[Freesurfer] postdoc position at Karolinska Institutet (Sweden)
External Email - Use Caution Dear everyone, We are recruiting a postdoc with expertise in neuroimaging (PET and/or MRI). Please see announcement here. Last day for submitting your application is 23rd of February. https://secure-web.cisco.com/1vVDjWQTc49asVod0AwGjaQgTeUpNJConsZgW_WT7VGOM74sk2zw2_8i2LDitq1EPUUV09jHZ6nJnVs9tsZ_NnqvK5_ZAhFvJofVHwYsbm5HL-GqG37jDyXLxtea5y27-00yd_SgCAdZOaxDzqqjhRTmZtMqs240pZpnUouKrZe4pM_1gxEyeC3BSA3NgwhG5AbC0-XjqeEeEqxLFBdR8K273nBoqmR89VC8CTmv2i542F8tDd2gFLoQb9W7Va51JjN2SARFRf7Qua4xBlvlox7V04p31PbVoMjlFR0tIEg8Dyc_WZzz0YUSJjUsi9x45/https%3A%2F%2Fki.varbi.com%2Fen%2Fwhat%3Ajob%2FjobID%3A701365%2Ftype%3Ajob%2Fwhere%3A4%2Fapply%3A1 [https://secure-web.cisco.com/1k7ZG4EQGIYP_4wb9sxv-IR-zIj9LfC1Wb_V9GYXiBs6JxeiCj5Y1-x_BYOrENE1W4xlF9s9pHOSIAaa4b67UR1PwEEkRFBgnDZWffjnguLZf63IkXeRZugqvlk8Z9ttEczG_zyRVKSsbCDN7yZXM5tYgZ__IPjyH11QcCgL6lbc215lN8KXWHSol_Lvg8vaHTvkiWuMT-RnEwykr6RwYjbBYOi6wT0HctkJFI1OntE3mwHAS6QdFPSQtrQIco0xj7kJaUy2vwFD2i9ISBgWZae1-NkPJbdxUPJ_JMyj_CXOtLF2tNZHDZV_KKbSZL91X/https%3A%2F%2Fcdn.varbi.com%2F134%2Fadaed4ab1e525afdd163920c1c1cf824.jpg]<https://secure-web.cisco.com/1vVDjWQTc49asVod0AwGjaQgTeUpNJConsZgW_WT7VGOM74sk2zw2_8i2LDitq1EPUUV09jHZ6nJnVs9tsZ_NnqvK5_ZAhFvJofVHwYsbm5HL-GqG37jDyXLxtea5y27-00yd_SgCAdZOaxDzqqjhRTmZtMqs240pZpnUouKrZe4pM_1gxEyeC3BSA3NgwhG5AbC0-XjqeEeEqxLFBdR8K273nBoqmR89VC8CTmv2i542F8tDd2gFLoQb9W7Va51JjN2SARFRf7Qua4xBlvlox7V04p31PbVoMjlFR0tIEg8Dyc_WZzz0YUSJjUsi9x45/https%3A%2F%2Fki.varbi.com%2Fen%2Fwhat%3Ajob%2FjobID%3A701365%2Ftype%3Ajob%2Fwhere%3A4%2Fapply%3A1> Postdoctoral Researcher in neuroimaging in aging and dementia<https://secure-web.cisco.com/1vVDjWQTc49asVod0AwGjaQgTeUpNJConsZgW_WT7VGOM74sk2zw2_8i2LDitq1EPUUV09jHZ6nJnVs9tsZ_NnqvK5_ZAhFvJofVHwYsbm5HL-GqG37jDyXLxtea5y27-00yd_SgCAdZOaxDzqqjhRTmZtMqs240pZpnUouKrZe4pM_1gxEyeC3BSA3NgwhG5AbC0-XjqeEeEqxLFBdR8K273nBoqmR89VC8CTmv2i542F8tDd2gFLoQb9W7Va51JjN2SARFRf7Qua4xBlvlox7V04p31PbVoMjlFR0tIEg8Dyc_WZzz0YUSJjUsi9x45/https%3A%2F%2Fki.varbi.com%2Fen%2Fwhat%3Ajob%2FjobID%3A701365%2Ftype%3Ajob%2Fwhere%3A4%2Fapply%3A1> Do you want to contribute to top quality medical research? We are looking for a postdoctoral fellow for studies of brain degeneration in Lewy Body dementia (DLB) using advanced brain imaging methods. ki.varbi.com All the best Dani -- Daniel Ferreira, PhD, Docent (Associate Professor) Director of Center for Alzheimer Research Karolinska Institutet, Sweden Department of Neurobiology, Care Sciences and Society (NVS) Center for Alzheimer Research Division of Clinical Geriatrics NEO floor 7th, SE 141 83 Huddinge daniel.ferreira.padi...@ki.se När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/1N82OsVZfbL6tc69_tJ91s2Fb22PUAN8UekFfodgpRrBl4TxlxBvMJKXIhx8qYicbtjjnXpJCh9t8O3BbGkyZhzevnzbyLPGu3h6HsYBM39OeN71k5dcc-QllnZVaD6Zuqwarhsw2QDRAs6BPRvbuoKfgywwjJeSIdXkY5adxbOjqx1acJT2FQQXSUiaRWXf9cc1RX12PnEG9OtZ7BZ3k8PwIvvf7iqFMKut6vU5mU1ICJ1QCHM2tDi0UGCzGrEvXPRdalIQedF0D-LqFnG5cDn9vErplx_IQkf6eLiLE5Bf8lroE35GcmIm8HlQkqQfO/https%3A%2F%2Fki.se%2Fmedarbetare%2Fintegritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1HBPUsdG40yRZJSAKuTROqyF-SgSZqmGX671qFGlFwaTlbj5vwrjvWcVBsqHGffYPPrA7WVslVuW0dfD31m6ZVdUKAaqgDM3PENyzCuxo_36t72oIUEJ0NYOPsBlijML1kKj6cpCQN2Z6RCABIV_8sogy3ya8E1BmaVAFK_3lHSeUmM-WK2jrmfL3sOFHdBCQEXgQa9YXjMFGPzrjZBQMwMTkdV9a6Bv0JwTzvqW8TUj6Aqen-RgVPMe9HR7uhZ9IcKuJoExjGtVJQJ56OEzHCz6-C1gomdvHBXkYZNp62CFPxUJf19as3C28u0bZn_BF/https%3A%2F%2Fki.se%2Fen%2Fstaff%2Fdata-protection-policy>. ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] Talairach Transform failure
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. > > (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) > > > LoadVol1 > > > 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; > > > 0.0 0.0 0.0 1.0; > > > 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; > > > 0.0 0.0 0.0 1.0; > > > - > > > INFO: changing target type to float > > > Ttarg: > > > -1.0 0.0 0.0 128.0; > > > 0.0 0.0 1.0 -128.0; > > > 0.0 -1.0 0.0 128.0; > > > 0.0
Re: [Freesurfer] Talairach Transform failure
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>) 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)
> > LoadVol1
> > 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;
> > 0.0 0.0 0.0 1.0;
> > 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;
> > 0.0 0.0 0.0 1.0;
> > -
> > INFO: changing target type to float
> > Ttarg:
> > -1.0 0.0 0.0 128.0;
> > 0.0 0.0 1.0 -128.0;
> > 0.0 -1.0 0.0 128.0;
> > 0.0 0.0 0.0 1.0;
> > INFO: loading movable /usr/local/freesurfer-6.0.0/average/mni305.cor.mgz
> > INFO: changing move type to float
> > Tmov:
> > -1.0 0.0 0.0 128.0;
