Re: [Freesurfer] Question re. Tracula motion measures
Hi, I ran our pipeline script that contains DTI_prep and Tracula, and when I extracted the individual motion data, they are mostly zeros (see below) Is this normal? If this is a problem, can anyone please let me know if there any way to fix this (e.g. re-run the motion script..)? Your help would be greatly appreciated! ps: I just need to examine the motions between 2 groups (below are all data from the 2 groups). AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0.0419463 1.02647 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0.370763 1.23369 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0.414365 1.13071 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 Thanks so much for helping! ___ 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] Statistical tests on Tracula's path spline
Hi,
Thanks for the great FreeSurfer Course this past week.
After running through Tracula and extracted the path stats (by voxel) across
all subjects, can I apply mri_glmfit to test the group differences using the
generated txt file that has all subject's diffusion meassure (e.g., FA) along
particular spline voxels (the pathstats.byvoxel.txt, for example)?
Thanks!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
freesurfer-requ...@nmr.mgh.harvard.edu [freesurfer-requ...@nmr.mgh.harvard.edu]
Sent: 01 October 2015 12:00
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 140, Issue 3
Send Freesurfer mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
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Today's Topics:
1. WM segmentation error longitudinal stream (Adam, Ruth)
2. Test incoming emails - (pablo najt)
3. Re: dt_recon (Alshikho, Mohamad J.)
4. mri_convert doubles file size when changing TR header
information (Shaun Patel)
5. Re: PVE correction tool within the V 6 beta (m.ba...@ulg.ac.be)
6. Re: Error Messages for Accessing Bin (Bruce Fischl)
7. Re: Calculate the cortical thickness in patients with brain
tumor (Bruce Fischl)
8. Re: Calculating local gyrification using CIVET's surface file
('.obj') (Bruce Fischl)
--
Message: 1
Date: Thu, 1 Oct 2015 14:35:30 +0200
From: "Adam, Ruth"
Subject: [Freesurfer] WM segmentation error longitudinal stream
To: Freesurfer support list
Message-ID:
Content-Type: text/plain; charset="us-ascii"
Hi all,
We have run longitudinal analysis on two time points.
The resulting longitudinal WM surface for both time points excludes large parts
of the cortex.
The cross sectional surfaces and the wm.mgz are correct.
The base wm.mgz also seems to be fine, however, the base white and pial
surfaces do not follow the wm volume properly.
We have rerun the longitudinal anlaysis (recon-all -long) according to the
cheat sheet:
1. marking the base wm.mgz border with 255 voxel value (instead of 110)
2. adding control points to the base wm.mgz
but it did not change the original result.
Any idea how this can be fixed?
Thank you very much in advance!
Best,
ruthi
--
Message: 2
Date: Thu, 1 Oct 2015 13:27:37 +
From: pablo najt
Subject: [Freesurfer] Test incoming emails -
To: "freesurfer@nmr.mgh.harvard.edu"
Message-ID:
Content-Type: text/plain; charset="iso-8859-1"
I am sending this message as a test since my income emails from FS stopped
working on the 29 of September.Regards
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Message: 3
Date: Thu, 1 Oct 2015 14:03:27 +
From: "Alshikho, Mohamad J."
Subject: Re: [Freesurfer] dt_recon
To: Freesurfer support list
Message-ID:
Content-Type: text/plain; charset="us-ascii"
Hi Doug,
Thank you very much for your answers!
Kindly I have one more question:
At the end of DTI analysis using the tool "dt_recon" we will have " stats"
file including the FA value for every segment and parcellate in the brain.
Depending on this output can we use the term " DTI morphometry" to describe the
analysis?
Thanks
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Monday, September 28, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon
On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals
f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>>
I need to generate the final statistics ( FA for every parcellate and segment
in aseg and wmparc atlases) using the command "mri_segstats"
In order to do so I need to move "fa.nii" to anatomical space using the command:
mri_vol2vol -mov fa.nii -lta register.lta -fstarg -o fa.anat.mgh
<<< source: Freesurfer wiki>>>
My questions are about the file "register.lta" :
1. What is the difference between this file and the file "register.dat" (
which I can see it as an output of the command " bbregister" in the final
analysis using the command "dt_recon")
They hold the same basic
Re: [Freesurfer] dmri_pathstats error
Dear DTI experts: I am wondering if anyone could help find the solution for this tracula script error: RuntimeError: Command: dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Below I pasted the last bits of the log including the error messages. Your help is being greatly appreciated. Yuwen 170712-12:28:30,168 interface INFO: stdout 2017-07-12T12:28:30.165030:Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... 170712-12:28:30,168 interface INFO: stdout 2017-07-12T12:28:30.165030:ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Traceback (most recent call last): File "/home/yuwenh/script/dti_2017pipeline_YHMK.py", line 292, in make_tables(args.subject) File "/home/yuwenh/script/dti_2017pipeline_YHMK.py", line 262, in make_tables cmd.run() File "/om/user/yuwenh/envs/CEMO_env/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1085, in run runtime = self._run_wrapper(runtime) File "/om/user/yuwenh/envs/CEMO_env/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1728, in _run_wrapper runtime = self._run_interface(runtime) File "/om/user/yuwenh/envs/CEMO_env/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1762, in _run_interface self.raise_exception(runtime) File "/om/user/yuwenh/envs/CEMO_env/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1686, in raise_exception **runtime.dictcopy())) RuntimeError: Command: dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Standard output: cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610 cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit Pathway name: lh.cst Subject name: START_610 Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Lower threshold for probability: 0.20 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Standard error: ___ 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] dmri_pathstats error
Dear DTI experts: I am wondering if anyone knows a solution to this tracula script error: dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610 cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug sysname Linux hostname node031 machine x86_64 user yuwenh Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit Pathway name: lh.cst Subject name: START_610 Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Lower threshold for probability: 0.20 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Your help would be greatly appreciated, Yuwen ___ 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] what program generates "path.map.txt" for dmri_pathstats to run?
