Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] reposition surface for pial surface
by Antonin Skoch 11 Jan '17

11 Jan '17

Dear Paul, I cannot see your attachment since I am only getting mail digest (without attachments) and the mail archive does not store attachments. I do not know for which option of surface reposition your question refers to. But, I hope when you play with the tool, you will figure out, as I did. Also, what do you mean, what step you should start? In case of "volume based" reposition, when you click on "apply", you internally invoke customized mris_make_surfaces code on the surface you want to modify. The run takes several seconds and when it is finished, you will see the result of reposition. Then you inspect the surface and when you are satisfied, you save the modified surface (by the proper name, i.e. overwriting the original surface, you can save it by different name before using this tool to be able to get back). Then you should rerun remaining steps of recon-all, which for example in case of V6beta after repositioning pial surface means running recon-all -s my_subject -cortribbon -parcstats -cortparc2 -parcstats2 -cortparc3 -pctsurfcon -hyporelabel -aparc2aseg -apas2aseg -segstats -wmparc -balabels Antonin Thank you very much Antonin. I do appreciate it. Do I need to insert a vertex number or just the coordinates? Because when i clicked on the surface outside the pial (see screenshot) the vertex = N/A ( see screenshot). ALso, what step of recon-all should i start? (autorecon-2 or autorecon3)? Best, PaulOn Tue, Jan 10, 2017 at 3:52 PM, Antonin Skoch <a...(a)ikem.cz> wrote: > Dear Paul, > > I could chime in with my current limited experiences with this tool (using > V6beta version of freeview). Maybe they could be helpful for you. > > Most straigthforward is using "edit coordinate": > > Select the surface you want to edit. > Select tools-reposition surface - edit coordinate. > With shift + left mouse button click on the surface to pick particular > vertex. > Manually enter new coordinates of the vertex. > Save surface to store edits. > This is prohibitively time consuming in case of large error, so it is > usable only in case of small errors. > > However, you can try to use combination of "edit coordinate" and "smooth". > By smoothing you can nudge some area of adjacent vertices to desired > position. > > I was partially successful also with using > reposition surface - volume based - coordinate: > With shift + left mouse button select particular vertex > In "volumes", load volume according to what you want to reposition the > surface. > With shift + ctrl + left mouse button click at the coordinate you want to > reposition the surface to. > Save surface to store edits. > > Regarding the parameters: > The "size" textfield determine the extent of the vertex neighbourhood > which would be repositioned. Do not use too large value since then the > behaviour is unpredictable, in my case the maximal resonable value is > around 5. > I am not sure about "sigma" parameter, maybe it has to do something with > the smoothing (of the underlying volume?), however in my case altering > this parameter did not change behaviour much. > Also, the "gradient direction" in my case did not change much, in many > cases it produced identical result regardless of the gradient direction > selected. > > In most cases, I was not satisfied with the result of the reposition, the > particular vertex moved to desired position, however position of adjacent > vertices did not make sense, mostly the surface got very jagged and > irregular, with worsening of the position in areas where the position was > good previously, etc. However, subsequent using of "smooth" usually > improved the shape and after many iterations I finally arrived to desired > shape of surface. > > I also tried to study the relevant source code to learn the behavior of > this tool and the significance of the parameters, but it is very > complicated to me to comprehend (so far..). > > Note that after using this tool you should rerun remaining code of > recon-all > > ReconAllDevTable > https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable > (for development version) would tell you which particular steps should be > rerun. > Please note that in case of rerun of recon-all from start you will lose > all modifications of surfaces you achieved using this tool. > > And, particularly, many surface errors can be corrected by editing the > volume (particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control > points to the white matter. > Large errors of ?h.white (and subsequently ?h.pial) can be caused of > wrongly corrected topological defect (which you can diagnose by inspecting > ?h.orig.nofix and ?h.orig). In that case editing of wm.mgz or aseg.mgz > would help to correct the issue. > I also came across the error when ?h.white was cut off the particular > gyrus near midline, which was caused by erroneous labeling of cortex in > aseg.mgz (gyrus was attributed to contralateral hemisphere). Editing of > aseg.mgz by assignment of the gyrus to correct hemisphere corrected the > error. > > Also, altering several of global parameters of mris_make_surfaces, as > listed for example here > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37990.html > > could help you to get satisfactory results (however, the altering of these > parameters should be done in my opinion for all subjects in the study to > avoid bias). > > Regards, > > Antonin > > Thanks bruce for your response. Since there is no documentation, how can i > use it because I seen trends on the forum where it was suggested to use > reposition surface ( > e.g.https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/0261…) > Use = directions and parameters to input. Thanks > Best, > Paul > > On Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl <fis...(a)nmr.mgh.harvard.edu> > wrote: > > > Hi Paul > > > > sorry, this is something that Ruopeng put together for me to mess around > > with - there isn't any documentation > > > > cheers > > Bruce > > > > On Tue, 10 Jan 2017, miracle ozzoude wrote: > > > > Hello Freesurfer, I would like to learn how to use the reposition surface > >> tool in freeview. Specifically, what parameters to enter in the gui (see > >> screenshots). Is there any documentation on how to use it if not, can > >> someone with experience work me through it. Thank you. > >> best, > >> Paul >

