these same types of analyses with kurtosis maps or other types of dMRI data?
I’ve been working mainly with Tracula 6.0 as I have received an as yet unresolved mri_binarize error with Tracula 7.2. However, I am curious if the above is possible with either or both versions.
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
External Email - Use Caution
Hi Anastasia,
Thank you so much! This is extremely helpful.
Quick follow up: If my non-dtifit maps are in a different orientation than the dtifit maps (and other Tracula outputs), will I need to manually reorient my non-dtifit maps?
On a related note: I submitted a question back on 3/2/22 entitled “mri_binarize error when using trac-all –prep”. This error is still stopping me from being able to use 7.2. Would it be possible for you or another one of the Freesurfer folks to try to help me debug this error? That way I can make use of the method below you’ve kindly written for me. ☺
Thank you!
Kayti Thorn (she/her) Database Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Thursday, March 17, 2022 9:40 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
CAUTION: External Hi Kayti - Yes, there is a way to get stats from other maps, in 7.2. We just haven't had a chance to document it yet 🙂
If you look in your trac-all.log or trac-all.cmd file, you'll find the dmri_pathstats command lines that produce the stats. You can use a modified version of those commands to indicate the path to the map you want to get stats from, and the name that you want it to have in the output stats tables.
For example, let's say you have mean kurtosis (mk) maps that you saved in every subject's dmri/ directory, and you want to get both overall and along-the-tract stats on the SLF1:
dmri_pathstats --intrc subject1/dpath/rh.slf1_avg16_syn_bbr --meas subject1/dmri/dkifit_mk.nii.gz --measname mk --path rh.slf1 --subj subject1 --out subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.overall.txt --outvox subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.byvoxel.txt
Let us know if this works! Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thorn, Kathryn <keithka@musc.edumailto:keithka@musc.edu> Sent: Tuesday, March 15, 2022 4:36 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Freesurfer/Tracula experts,
I would like to use my own diffusivity and anisotropy maps (FA, MD, etc) with Tracula as opposed to the maps generated by dtifit during the course of trac-all –prep. I see that there is a –notensor option to stop dtifit from producing metric maps; however I am wondering if there’s any way to get Tracula to recognize alternative metric maps that I supply to it.
My main goal is to sub in my own metric maps for the purposes of having Tracula generate tract profiles (pathstats.byvoxel.txt) with metric maps I generated via an alternative fitting method to dtifit. Is there any way to do this?
Additionally, is there any way to have Tracula perform these same types of analyses with kurtosis maps or other types of dMRI data?
I’ve been working mainly with Tracula 6.0 as I have received an as yet unresolved mri_binarize error with Tracula 7.2. However, I am curious if the above is possible with either or both versions.
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
Hi Kayti - About the orientation, you can put your other maps in the same orientation by running the orientLAS command on them.
About mri_binarize, did you see the response I just sent to another user? I wonder if it's the same thing.
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Thorn, Kathryn keithka@musc.edu Sent: Thursday, March 17, 2022 3:37 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Anastasia,
Thank you so much! This is extremely helpful.
Quick follow up: If my non-dtifit maps are in a different orientation than the dtifit maps (and other Tracula outputs), will I need to manually reorient my non-dtifit maps?
On a related note: I submitted a question back on 3/2/22 entitled “mri_binarize error when using trac-all –prep”. This error is still stopping me from being able to use 7.2. Would it be possible for you or another one of the Freesurfer folks to try to help me debug this error? That way I can make use of the method below you’ve kindly written for me. :)
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Thursday, March 17, 2022 9:40 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
CAUTION: External
Hi Kayti - Yes, there is a way to get stats from other maps, in 7.2. We just haven't had a chance to document it yet ??
If you look in your trac-all.log or trac-all.cmd file, you'll find the dmri_pathstats command lines that produce the stats. You can use a modified version of those commands to indicate the path to the map you want to get stats from, and the name that you want it to have in the output stats tables.
