External Email - Use Caution The image quality is quite good. GM and WM contrast is excellent. There are no scanning artifacts. The only remarkable finding is that this individual has moderate brain atrophy, enlarged ventricles, and large white matter signal abnormalities (hypointensities in the T1-w sequence). This could probably affect registration. If so, is there any way to fix this?
Thank you. Best regards Dani El jue., 17 ene. 2019 a las 16:58, Greve, Douglas N.,Ph.D. (< dgr...@mgh.harvard.edu>) escribió: > The first thing to do is to check your input data to make sure that > something is not really wrong. Eg, a large artifact or unusual anatomy. > > On 1/17/19 5:35 AM, Daniel Ferreira wrote: > > > > External Email - Use Caution > > > > Thanks Greve. Yes, I mean that the moveable is completely black. How > > should I continue from here? If the registration is so far off that it > > is out > > of the field of view, what should I do next? > > > > Thanks > > > > Dani > > > > El mié., 16 ene. 2019 a las 22:54, Greve, Douglas N.,Ph.D. > > (<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>) escribió: > > > > when you say it does not load, do you mean that the moveable is > > blank/black? The terminal output indicates that it is being > > loaded. It > > is probably the case that the registration is so far off that it > > is out > > of the field of view > > > > On 1/16/19 11:30 AM, Daniel Ferreira wrote: > > > > > > External Email - Use Caution > > > > > > Hi Greve, > > > > > > Thanks for your quick reply. > > > > > > I mean that tkregister2 loads the target volume (I think the > > original > > > T1 it is) but it does not load the moveable volume as stated in > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview: > > > > > "You will see the subject's volume as the TARGET volume and your > > > Talairach volume as a fuzzy MOVEABLE volume ...". > > > > > > Below you will find the terminal output from tkregister2. Thanks in > > > advance. > > > > > > >> > > > > > > tkregister2 --mgz --s 0e63e2e7-d1e1-4e78-9106-150994a32c44 --fstal > > > tkregister_tcl /usr/local/freesurfer-6.0.0/tktools/tkregister2.tcl > > > INFO: no target volume specified, assuming FreeSurfer orig volume. > > > target volume orig > > > movable volume (null) > > > reg file (null) > > > LoadVol 1 > > > ZeroCRAS 1 > > > $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ > > > Diagnostic Level -1 > > > > > > %Tue Dec 11 11:32:27 2018>>> > > > /usr/local/freesurfer-6.0.0/mni/bin/minctracc -clobber -debug > > > /tmp/5039.1.all.q/mritotal_2474//src_8_dxyz.mnc > > > > > > > /usr/local/freesurfer-6.0.0/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc > > > > > transforms/talairach.auto.xfm -transformation > > > /tmp/5039.1.all.q/mritotal_2474//src_8tmp2c.xfm -lsq9 -xcorr > > > -model_mask > > > > > > > /usr/local/freesurfer-6.0.0/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc > > > > > -center -3.237066 24.478743 -30.435196 -step 4 4 4 -tol 0.004 > > -simplex 2 > > > > > > talairach.xfm --------------------- > > > 0.58327 0.88352 -0.65294 -43.57153; > > > -1.09786 0.44137 -0.38347 -72.94266; > > > -0.04069 0.75613 0.98680 212.60657; > > > 0.00000 0.00000 0.00000 1.00000; > > > INFO: loading target > > > > > > /home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri/orig.mgz > > > Zeroing CRAS of target > > > new xfm ----------------- > > > 0.58327 0.88352 -0.65294 -25.73127; > > > -1.09786 0.44137 -0.38347 -65.12145; > > > -0.04069 0.75613 0.98680 228.56956; > > > 0.00000 0.00000 0.00000 1.00000; > > > --------------------- > > > INFO: changing target type to float > > > Ttarg: -------------------- > > > -1.00000 