> > 0.0 0.0 1.0 -128.0;
> > 0.0 -1.0 0.0 128.0;
> > 0.0 0.0 0.0 1.0;
> > 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;
> > 0.0 0.0 0.0 1.0;
> > 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) 32.27.7
> > Func:(180 -142 42) ( -52.4 -86.4 270.1) OutOfBounds
> > --
Re: [Freesurfer] Talairach Transform failure
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)
LoadVol1
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;
0.0 0.0 0.0 1.0;
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;
0.0 0.0 0.0 1.0;
-
INFO: changing target type to float
Ttarg:
-1.0 0.0 0.0 128.0;
0.0 0.0 1.0 -128.0;
0.0 -1.0 0.0 128.0;
0.0 0.0 0.0 1.0;
INFO: loading movable /usr/local/freesurfer-6.0.0/average/mni305.cor.mgz
INFO: changing move type to float
Tmov:
-1.0 0.0 0.0 128.0;
0.0 0.0 1.0 -128.0;
0.0 -1.0 0.0 128.0;
0.0 0.0 0.0 1.0;
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;
0.0 0.0 0.0 1.0;
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) 32.27.7
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>) 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=from:%22Daniel+Ferreira%22>
> Wed, 09 Jan 2019 10:22:05 -0800
> <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=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., pval=0. < threshold
[Freesurfer] Talairach Transform failure
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=from:%22Daniel+Ferreira%22> Wed, 09 Jan 2019 10:22:05 -0800 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=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., pval=0. < 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 * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Talairach Transform failure
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., pval=0. < 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 * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies
External Email - Use Caution Hi Martin, Thank you very much for your answer. Best regards Dani 2018-09-04 16:38 GMT+02:00 Martin Reuter : > Hi Dani, > > the regular FreeSurfer stream samples everything to 1mm isotropic. This is > of course problematic, if you have one group scanned at 1mm and the other > at a different resolution (as group differences could be affected by the > different resolutions). You would never know how much of what you get is > group and how much is resolution. > > Similarly this is problematic if you switch scanner, software, head-coil, > resolution in a longitudinal study. Effects cannot be separated any longer > and all you can report in a paper is that what you find is longitudinal > effect plus resolution effects and you don’t know how much is which. > > FreeSurfers longitudinal stream therefore requires inputs to be the same > resolution. This safety feature (to prevent potentially meaningless > analysis) can be circumvented by manually sampling images first - at your > own risk. If you go that way, you should at least also interpolate the 1mm > images to a new position (at least then both images will have interpolation > artefacts, so that differences are only the acquisition resolution and not > additionally interpolation artefacts in one of the time points). > > As an example, taking the same image twice, mapping one to a different > location and back again produces interpolation artefacts that are > significant and at orders comparable with 1 year of neurodegenerative > disease. > > Best, Martin > > > > > > On 30. Aug 2018, at 18:22, Daniel Ferreira wrote: > > > > Dear colleagues, > > I was wondering if resampling voxel size is done during recon-all. > > Also, I have data with voxel resolution of 1x1x1 mm at baseline and > 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation > by default (or can be performed by any way) that minimizes these > differences in somehow. > > Thank you very much > > 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 * > ___ > 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 > > > 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. > > -- *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 * ___ 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] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies
External Email - Use Caution Dear colleagues, I was wondering if resampling voxel size is done during recon-all. Also, I have data with voxel resolution of 1x1x1 mm at baseline and 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation by default (or can be performed by any way) that minimizes these differences in somehow. Thank you very much 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 * ___ 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.