For example, let's say you have mean kurtosis (mk) maps that you saved in every subject's dmri/ directory, and you want to get both overall and along-the-tract stats on the SLF1:
dmri_pathstats --intrc subject1/dpath/rh.slf1_avg16_syn_bbr --meas subject1/dmri/dkifit_mk.nii.gz --measname mk --path rh.slf1 --subj subject1 --out subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.overall.txt --outvox subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.byvoxel.txt
Let us know if this works!
Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thorn, Kathryn <keithka@musc.edumailto:keithka@musc.edu> Sent: Tuesday, March 15, 2022 4:36 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Freesurfer/Tracula experts,
I would like to use my own diffusivity and anisotropy maps (FA, MD, etc) with Tracula as opposed to the maps generated by dtifit during the course of trac-all –prep. I see that there is a –notensor option to stop dtifit from producing metric maps; however I am wondering if there’s any way to get Tracula to recognize alternative metric maps that I supply to it.
My main goal is to sub in my own metric maps for the purposes of having Tracula generate tract profiles (pathstats.byvoxel.txt) with metric maps I generated via an alternative fitting method to dtifit. Is there any way to do this?
Additionally, is there any way to have Tracula perform these same types of analyses with kurtosis maps or other types of dMRI data?
I’ve been working mainly with Tracula 6.0 as I have received an as yet unresolved mri_binarize error with Tracula 7.2. However, I am curious if the above is possible with either or both versions.
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
External Email - Use Caution
Hi Anastatia – I didn’t know about orientLAS, thank you for that heads up!
I must have missed your recent reply to another user. I will see if I can find that thread.
Thank you so much!
Kayti Thorn (she/her) Database Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Thursday, March 17, 2022 3:50 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
CAUTION: External Hi Kayti - About the orientation, you can put your other maps in the same orientation by running the orientLAS command on them.
About mri_binarize, did you see the response I just sent to another user? I wonder if it's the same thing.
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thorn, Kathryn <keithka@musc.edumailto:keithka@musc.edu> Sent: Thursday, March 17, 2022 3:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Anastasia,
Thank you so much! This is extremely helpful.
Quick follow up: If my non-dtifit maps are in a different orientation than the dtifit maps (and other Tracula outputs), will I need to manually reorient my non-dtifit maps?
On a related note: I submitted a question back on 3/2/22 entitled “mri_binarize error when using trac-all –prep”. This error is still stopping me from being able to use 7.2. Would it be possible for you or another one of the Freesurfer folks to try to help me debug this error? That way I can make use of the method below you’ve kindly written for me. ☺
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Thursday, March 17, 2022 9:40 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
CAUTION: External
Hi Kayti - Yes, there is a way to get stats from other maps, in 7.2. We just haven't had a chance to document it yet 🙂
If you look in your trac-all.log or trac-all.cmd file, you'll find the dmri_pathstats command lines that produce the stats. You can use a modified version of those commands to indicate the path to the map you want to get stats from, and the name that you want it to have in the output stats tables.
For example, let's say you have mean kurtosis (mk) maps that you saved in every subject's dmri/ directory, and you want to get both overall and along-the-tract stats on the SLF1:
dmri_pathstats --intrc subject1/dpath/rh.slf1_avg16_syn_bbr --meas subject1/dmri/dkifit_mk.nii.gz --measname mk --path rh.slf1 --subj subject1 --out subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.overall.txt --outvox subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.byvoxel.txt
Let us know if this works!
Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thorn, Kathryn <keithka@musc.edumailto:keithka@musc.edu> Sent: Tuesday, March 15, 2022 4:36 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Freesurfer/Tracula experts,
I would like to use my own diffusivity and anisotropy maps (FA, MD, etc) with Tracula as opposed to the maps generated by dtifit during the course of trac-all –prep. I see that there is a –notensor option to stop dtifit from producing metric maps; however I am wondering if there’s any way to get Tracula to recognize alternative metric maps that I supply to it.
My main goal is to sub in my own metric maps for the purposes of having Tracula generate tract profiles (pathstats.byvoxel.txt) with metric maps I generated via an alternative fitting method to dtifit. Is there any way to do this?
Additionally, is there any way to have Tracula perform these same types of analyses with kurtosis maps or other types of dMRI data?