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vertex-wise ROI analysis
by Clara Kühn 11 Jan '17

11 Jan '17

Dear FreeSurfer experts, is it possible to do a vertex-wise analysis on ROIs? When I extract the values per subject for (e.g.) the superior temporal gyrus grom the aparc file it is a pretty big region to get only one value. I would like to analyze it on a vertex level so I can see where exactly the effects are. I'd be really happy for any suggestions! Thank you Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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pial surface vs. aparc segmentation inconsistency
by Gabor Perlaki 11 Jan '17

11 Jan '17

Dear all, In some of our subjects the border of ctx_lh_parahippocampal (green color) is inconsistent with the border of pial surface (red color) in the sense that some small region within the pial surface is segmented as cerebellum (orange) coming from the subcortical segmentation stream. This problem is present in all three planes. It is hard to decide whether the colored border of ctx_lh_parahippocampal or the pial surface is more realistic, but it would be nice to know which one is used for the parahippocampal statistics in lh.aparc.stats file. Do I need to correct for this inaccuracy? How should I correct this type of missegmentation? Best Regards, Gabor <petzinger.gabor(a)gmail.com>

1 0

Is the average surface in MNI space?
by Ling Zhao 10 Jan '17

10 Jan '17

Dear experts, 1. From the FreeSufer wiki we all knows all of the processing and the generated files are in the Talairach (MNI305) coordinate. The FreeSurfer operates in a conformed space, which is different from the original structural image space that it has received as an input. If I want to use the generated surfaces or labels as masks (which is in Talairach space) for DTI probtrackx (which is need in diffusion space). How should I do? 2. In your wiki I see the information as following: “Average Surface Construction The averagesurface is constructed by computing the Talairach (MNI305) coordinate at each vertex for each subject (based on the talairach.xfm matrix for that subject). These coordinates are then mapped into the common surface space and averaged together so that the coordinate of a vertex in the common surface space is the average of the Talairach coordinates from the corresponding surface locations of the individuals. This results in the averagesurface overlaying nicely on the average (MNI305) volume. ” Is the MNI305 in the MNI space? Can you tell me the meaning of the MNI305 in “Talairach (MNI305) coordinate”? After the averagesurface overlaying nicely on the average (MNI305) volume. Is the averagesurface in the MNI space or in the Talairach space / common surface space? Best wishes Ling Zhao -- Center for the Study of Applied Psychology, Key Laboratory of Mental Health and Cognitive Science of Guangdong Province, School of Psychology, South China Normal University, Guangzhou 510631, P. R. China