Re: [Freesurfer] FreeSurfer on MP2RAGE
Dear experts, I just wanted to come back to my previous question since we have not got any answer: We have been working quite extensively with Freesurfer over the years. We are now starting to collect a new large cohort and we are about to decide which T1-weighted sequence to use, MPRAGE or MP2RAGE (Siemens 3T Prisma, headcoil 20 Chanel). When we visually inspect the images we think there is a better contrast between GM and WM in the MP2RAGE over the traditional MPRAGE sequence. Both sequences seem to produce good Freesurfer output, but the cortex tend to be a bit thinner with MP2RAGE, possibly due to the better contrast, but we can of course not be sure of this. Freesurfer have always produced nice results with the MPRAGE sequence and the MPRAGE flag seems to work well. Do you think this flag will work as well on MP2RAGE? Of course it is difficult to say but we wonder if you have any opinion on which sequence to use? Thank you very much, Best regards Dani -- Daniel Ferreira, PhD. Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics (Karolinska Institute, Sweden) danif...@gmail.com | daniel.ferreira.padi...@ki.se 2016-09-28 10:15 GMT+01:00 Daniel Ferreira <danif...@gmail.com>: > Dear all, > > > We have been working quite extensively with Freesurfer over the years. We > are now starting to collect a new large cohort and we are about to decide > which T1-weighted sequence to use, MPRAGE or MP2RAGE (Siemens 3T Prisma, > headcoil 20 Chanel). When we visually inspect the images we think there is > a better contrast between GM and WM in the MP2RAGE over the traditional > MPRAGE sequence. Both sequences seem to produce good Freesurfer output, but > the cortex tend to be a bit thinner with MP2RAGE, possibly due to the > better contrast, but we can of course not be sure of this. Freesurfer have > always produced nice results with the MPRAGE sequence and the MPRAGE flag > seems to work well. Do you think this flag will work as well on MP2RAGE? Of > course it is difficult to say but we wonder if you have any opinion on > which sequence to use? > > > Thank you very much, > > > Best regards > > -- > Daniel Ferreira, PhD. > Department of Neurobiology, Care Sciences and Society, Division of > Clinical Geriatrics (Karolinska Institute, Sweden) > danif...@gmail.com | daniel.ferreira.padi...@ki.se > -- Daniel Ferreira, PhD. Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics (Karolinska Institute, Sweden) danif...@gmail.com | daniel.ferreira.padi...@ki.se ___ 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] FreeSurfer on MP2RAGE
Dear all, We have been working quite extensively with Freesurfer over the years. We are now starting to collect a new large cohort and we are about to decide which T1-weighted sequence to use, MPRAGE or MP2RAGE (Siemens 3T Prisma, headcoil 20 Chanel). When we visually inspect the images we think there is a better contrast between GM and WM in the MP2RAGE over the traditional MPRAGE sequence. Both sequences seem to produce good Freesurfer output, but the cortex tend to be a bit thinner with MP2RAGE, possibly due to the better contrast, but we can of course not be sure of this. Freesurfer have always produced nice results with the MPRAGE sequence and the MPRAGE flag seems to work well. Do you think this flag will work as well on MP2RAGE? Of course it is difficult to say but we wonder if you have any opinion on which sequence to use? Thank you very much, Best regards -- Daniel Ferreira, PhD. Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics (Karolinska Institute, Sweden) danif...@gmail.com | daniel.ferreira.padi...@ki.se ___ 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] -qcache of v5.0 data with newer versions
Dear experts, Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been recon-all -all with FS 5.0.0? Thanks Dani ___ 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] -qcache of v5.0 data with newer versions
Dear experts, Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been recon-all -all with FS 5.0.0? Thanks Dani ___ 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] using -cw256 as default is good?
Dear experts, Could you please help me with my previous comment (see below)? Thanks so much Daniel Ferreira Dear experts, We are processing a dataset that gives us this error quite often: ERROR! FOV=300.000 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. Is it ok if I use -cw256 by default to all my scans even for those with FOV=256 that do not need such flag? Thanks Best regards Dani ___ 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] using -cw256 as default is good?
Dear experts, We are processing a dataset that gives us this error quite often: ERROR! FOV=300.000 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. Is it ok if I use -cw256 by default to all my scans even for those with FOV=256 that do not need such flag? Thanks Best regards Dani ___ 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.
Re: [Freesurfer] longitudinal processing, template and flags
Thanks Martin for your reply, I am agree with you on point 1. What would you say in the case that we are interested in rates of decline from baseline to 12 months, but besides 6 months follow-up we also have 24 months?. Here I see more conceptual problems. In an hypothetical context of severe atrophy from 12 to 24 months, adding the 24 mo follow-up perhaps difficult registration more than improves it. What do you think? Thanks a lot Best Daniel Hi Daniel, 1. yes. But why not include 6 month in your study if you have those scans??? You will get much more reliable slope estimates with 3 time points compared to 2, so including that time point will not only help for the image processing part, but also in your statistics (you gain power). 2. I am not familiar with the mprage flag and think it mainly affects the normalization. If you are sure you need it, then also add it to the -base and -long runs, just to be safe. best, Martin On 01/29/2014 09:08 AM, Daniel Ferreira wrote: Dear experts, I have two questions regarding the longitudinal stream: - I am including Baseline and 12 months follow-up in my study. However, I also have 6 months follow-up. I wonder if it is conceptually right to include these 6 months scans in template creation with the idea of increasing registration. - I am applying the -mprage flag in the crossectional first step. Should I use it in the -base and -longs steps too? Thanks very much Daniel Ferreira ___ 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] longitudinal processing, template and flags
Dear experts, I have two questions regarding the longitudinal stream: - I am including Baseline and 12 months follow-up in my study. However, I also have 6 months follow-up. I wonder if it is conceptually right to include these 6 months scans in template creation with the idea of increasing registration. - I am applying the -mprage flag in the crossectional first step. Should I use it in the -base and -longs steps too? Thanks very much Daniel Ferreira ___ 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] acquisition in 1 session vs 2 sessions
