Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30066 discussions

Masking option for tractstats2table
by Derek A Pisner 19 Jul '17

19 Jul '17

Hi Anastasia or Krish, Is there a version of tractstats2table floating around that allows me to apply a binarized mask to extract stats for sub-sections of tracts? If not, I can write my own—just wanting to see if such a function already exists so that I don’t reinvent the wheel… Derek Pisner Doctoral Student CLA 4.600 Mood Disorders Laboratory (MDL) Department of Psychology | The University of Texas at Austin

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dmri_motion -T threshold
by Buckless, Colleen 19 Jul '17

19 Jul '17

Hi All, I've been using dmri_motion to quantify motion in our DTI data. We are uncertain how to determine what the -T threshold should be. We have read through the wiki and the related papers and are confused what this number represents, how it effects the output, and the rational for selecting a specific threshold value. We have tried the default (100) and almost all of our scans have the floor values (0 and 1) for percent bad slices and average dropout score, and we are concerned that this value is most likely inappropriate for our data. We have tried other values but are unsure what a suitable threshold value should be for our data. We are concerned that this number effects the output, and want to make sure we are using an appropriate value. What is the best way to select the -T threshold and the rational for selecting one value versus another? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless(a)kennedykrieger.org ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: [Freesurfer] what program generates "path.map.txt" for dmri_pathstats to run?
by Yuwen Hung 18 Jul '17

18 Jul '17

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(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Friday, July 14, 2017 4:14 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 25 Send Freesurfer mailing list submissions to freesurfer(a)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(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)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(a)virgilio.it) 7. R: R: Re: 3G1V.fsgd (stdp82(a)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(a)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 <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PETsurfer AC/TOF To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <d5234734-a0cc-e310-cd02-d73229c9437c(a)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(a)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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/ ------------------------------ Message: 2 Date: Thu, 13 Jul 2017 16:30:54 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] 3G1V.fsgd To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1139ca82-1846-fbb5-9650-f10a5ad867c4(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 07/13/2017 10:37 AM, stdp82(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/ ------------------------------ Message: 3 Date: Thu, 13 Jul 2017 16:38:21 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] GLM Analysis Number of vertices and Area To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <7ef1f42e-31d6-fe1e-7e89-9e04338a8a9d(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/ ------------------------------ Message: 4 Date: Thu, 13 Jul 2017 22:48:03 +0200 From: Antonin Skoch <ansk(a)ikem.cz> Subject: [Freesurfer] Regression diagnostic in context of surface-based analysis To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1034294575-17116(a)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

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WM edits not being applied to surfaces
by Dan Grupe 18 Jul '17

18 Jul '17

Hi all, We are making manual white matter edits using the "voxel edit" tool in freeview with “recon editing” selected. These edits are being saved to wm.mgz but not applied to the white matter surfaces (using the command: recon-all -autorecon2-wm -autorecon3 -subjid). We are using FreeSurfer v5.3 on OS X version 10.11.6. I have seen this question posed by others on the message board in the last few months, but haven’t figured out if there is a known solution. Thanks for any suggestions or support! -Dan ------ Dan Grupe, Ph.D. Assistant Scientist Center for Healthy Minds University of Wisconsin-Madison ------ grupe(a)wisc.edu<mailto:grupe@wisc.edu> 608-263-7572 http://brainimaging.waisman.wisc.edu/~dgrupe

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mris_label2annotation error
by francesca bottino 18 Jul '17

18 Jul '17

Hello FreeSurfer Developers, I'm attempting to convert only one file.label in one file.annot. I'm using the command MRIS_LABEL2ANNOTATION. mris_label2annot --s fsaverage --h lh --l '/home/mlucignani/Desktop/TUTTO/merge/MERGE_AREA_1/originali_lh/lh_FILE_1.label' ERROR: need to specify color table file I don't know wich color table file insert

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Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness
by M Janani 18 Jul '17

