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: 0.200000 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request@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
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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 (stdp82@virgilio.it) 7. R: R: Re: 3G1V.fsgd (stdp82@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 and seg - VolumeROICorticalThickness (M Janani) 13. R: Re: R: Re: 3G1V.fsgd (stdp82@virgilio.it) 14. problems with recon-all in 6.0 (Lars M. Rimol)
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Message: 1 Date: Thu, 13 Jul 2017 16:28:24 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PETsurfer AC/TOF To: freesurfer@nmr.mgh.harvard.edu Message-ID: d5234734-a0cc-e310-cd02-d73229c9437c@nmr.mgh.harvard.edu 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:greve@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
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Hi Yuwen - This file is generated by the command dmri_paths, which is run before the dmri_pathstats command. You can see the exact command lines in scripts/trac-all.cmd (and the full output in scripts/trac-all.log).
Best,
a.y
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yuwen Hung [yuwenh@mit.edu] Sent: Friday, July 14, 2017 8:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: 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: 0.200000 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request@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-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@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 (stdp82@virgilio.it) 7. R: R: Re: 3G1V.fsgd (stdp82@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 and seg - VolumeROICorticalThickness (M Janani) 13. R: Re: R: Re: 3G1V.fsgd (stdp82@virgilio.it) 14. problems with recon-all in 6.0 (Lars M. Rimol)
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Message: 1 Date: Thu, 13 Jul 2017 16:28:24 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PETsurfer AC/TOF To: freesurfer@nmr.mgh.harvard.edu Message-ID: d5234734-a0cc-e310-cd02-d73229c9437c@nmr.mgh.harvard.edu 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:greve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Message: 2 Date: Thu, 13 Jul 2017 16:30:54 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3G1V.fsgd To: freesurfer@nmr.mgh.harvard.edu Message-ID: 1139ca82-1846-fbb5-9650-f10a5ad867c4@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8; format=flowed
On 07/13/2017 10:37 AM, stdp82@virgilio.it wrote:
Dear FS group,
I don't understand how I should build the contrast for 3 groups 1 covariate. No specific example is provided within fsgd example and also other colleagues report the same problem in the mail list. Please could you provide us details on this topic? Especially, how should be the g3v1.intercept and g31v.slope?
1 -1 0 0 0 0 1 0 -1 0 0 0 for g3v1.intercept.mtx
This is the main effect of group on the intercept regressing out the effect of covariate.
and 0 0 0 1 -1 0 0 0 0 1 0 -1 for g3v1.slope.mtx
This is the main effect of group on the slope regressing out the effect of group intercept.
are corrected?
Waiting for you very wellcome suggestions
Thanks and kind regards
Stefano
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Message: 3 Date: Thu, 13 Jul 2017 16:38:21 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM Analysis Number of vertices and Area To: freesurfer@nmr.mgh.harvard.edu Message-ID: 7ef1f42e-31d6-fe1e-7e89-9e04338a8a9d@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8; format=flowed
I'm not sure what you mean. Do you want stats for every cluster regardless of significance? If so, you can run the monte carlo correction with a clusterwise p-value (--cwp in mri_glmfit-sim) of 1.0
On 07/13/2017 11:52 AM, Aman Montazeri wrote:
Hello Friends,
Sorry for the simple question.
I am doing GLM analysis using QDEC between two groups (one discrete variable), then I run the Monte-Carlo clustering and got the stats of my cluster.
My supervisor asked me to get the Stats of blobs/clusters (area and number of vertices in each area) before applying the Monte-Carlo (only after GLM analysis/comparison) I would really appreciate if you could help me with getting those stats, as I can't figure out how to do it.
Thank you, Aman
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Message: 4 Date: Thu, 13 Jul 2017 22:48:03 +0200 From: Antonin Skoch ansk@ikem.cz Subject: [Freesurfer] Regression diagnostic in context of surface-based analysis To: freesurfer@nmr.mgh.harvard.edu Message-ID: 1034294575-17116@posta.medicon.cz Content-Type: text/plain; charset="utf-8"
Dear experts,
I am looking for a way how to effectively run a regression model diagnostic in context of surface-based analysis.
My example case is the regression model where response variable is cortical thickness and explanatory variable is continuous (disease duration). The statistical linear modelling uses several principial approaches to find model which best describes the studied relation in the data, namely:
1. model simplification by elimination of insignificant effects 2. transformation of dependent variable to improve normality of residuals 3. transformation of explanatory variable to improve model fit or use of linear combination of various terms in explanatory variable (for example apart from linear term to include also quadratic and higher-order polynomial terms)
My question is, how to effectively exploit methods 2 and 3 in context of vertex-wise surface-based analysis? Could you please comment on what tools inside FreeSurfer framework can be used for this purpose? What is your common aproach to find regression model which best approximates the relation present in the data?
Thank you in advance for pointing me to right direction.
Regards,
Antonin Skoch
freesurfer@nmr.mgh.harvard.edu
-
Yendiki, Anastasia -
Yuwen Hung