Dear experts, We are designing a study including a long MR protocol: 1) Localizer 2) Cal 3) T1-FSPGR 4) FLAIR 3D 5) DTI 1 6) DTI 2 7) fMRI Due to patients characteristics we were thinking on splitting the acquisition in two different sessions (session 1: sequences 1, 2, 3, 4; session 2: sequences 1, 2, 5, 6, 7). Do you think we should do the same for the healthy controls or we can scan them in just one single session? I wonder how system session-related artifacts could differentially affect the two kinds of protocol (spitted vs. single). I also wonder how FreeSurfer processing can be affected by this issues. Thanks a lot. Daniel Ferreira ___ 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] Fwd: missing eTIV in asegstats2table
Hi Douglas, You are right, sorry for not including the thread. Below I paste our previous conversation. I also attach again the files you asked me for. Thanks, best Daniel Message: 13 Date: Wed, 23 Oct 2013 10:49:44 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5267e208.4090...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 Hi Daniel, what is this in reference to? If this is a follow up on a previous thread, please include the rest of the thread and the file in the same email. I go through way too many emails to keep track of who's doing what. thanks! doug On 10/23/13 4:13 AM, Daniel Ferreira wrote: Dear Douglas, Please, find attached aseg.stats files for subj1 and subj2. Thanks Daniel Message: 4 Date: Tue, 08 Oct 2013 11:39:11 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5254271f.4040...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Can you send the aseg.stats file for subj1 and subj2? On 10/08/2013 07:53 AM, Daniel Ferreira wrote: Dear Douglas, I generated my table with version 5.3. Attached is an example for two subjects (in .txt and .xls formats). Best regards Dani Message: 18 Date: Mon, 07 Oct 2013 11:05:51 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5252cdcf.9050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed what version was the table generated with? 5.3 does not use ICV in the table anymore. It uses eTIV. Can you send an example of one of your tables? On 10/07/2013 03:12 AM, Daniel Ferreira wrote: Dear Douglas and Martin, Thanks for your replies. So far I have always been able to get eTIV when running asegstats2table (last column on the spreadsheet). But my current FreeSurfer version (5.3.0) is not grabbing it. I can found eTIV in the header and extract it for all the subjects with mri_segstats (as below in blue), but output is quite messy. I would rather prefer to get it as in asegstats2table format. Any idea? Thanks a lot, Dani for i in FAD*; do echo $i; mri_segstats --subject $i --etiv-only table_eTIV; done Message: 4 Date: Wed, 2 Oct 2013 08:50:23 +0200 From: Daniel Ferreira dani...@ull.es Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer@nmr.mgh.harvard.edu Message-ID: CACNza6eGqfsZ2Sfj9EVJxDD4pQv8PW7=nbcywwmepter0c0...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear Douglas, Thanks for your quick answer. Yes, all my subjects have the measure EstimatedTotalIntraCranialVol in their aseg.stats file. The problem is that when I run asegstats2table, this variable is not exported to the created text file. I wonder if there is some way to extract eTIV for all my subjects at the same time. I manage to do it with mri_segstats, but what I get is individual values for all my subjects in the terminal, so it is quite boring to pass all the values to a table. Thanks a lot, Dani Message: 1 Date: Tue, 01 Oct 2013 11:58:57 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer@nmr.mgh.harvard.edu Message-ID: 524af141.3060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed It should still be there. I changed the name to EstimatedTotalIntraCranialVol, eg the line now looks like # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1509814.835086, mm^3 On 10/01/2013 10:50 AM, Daniel Ferreira wrote: Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a lot Dani -- Daniel Ferreira, PhD. Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics (Karolinska Institute, Sweden) danif...@gmail.com | daniel.ferreira.padi...@ki.se aseg.stats_subj2 Description: Binary data aseg.stats_suj1 Description: Binary data ___ 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.
Re: [Freesurfer] missing eTIV in asegstats2table
Dear Douglas, Please, find attached aseg.stats files for subj1 and subj2. Thanks Daniel aseg.stats_subj2 Description: Binary data aseg.stats_suj1 Description: Binary data ___ 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.
Re: [Freesurfer] missing eTIV in asegstats2table
Dear Douglas, I generated my table with version 5.3. Attached is an example for two subjects (in .txt and .xls formats). Best regards Dani Measure:volume Left-Lateral-Ventricle Left-Inf-Lat-Vent Left-Cerebellum-White-MatterLeft-Cerebellum-Cortex Left-Thalamus-Proper Left-CaudateLeft-PutamenLeft-Pallidum 3rd-Ventricle 4th-Ventricle Brain-Stem Left-HippocampusLeft-Amygdala CSF Left-Accumbens-area Left-VentralDC Left-vessel Left-choroid-plexus Right-Lateral-Ventricle Right-Inf-Lat-Vent Right-Cerebellum-White-Matter Right-Cerebellum-Cortex Right-Thalamus-Proper Right-Caudate Right-Putamen Right-Pallidum Right-Hippocampus Right-Amygdala Right-Accumbens-area Right-VentralDC Right-vesselRight-choroid-plexus5th-Ventricle WM-hypointensities Left-WM-hypointensities Right-WM-hypointensities non-WM-hypointensities Left-non-WM-hypointensities Right-non-WM-hypointensitiesOptic-ChiasmCC_Posterior CC_Mid_PosteriorCC_Central CC_Mid_Anterior CC_Anterior BrainSegVol lhCortexVol rhCortexVol CortexVol lhCorticalWhiteMatterVolrhCorticalWhiteMatterVol CorticalWhiteMatterVol SubCortGrayVol TotalGrayVolSupraTentorialVol subj1 5343.2 185.8 15272.1 57503.0 8013.4 3732.3 5224.4 1542.7 624.6 1321.7 23517.9 5268.2 1714.3 947.4 545.6 4407.0 40.61229.3 4173.7 629.6 14334.8 62027.1 8240.2 3533.1 4751.1 1092.3 5135.4 1803.8 561.9 4040.1 36.41081.3 1.0 1095.8 0.0 0.0 7.6 0.0 0.0 205.9 1077.2 545.6 545.7 662.8 964.0 1314656.0 260454.002492 261474.048616 521928.051108 280252.449542 288274.518791 568526.968333 61396.0 702365.051108 1166113.01944 subj2 8976.7 294.3 15010.4 59048.6 8014.8 3254.2 4974.7 1488.2 900.2 1479.6 23413.8 4062.2 1504.7 851.9 473.1 4260.6 50.61160.8 8663.1 471.4 13077.3 60351.0 7282.0 3222.3 4726.0 1513.7 3903.7 1469.1 441.7 4121.5 33.31484.0 9.2 763.6 0.0 0.0 9.4 0.0 0.0 163.4 948.2 367.0 352.1 400.4 879.7 1127482.0 213354.37781 212733.44631426087.82412236284.606211 238324.80152474609.407731 56308.0 601390.82412979372.231851 aseg_volume.xls Description: MS-Excel spreadsheet ___ 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.