2 1

reposition surface for pial surface
by Antonin Skoch 10 Jan '17

10 Jan '17

Dear Paul, I could chime in with my current limited experiences with this tool (using V6beta version of freeview). Maybe they could be helpful for you. Most straigthforward is using "edit coordinate": Select the surface you want to edit. Select tools-reposition surface - edit coordinate. With shift + left mouse button click on the surface to pick particular vertex. Manually enter new coordinates of the vertex. Save surface to store edits. This is prohibitively time consuming in case of large error, so it is usable only in case of small errors. However, you can try to use combination of "edit coordinate" and "smooth". By smoothing you can nudge some area of adjacent vertices to desired position. I was partially successful also with using reposition surface - volume based - coordinate: With shift + left mouse button select particular vertex In "volumes", load volume according to what you want to reposition the surface. With shift + ctrl + left mouse button click at the coordinate you want to reposition the surface to. Save surface to store edits. Regarding the parameters: The "size" textfield determine the extent of the vertex neighbourhood which would be repositioned. Do not use too large value since then the behaviour is unpredictable, in my case the maximal resonable value is around 5. I am not sure about "sigma" parameter, maybe it has to do something with the smoothing (of the underlying volume?), however in my case altering this parameter did not change behaviour much. Also, the "gradient direction" in my case did not change much, in many cases it produced identical result regardless of the gradient direction selected. In most cases, I was not satisfied with the result of the reposition, the particular vertex moved to desired position, however position of adjacent vertices did not make sense, mostly the surface got very jagged and irregular, with worsening of the position in areas where the position was good previously, etc. However, subsequent using of "smooth" usually improved the shape and after many iterations I finally arrived to desired shape of surface. I also tried to study the relevant source code to learn the behavior of this tool and the significance of the parameters, but it is very complicated to me to comprehend (so far..). Note that after using this tool you should rerun remaining code of recon-all ReconAllDevTable https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable (for development version) would tell you which particular steps should be rerun. Please note that in case of rerun of recon-all from start you will lose all modifications of surfaces you achieved using this tool. And, particularly, many surface errors can be corrected by editing the volume (particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control points to the white matter. Large errors of ?h.white (and subsequently ?h.pial) can be caused of wrongly corrected topological defect (which you can diagnose by inspecting ?h.orig.nofix and ?h.orig). In that case editing of wm.mgz or aseg.mgz would help to correct the issue. I also came across the error when ?h.white was cut off the particular gyrus near midline, which was caused by erroneous labeling of cortex in aseg.mgz (gyrus was attributed to contralateral hemisphere). Editing of aseg.mgz by assignment of the gyrus to correct hemisphere corrected the error. Also, altering several of global parameters of mris_make_surfaces, as listed for example here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37990.html could help you to get satisfactory results (however, the altering of these parameters should be done in my opinion for all subjects in the study to avoid bias). Regards, Antonin Thanks bruce for your response. Since there is no documentation, how can i use it because I seen trends on the forum where it was suggested to use reposition surface ( e.g. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.h…) Use = directions and parameters to input. Thanks Best, PaulOn Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl <fis...(a)nmr.mgh.harvard.edu> wrote: > Hi Paul > > sorry, this is something that Ruopeng put together for me to mess around > with - there isn't any documentation > > cheers > Bruce > > On Tue, 10 Jan 2017, miracle ozzoude wrote: > > Hello Freesurfer, I would like to learn how to use the reposition surface >> tool in freeview. Specifically, what parameters to enter in the gui (see >> screenshots). Is there any documentation on how to use it if not, can >> someone with experience work me through it. Thank you. >> best, >> Paul

2 1

Help - Error: cannot unpack mosaics without ASCII header
by Caleb Comoglio 10 Jan '17

10 Jan '17

Hello, I am having trouble with the MRI_convert portion of recon-all. I get the error below when I run recon-all and when I run MRI_convert independently of recon-all. WARNING: file Desktop/3T_20161201_131733544/MR000004 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header Prior to getting the error I get the following message: Scanning Directory INFO: Found 2316 files in Desktop/3T_20161201_131733544 INFO: Scanning for Series Number 2 INFO: found 192 files in series INFO: loading series header info. INFO: sorting. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 192, Files Expected (lRep+1): 1 Do you have any suggestions? Additional system info is below: 1) OS: MacOS Sierra (10.12.2) 2) FS software version: freesurfer-Darwin-lion-stable-pub-v5.3.0 3) Data is MPRAGE directly from a siemens machine *Caleb C. Comoglio, BSBME* Graduate Research Fellow Bioelectronics Laboratory, IUPUI ccomogli(a)iupui.edu (574) 727-1620