0.00000 0.00000 128.00000; > > > 0.00000 0.00000 1.00000 -128.00000; > > > 0.00000 -1.00000 0.00000 128.00000; > > > 0.00000 0.00000 0.00000 1.00000; > > > INFO: loading movable > > /usr/local/freesurfer-6.0.0/average/mni305.cor.mgz > > > INFO: changing move type to float > > > Tmov: -------------------- > > > -1.00000 0.00000 0.00000 128.00000; > > > 0.00000 0.00000 1.00000 -128.00000; > > > 0.00000 -1.00000 0.00000 128.00000; > > > 0.00000 0.00000 0.00000 1.00000; > > > mkheaderreg = 0, float2int = 0 > > > ---- Input registration matrix -------- > > > 0.58327 0.88352 -0.65294 -25.73127; > > > -1.09786 0.44137 -0.38347 -65.12145; > > > -0.04069 0.75613 0.98680 228.56956; > > > 0.00000 0.00000 0.00000 1.00000; > > > Determinant 1.92442 > > > subject = 0e63e2e7-d1e1-4e78-9106-150994a32c44 > > > Zoom Factor = 2, SQR() = 4 > > > FOV = 256 > > > Opening window 0e63e2e7-d1e1-4e78-9106-150994a32c44 > > > Opening 0e63e2e7-d1e1-4e78-9106-150994a32c44, xnum = 256, xdim = > 512 > > > Setting scale > > > tkregister2: interface: > > > /usr/local/freesurfer-6.0.0/tktools/tkregister2.tcl > > > tkregister.tcl: startup done > > > tkregister.tcl: default macro interface (to change: > > macro,mini,micro) > > > tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro} > > > % ------------------------------------------------------------ > > > Screen: 249 340 (28,28,28), inorm = 1, mov_frame = 0 > > > Anat: (124 85 127) ( 4.0 -1.0 43.0) 32.0000 27.7 > > > Func: (180 -142 42) ( -52.4 -86.4 270.1) OutOfBounds > > > -------------------------------------------------------------- > > > > > > > > > > > > > > > > > > El mié., 16 ene. 2019 a las 15:35, Greve, Douglas N.,Ph.D. > > > (<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>>) > > escribió: > > > > > > What do you mean that the tal volume does not load as a mov > > > volume? Can you send the terminal output from tkregister2? > > > > > > On 1/16/19 10:01 AM, Daniel Ferreira wrote: > > >> > > >> External Email - Use Caution > > >> > > >> Dear Bruce, Martin, and experts, > > >> > > >> > > >> I posted an issue a few days ago. I have been looking > > through the > > >> archives but can not figure out the solution myself. I was > > >> wondering if you would have any suggestion on how to fix the > > >> issue described further down? > > >> > > >> Thank you very much in advance > > >> > > >> Dani > > >> > > >> ---- > > >> > > >> Daniel Ferreira > > >> > > < > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Daniel+Ferreira%22 > > > > >> Wed, 09 Jan 2019 10:22:05 -0800 > > >> > > < > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20190109 > > > > >> > > >> 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.padi...@ki.se > > <mailto:email%3adaniel.ferreira.padi...@ki.se> > > <mailto:daniel.ferreira.padi...@ki.se > > <mailto:daniel.ferreira.padi...@ki.se>> > > <daniel.ferreira.padi...@ki.se > > <mailto:daniel.ferreira.padi...@ki.se> > > <mailto:daniel.ferreira.padi...@ki.se > > <mailto:daniel.ferreira.padi...@ki.se>>>* > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > -- > > > > > > *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.padi...@ki.se > > <mailto:daniel.ferreira.padi...@ki.se> > > > <mailto:daniel.ferreira.padi...@ki.se > > <mailto:daniel.ferreira.padi...@ki.se>>/ > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > > > > *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.padi...@ki.se > > <mailto:daniel.ferreira.padi...@ki.se>/ > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *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.padi...@ki.se <daniel.ferreira.padi...@ki.se>*
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