Re: [Freesurfer] missing eTIV in asegstats2table
Dear Douglas and Martin, Thanks for your replies. So far I have always been able to get eTIV when running asegstats2table (last column on the spreadsheet). But my current FreeSurfer version (5.3.0) is not grabbing it. I can found eTIV in the header and extract it for all the subjects with mri_segstats (as below in blue), but output is quite messy. I would rather prefer to get it as in asegstats2table format. Any idea? Thanks a lot, Dani for i in FAD*; do echo $i; mri_segstats --subject $i --etiv-only table_eTIV; done ___ 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.
Re: [Freesurfer] missing eTIV in asegstats2table
Hi, Thanks Marcos for your reply. My problem is that asegstats2table does not output values for eTIV. I do not manage to figure out why. But maybe your script could work. Anyone knows what is the corresponding FieldName Index for eTIV?? I checked a aseg.stats file and did not find it. Thanks a lot Dani Message: 7 Date: Wed, 02 Oct 2013 10:32:51 -0300 From: Marcos Martins da Silva marc...@hucff.ufrj.br Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: Daniel Ferreira dani...@ull.es Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: 1380720771.1845.9.camel@alien Content-Type: text/plain; charset=utf-8 You can use in a loop with your subjects. It extracts the fields I want and some others including the etiv to a table named AsegVol. You may change the number of the fields to get what you need. The code I am sending you addresses hippocampus, putamen and caudate (both sides). for i in $(ls -d suj*) do asegstats2table --segno 11 12 17 50 51 53 -s $i --tablefile AsegVol done Notice that suj is the prefix of all my subjects in freesurfer/subjects folder I hope it helps you. Em Qua, 2013-10-02 ___ 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.
Re: [Freesurfer] missing eTIV in asegstats2table
Dear Douglas, Thanks for your quick answer. Yes, all my subjects have the measure EstimatedTotalIntraCranialVol in their aseg.stats file. The problem is that when I run asegstats2table, this variable is not exported to the created text file. I wonder if there is some way to extract eTIV for all my subjects at the same time. I manage to do it with mri_segstats, but what I get is individual values for all my subjects in the terminal, so it is quite boring to pass all the values to a table. Thanks a lot, Dani Message: 1 Date: Tue, 01 Oct 2013 11:58:57 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer@nmr.mgh.harvard.edu Message-ID: 524af141.3060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed It should still be there. I changed the name to EstimatedTotalIntraCranialVol, eg the line now looks like # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1509814.835086, mm^3 On 10/01/2013 10:50 AM, Daniel Ferreira wrote: Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a lot Dani ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 116, Issue 7 ___ 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] missing eTIV in asegstats2table
Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a lot Dani ___ 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.
Re: [Freesurfer] average measure of cortical thickness
Hi Douglas, Well, I usually use aparcstats2table with -m thickness, but what I get is the thickness for all those 34 hemisphere regions, but not that measure of mean thickness for the hemisphere. Could I be missing something? thanks Daniel Message: 15 Date: Tue, 30 Oct 2012 11:17:56 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average measure of cortical thickness To: freesurfer@nmr.mgh.harvard.edu Message-ID: 508fefa4.9070...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed You can get thickness with aparcastats2table with the -m thickness option. This gives you a measure of mean thickness for the hemisphere as well. do8ug 2012/10/30 Daniel Ferreira dani...@ull.es Please, is there any automatic way to extract this Mean Thickness values for lh and rh for a big group of subjects? As for example aparcstats2table? thank you very much Daniel 2012/10/30 Bruce Fischl fis...@nmr.mgh.harvard.edu yes, I think so Bruce On Tue, 30 Oct 2012, Daniel Ferreira wrote: So, as a measure of whole brain cortical thickness average is it better to Mean Thickness from aparc.stats file? 2012/10/30 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel the parcellations are not uniform in size, and therefore the average of them will not be the same as averaging over the cortex. cheers Bruce On Tue, 30 Oct 2012, Daniel Ferreira wrote: Hi, I was wondering what should I use as an average of cortical thickness for the whole cortex. The aparc.stats output gives a value of Mean Thickness for each hemisphere. But this value does not coincide with the one I get if I average the 34 variables from aparc.stats. Do you know why? thanks so much in advance Daniel 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/**compliancelinehttp://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 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.
Re: [Freesurfer] Talairach Failure Detection
Hi, I see. But why does it happen? If I look at the initial Dicom it is normal, no wrapped, as usually looks like. thanks 2012/10/23 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel it looks like you have too much wrap in your image, with a significant amount of brain wrapping to the top. Nothing will work on this sorry Bruce On Tue, 23 Oct 2012, Daniel Ferreira wrote: Hi Nick, Here comes attached the tkmedit orig.mgz thanks Daniel 2012/10/22 Nick Schmansky ni...@nmr.mgh.harvard.edu what does orig.mgz look like in tkmedit? n. On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote: Hi, I did recon-all -i dicoms -s id and then what Nick posted. 2012/10/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel what was your original data format? Did you start with dicoms? Bruce On Thu, 18 Oct 2012, Daniel Ferreira wrote: Thanks Nick very much for your suggestion. Unfortunately it did not fix the error. I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached. What can be happening here? Any idea to fix it? thanks Daniel 2012/10/17 Nick Schmansky ni...@nmr.mgh.harvard.edu Daniel, See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release: https://surfer.nmr.mgh.** harvard.edu/fswiki/TalFailV5.1https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 Nick On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: Dear experts, Please, I'm getting the Talairach Failure Detection problem in one of my subjects (message enclosed below). I tried to follow the tutorial to fix a bad Talairach with: 1) tkregister2 --mgz -s id --fstal -- not green lines appear, I attach a screenshot. Both the standard and my MRI are slided down to the bottom of the window. See also attached tkmedit file. 2) Anyway, I tried also -notal-check to see if something changed in spite Talairach failed, but it fails also (off course). 3) I used -use-mritotal but I still get the same. However, this time processing finishes without errors, but my MRI is still at the bottom of the window and output cut all what is between middle temporal regions and neck. Please, any idea? Thanks a lot Daniel #@# Talairach Failure Detection Wed Oct 10