18 Jul '17

Hi Douglas Greve, Yes, I'm getting the same result as mentioned below. Regards, Janani ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Did you get exactly the same error? On 07/14/2017 02:05 AM, M Janani wrote: > > Hi Douglas Greve > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…>, > > Thanks for your support. > > I tried with the --reshape-factor 6. But it didn't work for me. > > The segmentation was created using the below mentioned data > > 1.SPM standard ROI > > 2..dat file generated using the T1.nii(available in SPM8 template) and > fsaverage. > > Please help us to proceed further. > > Regards, > > Janani > > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > How did you create the segmentation? You can change the shape of the > seg with mri_surf2surf --reshape 6 --s fsaverage --hemi lh --sval > seg.mgh --tval seg.reshape.mgh > > On 7/7/17 10:15 AM, M Janani wrote: > Hi Team, > > I'm attempting to extract cortical thickness values for a > region-of-interest (ROI) defined in volume spacesubject for PiB MRI. > > I got the below mentioned error while computing the stats value > cwd > > cmdline mri_segstats --seg > freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh --in > lh.thickness.fsaverage.mgh --sum segstats-CBLROI.txt > > sysname Linux > hostname teslak80 > machine x86_64 > user lakshman > UseRobust 0 > Loading /freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh > Loading lh.thickness.fsaverage.mgh > ERROR: dimension mismatch between input volume and seg > input 27307 1 6 > seg 23406 1 7 > > I tried with the solution provided in the below mail, but it didn't > work for me > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-January/027405.…<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.h…> > > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.h…> > > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.h…> > > Any help would be really helpful. > Regards, > Janani > ::DISCLAIMER:: > ---------------------------------------------------------------------------------------------------------------------------------------------------- > > The contents of this e-mail and any attachment(s) are confidential and > intended for the named recipient(s) only. E-mail transmission is not > guaranteed to be secure or error-free as information could be > intercepted, corrupted, lost, destroyed, arrive late or incomplete, or > may contain viruses in transmission. The e mail and its contents (with > or without referred errors) shall therefore not attach any liability > on the originator or HCL or its affiliates. Views or opinions, if any, > presented in this email are solely those of the author and may not > necessarily reflect the views or opinions of HCL or its affiliates. > Any form of reproduction, dissemination, copying, disclosure, > modification, distribution and / or publication of this message > without the prior written consent of authorized representative of HCL > is strictly prohibited. If you have received this email in error > please delete it and notify the sender immediately. Before opening any > email and/or attachments, please check them for viruses and other > defects. > > ---------------------------------------------------------------------------------------------------------------------------------------------------- > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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bbregister + mri_vol2vol different results
by Paul Glad Mihai 18 Jul '17

18 Jul '17

Hello, I'm getting two different results from the coregistration step. When I run bbregister on the mean epi it coregisters properly and writes out _bbreg.nii. The next step involves registering the realigned epi time series to the T1 image using the same transform matrix calculated from the mean image. But the results fail miserably. I've attached some sample images. I came across the same result after transforming the matrix it to ITK space and applying the transform using ANTs' applyTransform, which tells me that the ITK conversion works, but this registration goes wrong. Or I may not really understand what I'm doing, lol. Here are the commands: bbregister --t2 --epi-mask --init-header --fslmat /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat --reg /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat --o /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii --mov /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii --s sub-01 mri_vol2vol --fsl /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat --mov /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii --targ /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz --o /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii Regards, Glad -- Paul Glad Mihai, PhD Independent Research Group "Neural Mechanisms of Human Communication" Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A, 04103 Leipzig, Germany Phone: +49 (0) 341-9940-2478 E-mail: mihai(a)cbs.mpg.de

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how to extract data that are removed effects of covariates
by hiroki.sato＠med.tohoku.ac.jp 18 Jul '17

18 Jul '17

Dear experts, I’m new to analysis with use of the Freesurfer. I compared grey matter thickness between two groups using Qdec with several covariates (i.e. nuisance factors) such as age, gender and intracranial volume (ICV). I found regions that significantly differed between the two groups. I would like to ask about how to extract data in these regions in each subject related with the effect of groups after effects of covariates were removed. On the discussion forum, I found the solutions to extract raw data in the ROIs. But in the communication, they did not discuss about how to remove covariate’s effects. I would appreciate if you could let me know about how to extract values related with the effect of group or how to remove covariate’s effects from raw data. Thank you for your guidance! Best, Hiroki

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RBV PVC: Saving output file before upsampling
by SudEEpti 18 Jul '17

18 Jul '17

Hello, Is there a way to save the PVC (RBV) output in native PET resolution, before upsampling? Would you also be able to share the command that is used for upsampling? I would like to play with a different type of interpolation. Thank you very much. Su