Dear DTI experts: I am wondering if anybody could provide any information to help me out with this constant error that I am desperate to resolve? I just need to know what program generates this "path.map.txt" for the tracula script dmri_pathstats to run through? dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610 cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug sysname Linux hostname node031 machine x86_64 user yuwenh Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit Pathway name: lh.cst Subject name: START_610 Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Lower threshold for probability: 0.20 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Your help is being greatly appreciated, Yuwen -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of freesurfer-requ...@nmr.mgh.harvard.edu Sent: Friday, July 14, 2017 4:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 25 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: PETsurfer AC/TOF (Douglas N Greve) 2. Re: 3G1V.fsgd (Douglas N Greve) 3. Re: GLM Analysis Number of vertices and Area (Douglas N Greve) 4. Regression diagnostic in context of surface-based analysis (Antonin Skoch) 5. bbregister + mri_vol2vol different results (Paul Glad Mihai) 6. R: Re: 3G1V.fsgd (std...@virgilio.it) 7. R: R: Re: 3G1V.fsgd (std...@virgilio.it) 8. Re: R: Re: 3G1V.fsgd (Douglas N Greve) 9. Mid point on Freeview (Trisanna Sprung-Much) 10. vertex-wise contra-lateral mapping on an ico surface (Burke Rosen) 11. Re: Mid point on Freeview (Bruce Fischl) 12. Re: ERROR: dimension mismatch between input volume andseg - VolumeROICorticalThickness (M Janani) 13. R: Re: R: Re: 3G1V.fsgd (std...@virgilio.it) 14. problems with recon-all in 6.0 (Lars M. Rimol) -- Message: 1 Date: Thu, 13 Jul 2017 16:28:24 -0400 From: Douglas N Greve Subject: Re: [Freesurfer] PETsurfer AC/TOF To: freesurfer@nmr.mgh.harvard.edu Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed Sorry, I don't know what the difference is. I always use the mean update volume as the template for registration. On 07/13/2017 01:57 PM, Fu, Jason (NIH/NINDS) [F] wrote: > ac/tof is attenuation corrected/time of flight. Ac/hd is attenuation > corrected/head. > > -Original Message- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Thursday, July 13, 2017 12:52 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] PETsurfer AC/TOF > > sorry, what is an ac/tof file? > > > On 07/13/2017 12:12 PM, Fu, Jason (NIH/NINDS) [F] wrote: >> Hi, >> >> I am currently using PETsurfer PVC to determine glucose metabolism >> differences in certain structures between the brain hemispheres. I am >> currently using ac/tof files to coregister to the anatomy. One of the >> patients did not have the ac/tof files, would ac/hd files work instead? >> >> Thanks, >> Jason Fu >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax:
Re: [Freesurfer] Help for dmri_pathstats error
Dear DTI Experts: I wonder if there is anyone that might know a direction to look into this error? I just need to know what program generates this "path.map.txt" for the tracula script dmri_pathstats to run through. dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610 cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug sysname Linux hostname node031 machine x86_64 user yuwenh Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit Pathway name: lh.cst Subject name: START_610 Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Lower threshold for probability: 0.20 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Any thought would be greatly appreciated. Thank you - Yuwen ___ 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] Brain editing for TRACULA?
Dear DTI Expert: I wonder I may get help with this quick question - Is the brain editing necessary (or critical) for TRACULA processing? Thank you! Yuwen ___ 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] Re. TRACULA configuration file
External Email - Use Caution Dear TRACULA expert: I wonder if it is recommended to turn on performing of registeration-based B0-inhomogeneity compensation (set dob0 = 1) and utilise the field map magnitude and phase dicom files? The default is set to not to use these functions, but I wonder whether using them may result in better outcomes? Thank you, Yuwen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re. Help with TRACULA configuration file
External Email - Use Caution Dear TRACULA expert: I wonder if it is recommended to turn on performing of registeration-based B0-inhomogeneity compensation (set dob0 = 1) and utilise the field map magnitude and phase dicom files? The default is set to not to use these functions, but I wonder whether using them may result in better outcomes? Thank you, Yuwen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