Re: [Freesurfer] cortical parcellation question
Thanks for all the information given. We finally have managed to solve it thanks to your comments. Cheers Daniel 2012/10/17 Bruce Fischl fis...@nmr.mgh.harvard.edu there is no volume associate with them any longer. As a short-cut I think Doug ran the aparc on fsaverage, so you could try sampling it into the volume (or just using the aparc+aseg.mgz that is distributed with fsaverage) cheers Bruce On Wed, 17 Oct 2012, Daniel Ferreira wrote: Hello again, Thanks for all the information Bruce. Is it not possible to back-project the regions defined in the 2D surface-based spherical coordinate system onto the mean_intensity.nii image? As those regions in the 2D surface-based coordinate system would have been initially defined on a 3D volume(s) and transformed (inflated) to the 2D spherical surface? Daniel -- Forwarded message -- From: Bruce Fischl fis...@nmr.mgh.harvard.edu Date: 2012/10/11 Subject: Re: [Freesurfer] cortical parcellation question To: Daniel Ferreira danif...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Hi Daniel, no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable). Bruce On Thu, 11 Oct 2012, Daniel Ferreira wrote: Thanks for the detailed information. The mean intensity image (mean_intensity.nii) generated from frame #1 is almost exactly what I need. This image has all the sub-cortical regions assigned a discrete integer number (i.e. all the voxels in the left cerebelllar grey matter = 8 and right = 47). However the whole of the neocortex is defined as left (intensity = 3) and right (intensity = 42) only, there are no cortical sub-divisions. Is it possible to have the individual neocortical regions assigned a discrete integer number; (obviously not one already assigned to the other regions in the mean_intensity.nii image)? For example all inferior temporal voxels = 9; middle temporal voxels = 10; superior temporal voxels = 11. So each of the regions defined in the colortable_desikan_killiany.**txt file found in the FREESURFER_HOME/average/ directory are also defined in the mean_intensity.nii image? Thanks 2012/10/6 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel it's in .gca format, and includes information that wouldn't fit in a nifti file (e.g. markov relationships). You can use mri_convert to extract some of the basic info though (e.g. the most likely class at each location and the mean intensity of the most likely class) using mri_convert. For example: mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#0 ./labels.nii mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#1 ./mean_intensity.nii where the #n syntax mean extract the nth frame from the 4D gca volume. Frame 0 is the most likely label and frame 1 is the mean intensity. Note however that there is lots more info in the .gca that this doesn't capture such as the MRF parameters I mentioned above, class variances, other class probabilities, etc cheers Bruce On Thu, 4 Oct 2012, Daniel Ferreira wrote: Thanks Bruce, When you say the atlas itself is included in the Freesurfer distribution, do you mean there is a 3D version of it available in the download? Also, I am not looking for the individual subjects' images, I just want a copy of the final atlas as a 3D image in analyze/nifti format. (i.e. in the same format as the Harvard-Oxford atlas that is downloaded with FSL). Thanks a lot. Daniel Ferreira 2012/10/3 Bruce Fischl fis
[Freesurfer] average measure of cortical thickness
Hi, I was wondering what should I use as an average of cortical thickness for the whole cortex. The aparc.stats output gives a value of Mean Thickness for each hemisphere. But this value does not coincide with the one I get if I average the 34 variables from aparc.stats. Do you know why? thanks so much in advance Daniel ___ 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.
Re: [Freesurfer] Talairach Failure Detection
Well, in the PACs looks fine. When converting to nii it is already wrapped. I will go to the machine again and see. Thanks! 2012/10/30 Bruce Fischl fis...@nmr.mgh.harvard.edu really? In what viewer? Does it happen in the rawavg.mgz? On Tue, 30 Oct 2012, Daniel Ferreira wrote: Hi, I see. But why does it happen? If I look at the initial Dicom it is normal, no wrapped, as usually looks like. thanks 2012/10/23 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel it looks like you have too much wrap in your image, with a significant amount of brain wrapping to the top. Nothing will work on this sorry Bruce On Tue, 23 Oct 2012, Daniel Ferreira wrote: Hi Nick, Here comes attached the tkmedit orig.mgz thanks Daniel 2012/10/22 Nick Schmansky ni...@nmr.mgh.harvard.edu what does orig.mgz look like in tkmedit? n. On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote: Hi, I did recon-all -i dicoms -s id and then what Nick posted. 2012/10/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel what was your original data format? Did you start with dicoms? Bruce On Thu, 18 Oct 2012, Daniel Ferreira wrote: Thanks Nick very much for your suggestion. Unfortunately it did not fix the error. I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached. What can be happening here? Any idea to fix it? thanks Daniel 2012/10/17 Nick Schmansky ni...@nmr.mgh.harvard.edu Daniel, See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release: https://surfer.nmr.mgh.**harvard.edu/fswiki/TalFailV5.1https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 Nick On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: Dear experts, Please, I'm getting the Talairach Failure Detection problem in one of my subjects (message enclosed below). I tried to follow the tutorial to fix a bad Talairach with: 1) tkregister2 --mgz -s id --fstal -- not green lines appear, I attach a screenshot. Both the standard and my MRI
Re: [Freesurfer] average measure of cortical thickness
So, as a measure of whole brain cortical thickness average is it better to Mean Thickness from aparc.stats file? 2012/10/30 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel the parcellations are not uniform in size, and therefore the average of them will not be the same as averaging over the cortex. cheers Bruce On Tue, 30 Oct 2012, Daniel Ferreira wrote: Hi, I was wondering what should I use as an average of cortical thickness for the whole cortex. The aparc.stats output gives a value of Mean Thickness for each hemisphere. But this value does not coincide with the one I get if I average the 34 variables from aparc.stats. Do you know why? thanks so much in advance Daniel 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/**compliancelinehttp://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 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.