I’ve been working mainly with Tracula 6.0 as I have received an as yet unresolved mri_binarize error with Tracula 7.2. However, I am curious if the above is possible with either or both versions.
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
Hi Kayti - This was the one: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg72181.html
Anastasia.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Thorn, Kathryn keithka@musc.edu Sent: Thursday, March 17, 2022 5:06 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Anastatia – I didn’t know about orientLAS, thank you for that heads up!
I must have missed your recent reply to another user. I will see if I can find that thread.
Thank you so much!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Thursday, March 17, 2022 3:50 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
CAUTION: External
Hi Kayti - About the orientation, you can put your other maps in the same orientation by running the orientLAS command on them.
About mri_binarize, did you see the response I just sent to another user? I wonder if it's the same thing.
Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thorn, Kathryn <keithka@musc.edumailto:keithka@musc.edu> Sent: Thursday, March 17, 2022 3:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Anastasia,
Thank you so much! This is extremely helpful.
Quick follow up: If my non-dtifit maps are in a different orientation than the dtifit maps (and other Tracula outputs), will I need to manually reorient my non-dtifit maps?
On a related note: I submitted a question back on 3/2/22 entitled “mri_binarize error when using trac-all –prep”. This error is still stopping me from being able to use 7.2. Would it be possible for you or another one of the Freesurfer folks to try to help me debug this error? That way I can make use of the method below you’ve kindly written for me. :)
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Thursday, March 17, 2022 9:40 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
CAUTION: External
Hi Kayti - Yes, there is a way to get stats from other maps, in 7.2. We just haven't had a chance to document it yet ??
If you look in your trac-all.log or trac-all.cmd file, you'll find the dmri_pathstats command lines that produce the stats. You can use a modified version of those commands to indicate the path to the map you want to get stats from, and the name that you want it to have in the output stats tables.
For example, let's say you have mean kurtosis (mk) maps that you saved in every subject's dmri/ directory, and you want to get both overall and along-the-tract stats on the SLF1:
dmri_pathstats --intrc subject1/dpath/rh.slf1_avg16_syn_bbr --meas subject1/dmri/dkifit_mk.nii.gz --measname mk --path rh.slf1 --subj subject1 --out subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.overall.txt --outvox subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.byvoxel.txt
Let us know if this works!
Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thorn, Kathryn <keithka@musc.edumailto:keithka@musc.edu> Sent: Tuesday, March 15, 2022 4:36 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Freesurfer/Tracula experts,
I would like to use my own diffusivity and anisotropy maps (FA, MD, etc) with Tracula as opposed to the maps generated by dtifit during the course of trac-all –prep. I see that there is a –notensor option to stop dtifit from producing metric maps; however I am wondering if there’s any way to get Tracula to recognize alternative metric maps that I supply to it.
My main goal is to sub in my own metric maps for the purposes of having Tracula generate tract profiles (pathstats.byvoxel.txt) with metric maps I generated via an alternative fitting method to dtifit. Is there any way to do this?
Additionally, is there any way to have Tracula perform these same types of analyses with kurtosis maps or other types of dMRI data?
I’ve been working mainly with Tracula 6.0 as I have received an as yet unresolved mri_binarize error with Tracula 7.2. However, I am curious if the above is possible with either or both versions.
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
External Email - Use Caution
Thank you so much for all of your help, Anastasia!
