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30132 discussions

segmentation problem
by Manuela Costa 10 Jan '19

10 Jan '19

External Email - Use Caution Dear all, We have a subject for whom we would like to do hippocampal subfield and amygdalar nuclei segmentation. Unfortunately, this subject has a large lesion in the right hemisphere. Looking at the aseg, the segmentation of the bilateral amygdala are fine, but the right hippocampus becomes incorrectly segmented towards the posterior end (shown in the attached images). Is there any way that this can be corrected, manually or otherwise? Will there be further problems down the line when we proceed with the subfield segmentation? We are running freesurfer-linux-centos6_x86_64-dev-20181121-910b841. Thanks in advance! Regards, Manuela -- Manuela Costa, PhD Cognitive Neuroscientist Lab. for Clinical Neuroscience,CTB, Madrid <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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problem with contrast in 1st-level analysis
by xi star 10 Jan '19

10 Jan '19

External Email - Use Caution Hi! FS Experts! In the fMRI experiment, there are 2 conditions: 1# 3D picture 2# zero disparity picture interleaved with fixation block (0). To compare 3D-vs-zero disparity, I used command: mkcontrast-sess -a 1 -c 2 -nosumconds but the results showed more activation then expected. To find the problem, I compared 3D-vs-fix (-a 1 -c 0), the result shows the same as 3D-vs-zero disparity. My question is: why the two contrast ( [1 0; 0 -1] and [1 0] ) came to the same result? How can I compared the two conditions? Thanks a lot ! Yours, Star

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freeview.bin: Fatal IO error: client killed
by 이충섭 10 Jan '19

10 Jan '19

External Email - Use Caution Hello Freesurfer developers, First, the recon-all command was completed without errors. However, the following command results in the same error as the mail subject . freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red If i enter only freeview, it runs without error.. Can you tell me what's wrong? Thank you. 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) platform: Ubuntu 16.04.5 LTS 3)uname -a: Linux eclgpu4 4.4.0-135-generic #161-Ubuntu SMP Mon Aug 27 10:45:01 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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Yeo labels
by Tosun, Duygu 09 Jan '19

09 Jan '19

External Email - Use Caution Is there a recon-all flag similar to -label_v1 or -ba-labels to automatically create label and stat files for Yeo network parcellations?

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Talairach Transform failure
by Daniel Ferreira 09 Jan '19

09 Jan '19

External Email - Use Caution Dear experts, I am processing some data and one of my cases failed. I checked the recon-all.log and found the following: *#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET* */home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri* * talairach_afd -T 0.005 -xfm transforms/talairach.xfm * *ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)* *Manual Talairach alignment may be necessary, or* *include the -notal-check flag to skip this test,* *making sure the -notal-check flag follows -all* *or -autorecon1 in the command string.* *See:* *http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>* *ERROR: Talairach failed!* *Linux siv 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux* *recon-all -s 0e63e2e7-d1e1-4e78-9106-150994a32c44 exited with ERRORS at tis 11 dec 2018 11:32:31 CET* Next, I tried to fix the issue by using tkregister: tkregister2 --mgz --s tal_before --fstal However, the Talairach volume does not load as a MOVEABLE volume. When I check the available recon-all output I only have: orig/001 --> looks good rawavg --> looks good orig --> its awful (it looks like millions of white tiny voxels on a black background) nu --> it is empty transforms/talairach.xfm --> is available I was wondering if you would know about any way to fix this? Thank you in advance, Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padilla(a)ki.se <daniel.ferreira.padilla(a)ki.se>*

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field of view mis-displacement complication
by Nasiriavanaki, Zahra 09 Jan '19

09 Jan '19

Dear Freesurfers Hi I have a bunch of data which have field of view mis-displacement at the time of data aquisition, so when I overlay the functional data on the structural image, the top part of the brain is cut off. Below I have copied one of the subject's functional image overlaid on his structural image on the right and the result of first level analysis (single subject map) in two different thresholds on the left. I have also copied one of the registration slices on the bottom. My question is why there is activation on parts of the brain which doesn't really have a functional data? Should I preprocess these data in a different way than the usual way? Thanks a lot Mona [cid:f6b8ef2d-9ae4-4ef4-b29e-a124467450ff] [cid:38d232c1-8e53-4f08-aa06-07e13e52789d] Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Programs samples two surface parcellation into volumetric segmentation
by Yerong Li 09 Jan '19

09 Jan '19

External Email - Use Caution Dear Freesurfer experts: In notice "mris_sample_parc" samples a volumetric parcellation onto a surface, I am trying to find a program that samples "annot" files to volumetric parcellations. I need to know the connection between labels in [lh.aparc.annot, rh.aparc.annot] and labels in [aparc+aseg.mgz]. I am expecting a program with two inputs [lh.aparc.annot, rh.aparc.annot] and output [aparc+aseg.mgz] ** Basically I have fibers from tracking algorithms and I am reconstructing connectivity matrices on the surface parcellation, that's why I need the subcortical segmentation file aparc+aseg.mgz. Yerong