2 1

Multiple comparison correction on subcortical volume
by neuroimage analyst 10 Jan '17

10 Jan '17

Hi, I extracted thalamic, caudate, and putamen volume (left hemisphere), and cingulate thickness (right hemisphere) from freesurfer's parcellation. Then I compare these volumes and thickness across two groups using R and found significant differences in these measurements. Do I have to correct for multiple comparisons? If yes, how do I do that? Does this make sense to divide the p-value/4 and if the p-value < p-value/4 then the test is Bonferroni corrected? If no, what do I say in my results that the test statistic is not inflated? Thanks Regards --VM

2 1

autorecon1 crash (with nu_correct).
by Jamie Hanson 10 Jan '17

10 Jan '17

Hello Freesurfer List, I was running into issues processing subjects, with errors just getting through the autorecon1 step of the pipeline. My terminal outputs the following: ==== /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri /usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Tue Jan 10 12:53:44 EST 2017 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.129237 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.129237/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, -1.32349e-23, -1.32349e-23) j_ras = (0, 1.49012e-08, -1) k_ras = (0, 1, 1.49012e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.129237/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jan 10 12:53:47 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.129237/nu0.mnc ./tmp.mri_nu_correct.mni.129237/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.129237/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/pkg/freesurfer//mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 10007 exited with ERRORS at Tue Jan 10 12:53:47 EST 2017 For more details, see the log file /home/jamielh/Volumes/Hanson/ Pardini_Projects/K_award/10007/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting ==== Searching the FS list, I saw that I originally thought this was an incompatibility with the current stable Freesurfer version and the most recent MNI tools. To troubleshoot that issue, I installed the dev version of Freesurfer (as noted by this thread: https://mail.nmr.mgh. harvard.edu/pipermail///freesurfer/2016-September/047734.html) The error however still persists (even using the dev version). Anyone else run into this issue or have thoughts about troubleshooting it? Thanks much! Best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

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Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream
by Tamara Tavares 10 Jan '17

10 Jan '17

Hi Dr. Reuter, Thank you for the clarification. The differences I am seeing are also in the T1.mgz file in the longitudinal run folder. I assume it is okay to use the T1.mgz from the longitudinal outputs as the original image as I can easily compare the same slice across different time points? Also, on a related note, I have two scans (time 1 and time 2) that doesn't seem to align perfectly with the template or with each other. When I use the opacity slider to transition from the template to time 1 it looks like the brain is 'moving in'. When I transition from template to time 2 the brain seems to 'pop out'. Similarly, when I transition from time 1 to time 2, it looks like the brain is popping out. With my other images, there is a smooth transition from time 1 to time 2 and a relatively smooth transition from the template to the time points. Do you think this is problematic? Thank you again for your help. Best, Tamara Message: 4 Date: Wed, 28 Dec 2016 11:20:36 +0100 From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <F2352B06-D00A-409A-9FB3-7AE1FD6EA20B(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=us-ascii Hi Tamara, three out of how many? I would probably remove those three as whatever you measure in them could be driven by the acquisition differences, but it depends on what acquisition differences you have. If it is only small differences, like tiny deviations in the voxel size etc, it should be OK. I have no idea where the other intensity differences could come from. If you see them in the original inputs, maybe an MR physicist could take a look and advise. If you have a concrete case where the inputs are OK, but you think that in FS processed images show different contrast or intensities, I would need to have those images to see if I can replicate that. Best, Martin

2 1

reposition surface for pial surface
by miracle ozzoude 10 Jan '17

10 Jan '17

Hello Freesurfer, I would like to learn how to use the reposition surface tool in freeview. Specifically, what parameters to enter in the gui (see screenshots). Is there any documentation on how to use it if not, can someone with experience work me through it. Thank you. best, Paul

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