Re: [Freesurfer] average measure of cortical thickness
Please, is there any automatic way to extract this Mean Thickness values for lh and rh for a big group of subjects? As for example aparcstats2table? thank you very much Daniel 2012/10/30 Bruce Fischl fis...@nmr.mgh.harvard.edu yes, I think so Bruce On Tue, 30 Oct 2012, Daniel Ferreira wrote: So, as a measure of whole brain cortical thickness average is it better to Mean Thickness from aparc.stats file? 2012/10/30 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel the parcellations are not uniform in size, and therefore the average of them will not be the same as averaging over the cortex. cheers Bruce On Tue, 30 Oct 2012, Daniel Ferreira wrote: Hi, I was wondering what should I use as an average of cortical thickness for the whole cortex. The aparc.stats output gives a value of Mean Thickness for each hemisphere. But this value does not coincide with the one I get if I average the 34 variables from aparc.stats. Do you know why? thanks so much in advance Daniel 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/**compliancelinehttp://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 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.
Re: [Freesurfer] Talairach Failure Detection
Hi, I did recon-all -i dicoms -s id and then what Nick posted. 2012/10/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel what was your original data format? Did you start with dicoms? Bruce On Thu, 18 Oct 2012, Daniel Ferreira wrote: Thanks Nick very much for your suggestion. Unfortunately it did not fix the error. I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached. What can be happening here? Any idea to fix it? thanks Daniel 2012/10/17 Nick Schmansky ni...@nmr.mgh.harvard.edu Daniel, See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release: https://surfer.nmr.mgh.**harvard.edu/fswiki/TalFailV5.1https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 Nick On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: Dear experts, Please, I'm getting the Talairach Failure Detection problem in one of my subjects (message enclosed below). I tried to follow the tutorial to fix a bad Talairach with: 1) tkregister2 --mgz -s id --fstal -- not green lines appear, I attach a screenshot. Both the standard and my MRI are slided down to the bottom of the window. See also attached tkmedit file. 2) Anyway, I tried also -notal-check to see if something changed in spite Talairach failed, but it fails also (off course). 3) I used -use-mritotal but I still get the same. However, this time processing finishes without errors, but my MRI is still at the bottom of the window and output cut all what is between middle temporal regions and neck. Please, any idea? Thanks a lot Daniel #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 /home/daniel/FreeSurfer/**subjects/N001511_d2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. 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/**Talairachhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC 2011 x86_64 GNU/Linux recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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 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.
Re: [Freesurfer] cortical parcellation question
Hello again, Thanks for all the information Bruce. Is it not possible to back-project the regions defined in the 2D surface-based spherical coordinate system onto the mean_intensity.nii image? As those regions in the 2D surface-based coordinate system would have been initially defined on a 3D volume(s) and transformed (inflated) to the 2D spherical surface? Daniel -- Forwarded message -- From: Bruce Fischl fis...@nmr.mgh.harvard.edu Date: 2012/10/11 Subject: Re: [Freesurfer] cortical parcellation question To: Daniel Ferreira danif...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Hi Daniel, no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable). Bruce On Thu, 11 Oct 2012, Daniel Ferreira wrote: Thanks for the detailed information. The mean intensity image (mean_intensity.nii) generated from frame #1 is almost exactly what I need. This image has all the sub-cortical regions assigned a discrete integer number (i.e. all the voxels in the left cerebelllar grey matter = 8 and right = 47). However the whole of the neocortex is defined as left (intensity = 3) and right (intensity = 42) only, there are no cortical sub-divisions. Is it possible to have the individual neocortical regions assigned a discrete integer number; (obviously not one already assigned to the other regions in the mean_intensity.nii image)? For example all inferior temporal voxels = 9; middle temporal voxels = 10; superior temporal voxels = 11. So each of the regions defined in the colortable_desikan_killiany.**txt file found in the FREESURFER_HOME/average/ directory are also defined in the mean_intensity.nii image? Thanks 2012/10/6 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel it's in .gca format, and includes information that wouldn't fit in a nifti file (e.g. markov relationships). You can use mri_convert to extract some of the basic info though (e.g. the most likely class at each location and the mean intensity of the most likely class) using mri_convert. For example: mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#0 ./labels.nii mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#1 ./mean_intensity.nii where the #n syntax mean extract the nth frame from the 4D gca volume. Frame 0 is the most likely label and frame 1 is the mean intensity. Note however that there is lots more info in the .gca that this doesn't capture such as the MRF parameters I mentioned above, class variances, other class probabilities, etc cheers Bruce On Thu, 4 Oct 2012, Daniel Ferreira wrote: Thanks Bruce, When you say the atlas itself is included in the Freesurfer distribution, do you mean there is a 3D version of it available in the download? Also, I am not looking for the individual subjects' images, I just want a copy of the final atlas as a 3D image in analyze/nifti format. (i.e. in the same format as the Harvard-Oxford atlas that is downloaded with FSL). Thanks a lot. Daniel Ferreira 2012/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel, 1. Do you mean the atlas or the parcellation of your subjects? We cannot distribute the individual subjects in the atlas as the data was collected under an IRB long ago that didn't include this. The atlas itself (summary statistics derived from those subjects) is included in the FreeSurfer distribution. 2. The subcortical areas are the same, but not the cortical ones. That cortical parcellation is quite coarse, and while we did implement it we were never given permission to distribute the automated version, so it is not part of FreeSurfer. The boundaries that we define are thus different than that one (and since the Harvard-Oxford one is based on volumetric labeling of folding patterns we found that it contained a bunch of errors in which e.g. the wrong side of a sulcus was labeled) cheers Bruce On Wed, 3 Oct 2012, Daniel Ferreira wrote: Dear experts, I have a couple of questions regarding
[Freesurfer] cortical parcellation question
Dear experts, I have a couple of questions regarding the cortical parcellation atlas that is used in Freesurfer: 1) I would like to know if it is possible to obtain the Desikan-Killiany atlas in 3D analyze/nifti format. With each region of the brain assigned a discrete integer number (for example the all of the voxels of the left inferior temporal lobe have an intensity = 1, or the whole of the left hippocampus = 2). 2) Are the Harvard-Oxford cortical and subcortical atlases that can be downloaded with FSL the same as the cortical parcellation atlas that is used in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the left inferior temporal cortex in the Freesurfer cortical parcellation = the left inferior temporal cortex in the Harvard-Oxford atlas downloaded with FSL) Many thanks Daniel Ferreira ___ 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.