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t1 mri_convert fails
by clemens.schroeder＠uzh.ch 18 Jul '17

18 Jul '17

Hello Developers I am trying to run recon-all on a number of MP2RAGE T1 images but I fail. Using tkmedit, I noticed that orig/001.mgz looks fine but orig.mgz is all-0. Also, mri_convert assumes TE=0, which is false. Do you have any advice for me? The recon-all.log is attached FreeSurfer freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c My OS is OSX El Capitan 10.11.6 uname -a: Darwin MAC15-0004.local 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 Here is the print from the command: MAC15-0004:t1 clschr$ recon-all -s example -i example.nii -all -hippocampal-subfields-T1 Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Users/clschr/Desktop/7T/t1 Actual FREESURFER_HOME /Applications/freesurfer Darwin vpn-89-206-117-41.uzh.ch 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 /Users/clschr/Desktop/7T/t1/example \n mri_convert /Users/clschr/Desktop/7T/t1/example.nii /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz \n mri_convert.bin /Users/clschr/Desktop/7T/t1/example.nii /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/clschr/Desktop/7T/t1/example.nii... niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999967, 0.00331038, 0.00735774) j_ras = (0.00506133, 0.967573, 0.252542) k_ras = (0.00628314, -0.252571, 0.967558) writing to /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Jul 18 09:20:32 CEST 2017 Found 1 runs /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz \n /Users/clschr/Desktop/7T/t1/example \n mri_convert /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz --conform \n mri_convert.bin /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999967, 0.00331038, 0.00735774) j_ras = (0.00506133, 0.967573, 0.252542) k_ras = (0.00628314, -0.252571, 0.967558) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz... \n mri_add_xform_to_header -c /Users/clschr/Desktop/7T/t1/example/mri/transforms/talairach.xfm /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Jul 18 09:20:41 CEST 2017 /Users/clschr/Desktop/7T/t1/example/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Users/clschr/Desktop/7T/t1/example/mri /Applications/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin vpn-89-206-117-41.uzh.ch 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 Tue Jul 18 09:20:41 CEST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks(a)gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.37996 /Users/clschr/Desktop/7T/t1/example/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.37996/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.37996/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.82077e-10, -4.65661e-10) j_ras = (-4.65661e-10, 0, -1) k_ras = (3.49246e-10, 1, 1.49012e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.37996/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jul 18 09:20:45 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.37996/nu0.mnc ./tmp.mri_nu_correct.mni.37996/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.37996/0/ -iterations 1000 -distance 50 [clschr@vpn-89-206-117-41.uzh.ch:/Users/clschr/Desktop/7T/t1/example/mri/] [2017-07-18 09:20:45] running: /Applications/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.37996/0/ ./tmp.mri_nu_correct.mni.37996/nu0.mnc ./tmp.mri_nu_correct.mni.37996/nu1.imp Error: Composite mask volume is empty. Check for one of the following: 1) the user supplied mask is empty (all zeros) 2) the values within the region of interest are entirely less than one 3) the user supplied background threshold is too high 4) the intersection of the various masking options yields an empty mask nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Darwin vpn-89-206-117-41.uzh.ch 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64 Here is the header information of the image: % vpn-89-206-116-146:t1 clschr$ fslhd example.nii filename example.nii sizeof_hdr 348 data_type FLOAT32 dim0 3 dim1 180 dim2 256 dim3 256 dim4 1 dim5 1 dim6 1 dim7 1 vox_units Unknown time_units Unknown datatype 16 nbyper 4 bitpix 32 pixdim0 0.000000 pixdim1 0.800000 pixdim2 0.781000 pixdim3 0.781000 pixdim4 0.006900 pixdim5 0.000000 pixdim6 0.000000 pixdim7 0.000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 0.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name T1TFE intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 -0.799974 0.003954 0.004913 71.792442 qto_xyz:2 0.002648 0.755674 -0.197258 -65.335892 qto_xyz:3 0.005892 0.197235 0.755663 -137.084869 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Scanner Anat sform_code 1 sto_xyz:1 -0.799974 0.003953 0.004907 71.792442 sto_xyz:2 0.002648 0.755674 -0.197258 -65.335892 sto_xyz:3 0.005886 0.197235 0.755663 -137.084869 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 descrip phase=-y;TE=2.5;time=20170201134952; aux_file ;Philips;WIP MP2RAGE 0p

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