Kayti Thorn (she/her) Database Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Friday, March 18, 2022 2:41 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
CAUTION: External Hi Kayti - This was the one: https://secure-web.cisco.com/1xGBTJ_-jxkuO_PL9dYVHDMbJeZ2vpITpxbgFZf1tV9Dhr4...https://secure-web.cisco.com/14Y0I9hBTIgJb8GHZpozLtudbuJeDfCaJyRQcYZyH-eL8LlwerndYqzjpWEs_IVWzxOhuB4nSD4vfDV8giXmJINLql6XtLxMJGN3opsX_stNXC7ubrTFxVgmhZv3VX7_rbjgRxTii78L8rm_9Tae3bdegtUmiZ9WuV_JAm2PYjxxvVxSQrbHPqWESf3FKjNrZ7Eaa80e2UGdR4WEwFRqjNV20Z-o0Z-IzJ9bWFh9u7dCxtAhls4RAn0_7T-XIFIG7Ow71Uqx_UQ4x3MjtcM40k-V3u7oCOY-nXfDMpYwLEty2guWNgzAqYIh-E2P-bBYD/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg72181.html__;!!Ab1_Rw!W0iXiXL3mR5VSo3EU2U5LqYCgOV1fT2WioPMNBsKTuLjuOjL0Uae2tvMZFBphhcC$
Anastasia.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thorn, Kathryn <keithka@musc.edumailto:keithka@musc.edu> Sent: Thursday, March 17, 2022 5:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
External Email - Use Caution
Hi Anastatia – I didn’t know about orientLAS, thank you for that heads up!
I must have missed your recent reply to another user. I will see if I can find that thread.
Thank you so much!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Thursday, March 17, 2022 3:50 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
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Hi Kayti - About the orientation, you can put your other maps in the same orientation by running the orientLAS command on them.
About mri_binarize, did you see the response I just sent to another user? I wonder if it's the same thing.
Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thorn, Kathryn <keithka@musc.edumailto:keithka@musc.edu> Sent: Thursday, March 17, 2022 3:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
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Hi Anastasia,
Thank you so much! This is extremely helpful.
Quick follow up: If my non-dtifit maps are in a different orientation than the dtifit maps (and other Tracula outputs), will I need to manually reorient my non-dtifit maps?
On a related note: I submitted a question back on 3/2/22 entitled “mri_binarize error when using trac-all –prep”. This error is still stopping me from being able to use 7.2. Would it be possible for you or another one of the Freesurfer folks to try to help me debug this error? That way I can make use of the method below you’ve kindly written for me. ☺
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Thursday, March 17, 2022 9:40 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
CAUTION: External
Hi Kayti - Yes, there is a way to get stats from other maps, in 7.2. We just haven't had a chance to document it yet 🙂
If you look in your trac-all.log or trac-all.cmd file, you'll find the dmri_pathstats command lines that produce the stats. You can use a modified version of those commands to indicate the path to the map you want to get stats from, and the name that you want it to have in the output stats tables.
For example, let's say you have mean kurtosis (mk) maps that you saved in every subject's dmri/ directory, and you want to get both overall and along-the-tract stats on the SLF1:
dmri_pathstats --intrc subject1/dpath/rh.slf1_avg16_syn_bbr --meas subject1/dmri/dkifit_mk.nii.gz --measname mk --path rh.slf1 --subj subject1 --out subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.overall.txt --outvox subject1/dpath/rh.slf1_avg16_syn_bbr/my.pathstats.byvoxel.txt
Let us know if this works!
Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thorn, Kathryn <keithka@musc.edumailto:keithka@musc.edu> Sent: Tuesday, March 15, 2022 4:36 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps
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Hi Freesurfer/Tracula experts,
I would like to use my own diffusivity and anisotropy maps (FA, MD, etc) with Tracula as opposed to the maps generated by dtifit during the course of trac-all –prep. I see that there is a –notensor option to stop dtifit from producing metric maps; however I am wondering if there’s any way to get Tracula to recognize alternative metric maps that I supply to it.
My main goal is to sub in my own metric maps for the purposes of having Tracula generate tract profiles (pathstats.byvoxel.txt) with metric maps I generated via an alternative fitting method to dtifit. Is there any way to do this?
Additionally, is there any way to have Tracula perform these same types of analyses with kurtosis maps or other types of dMRI data?
I’ve been working mainly with Tracula 6.0 as I have received an as yet unresolved mri_binarize error with Tracula 7.2. However, I am curious if the above is possible with either or both versions.
Thank you!
Kayti Thorn
(she/her)
Database Specialist
Medical University of South Carolina
Department of Neurology
Center for Biomedical Imaging
135 Cannon St. CS101
Charleston, SC 29425
freesurfer@nmr.mgh.harvard.edu
-
Thorn, Kathryn -
Yendiki, Anastasia