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On relationship between aparc+aseg.mgz and ?h.aparc.annot
by Yerong Li 09 Jan '19

09 Jan '19

External Email - Use Caution Dear Freesurfer experts: I am on ROI analysis tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0 And I am trying to understand the relationship between: /label/?h.aparc.annot and /mri/aparc+aseg.mgz /label/?h.aparc.a2009s.annot and /mri/aparc.a2009s+aseg.mgz I understand /label/?h.aparc.annot corresponds to "Desikan-Killiany atlas" and its labels have 35 different labels (except unknown 0), while in several cases you mentioned that "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas", which I DO NOT understand. "/mri/aparc+aseg.mgz" to me are subcortical segmentations while "/label/?h.aparc.annot" are cortical(surface) parcellations. "Desikan-Killiany atlas" should mean "cortical (surface) parcellations". That's why I do not understand why "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas"? Could anyone help me understand this? Yerong

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Re: [Freesurfer] (no subject)
by Emil H.J. Nijhuis 09 Jan '19

09 Jan '19

External Email - Use Caution Dear Ruopeng, I tried the UpdateFreeview <https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview?action=fullsearch&…> procedure below, however I received the error message: >> This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix this problem. Abort << Any advice on how to solve this problem? With best regards, Emil Date: Mon, 7 Jan 2019 17:52:39 +0100 > From: "Larissa Bechtle" <Larissa.Bechtle(a)web.de> > Subject: Re: [Freesurfer] (no subject) > To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > > <trinity-2a602680-bd3f-4cdb-be33-806428c61a78-1546879959319@msvc-mesg-web003 > > > > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Ruopeng, > > Thank you very much for your quick answer and advice. So I am going to > update freeview! > Thanks! > Larissa > > Gesendet mit der WEB.DE Mail App > > Am 07.01.19 um 17:35 schrieb Ruopeng Wang > > > Hi Larissa, > > > > The latest development version of freeview supports drawing labels on > > surface. You can take a look here on how to update freeview: > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview > > > > In the latest version, you can draw paths on surface and use custom fill > > to create/edit labels, just like in tksurfer. > > > > Best, > > Ruopeng > > > > On 1/7/19 11:22 AM, Larissa Bechtle wrote: > > > External Email - Use Caution > > > > > > Hi everybody, > > > > > > after finishing my group analysis I am currently trying to run a ROI > analysis. > > > However I have some problems/general questions. > > > I am trying to draw a ROI on fsaverage in order to use the > mri_label2label command afterwards. > > > I opened Freeview, clicked on "load surface" first and then chose > lh.inflated_avg (fsaverage -> surf) which worked fine but I cant choose > "New ROI" (in order to crate the ROI). > > > > > > So is it possible to draw a ROI when focussing only on the surface? > And if this is the case why cant I? Did I chose the wrong file? > > > I am really thankful for any help!! > > > > > > Larissa > > > > > > > > > _______________________________________________ > > > 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 > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 179, Issue 11 > ******************************************* >

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mris_pmake version issue
by Raij, Tommi A. 08 Jan '19

08 Jan '19

Dear FreeSurfers, I am trying to update an mris_pmake command line that works with the pub v5.3.0 version with a new command line that works with pub v6.0.0 version. The purpose is to compute the distance between two vertex points on the pial surface using the cvs_avg35_inMNI152 brain. We are using CentOS (6.6 on the workstation running FS v5.3.0 and 7.4 on the workstation running FS v6.6.0) outside Martinos Center. nmr-std-env setenv SUBJECTS_DIR /usr/pubsw/packages/freesurfer/subjects setenv SUBJECT cvs_avg35_inMNI152 Old command line (gives a reasonable result on v5.3.0): mris_pmake --subject cvs_avg35_inMNI152_temp --hemi lh --surface0 pial --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:121981,endVertex:132633 Start->End vertices [ 121981->132633 ] Total path cost [ 29.668283 ] If I try to run this on v6.0.0, I receive the error: mris_pmake: unrecognized option '--surface0' I first tried removing --surface0 option, but then the error becomes mris_pmake: unrecognized option '--curv0' I then tried removing the --curv0 and eventually --curv 1 options as well, but these gave more similar errors (unrecognized option) or core dumped. Looking at older posts on the FreeSurfer list, I tried removing all three --surface0 --curv0 --curv 1 options, but this gives a clearly incorrect result where the startVertex and endVertex values are apparently not read from the command line: Start->End vertices [ 0->0 ] Total path cost [ 0.000000 ] I tried renaming --surface0 to --surface and --curv0 to --curv, as it seems that some of the options have been renamed, and to some degree this worked as there were no more 'unrecognized option' errors. However, the result is still Start->End vertices [ 0->0 ] Total path cost [ 0.000000 ] Any suggestions would be greatly appreciated. Btw the command line documentation (mris_pmake --help) does not seem to be quite match the version distributed with FS v6.0.0, at least when it comes to the option names for surface and curve, and if there are separate definitions for 0 and 1. Thank you! Best regards, Tommi Raij

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