Re: [Freesurfer] cortical parcellation question
Thanks Bruce, When you say the atlas itself is included in the Freesurfer distribution, do you mean there is a 3D version of it available in the download? Also, I am not looking for the individual subjects' images, I just want a copy of the final atlas as a 3D image in analyze/nifti format. (i.e. in the same format as the Harvard-Oxford atlas that is downloaded with FSL). Thanks a lot. Daniel Ferreira 2012/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel, 1. Do you mean the atlas or the parcellation of your subjects? We cannot distribute the individual subjects in the atlas as the data was collected under an IRB long ago that didn't include this. The atlas itself (summary statistics derived from those subjects) is included in the FreeSurfer distribution. 2. The subcortical areas are the same, but not the cortical ones. That cortical parcellation is quite coarse, and while we did implement it we were never given permission to distribute the automated version, so it is not part of FreeSurfer. The boundaries that we define are thus different than that one (and since the Harvard-Oxford one is based on volumetric labeling of folding patterns we found that it contained a bunch of errors in which e.g. the wrong side of a sulcus was labeled) cheers Bruce On Wed, 3 Oct 2012, Daniel Ferreira wrote: Dear experts, I have a couple of questions regarding the cortical parcellation atlas that is used in Freesurfer: 1) I would like to know if it is possible to obtain the Desikan-Killiany atlas in 3D analyze/nifti format. With each region of the brain assigned a discrete integer number (for example the all of the voxels of the left inferior temporal lobe have an intensity = 1, or the whole of the left hippocampus = 2). 2) Are the Harvard-Oxford cortical and subcortical atlases that can be downloaded with FSL the same as the cortical parcellation atlas that is used in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the left inferior temporal cortex in the Freesurfer cortical parcellation = the left inferior temporal cortex in the Harvard-Oxford atlas downloaded with FSL) Many thanks Daniel Ferreira 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/**compliancelinehttp://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 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] Fwd: How TE, TI and flip angle parameters affect the images and results?
Thanks for your answers! Following your comments, I have thought to select only first two sequences, as they are the more frequent in our database and only differ on the TE parameter. We will also create balanced groups. cheers Daniel 2012/8/18 Andre van der Kouwe an...@nmr.mgh.harvard.edu Hi Daniel, I agree, those flip angle differences are quite big and would make a difference to contrast. I suspect gray/white contrast is better for the higher TI and lower flip angles in those scans (and they could benefit from longer TR). So if you have a balanced study/control group it's ok but I wouldn't compare subjects with systematically different protocols like those below. Cheers, Andre. Bruce Fischl wrote: Hi Daniel those are pretty big differences in flip angle. I'll cc Andre van der Kouwe on this so he can comment, but I would be hesitant. The increased TE will have a big effect on dura (darkening it), but will also reduce gray/white contrast. cheers Bruce On Fri, 17 Aug 2012, Daniel Ferreira wrote: Dear all, We are designing a study based on clinical data. We want to work with a MPRAGE sequence but subjects have been given 4 different sets of parameters: - TR: 1900; TE: 4,38; TI: 1100; flip angle: 15 - TR: 1900; TE: 3,55; TI: 1100; flip angle: 15 - TR: 1900; TE: 3,39; TI: 900; flip angle: 9 - TR: 1900; TE: 3,39; TI: 900; flip angle: 15 I wonder how these differences could affect the images and thus the results. Can I combine all of them or at least some of them? Are they so different that I should just study them by separate? thank you very much on advance Daniel Ferreira 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/**compliancelinehttp://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 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] How TE, TI and flip angle parameters affect the images and results?
Dear all, We are designing a study based on clinical data. We want to work with a MPRAGE sequence but subjects have been given 4 different sets of parameters: - TR: 1900; TE: 4,38; TI: 1100; flip angle: 15 - TR: 1900; TE: 3,55; TI: 1100; flip angle: 15 - TR: 1900; TE: 3,39; TI: 900; flip angle: 9 - TR: 1900; TE: 3,39; TI: 900; flip angle: 15 I wonder how these differences could affect the images and thus the results. Can I combine all of them or at least some of them? Are they so different that I should just study them by separate? thank you very much on advance Daniel Ferreira ___ 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] when are uncorrected 0, 001 results permitted instead of FWE?
Dear all, I have heard that the FWE correction sometimes could be demanding and kill very subtle differences, overall for example in aging studies with normal people and narrow-age intervals, or young people, where changes are supposed to be not very big. So, do you know when uncorrected results are justified or at least permitted instead of FWE? Any paper or information about this specific FWE disadvantages in aid of p0,001 uncorrected results? Thank you very much in advance Daniel Ferreira ___ 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.
Re: [Freesurfer] Recon-all Error: _FindFacePath
Hello Khoa, Thank you very much for your suggestion. I checked both brainmask.mgz and wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope something can be done. Cheers! Daniel Ferreira 2011/9/13 Khoa Nguyen k...@nmr.mgh.harvard.edu Hi Daniel, Usually when I get the FindFacePath error, the wm.mgz is very bad. You can try placing control points on the wm and rerun -autorecon2 and -autorecon3. That worked for me. -Khoa On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote: Dear Bruce and experts, I would really appreciate if you can help me with my scans. I have successfully processed all my sample but got this same FindFacePath error with 2 subjects. I checked the brainmask and wm files and for me they look ok. So I do not know how can I fix this error. Thank you very much in advance ERROR: _FindFacePath: could not find path! Linux neuroimagen 2.6.35-30-generic #54-Ubuntu SMP Tue Jun 7 18:41:54 UTC 2011 x86_64 GNU/Linux recon-all -s GJ169_3D exited with ERRORS at Sat Aug 20 07:53:56 WEST 2011 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 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 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.
Re: [Freesurfer] Recon-all Error: _FindFacePath
Hi Fatima, I used the Martinos Center File drop ( https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html). Daniel 2011/9/14 Ahmed, F, Me fah...@sun.ac.za fah...@sun.ac.za Hi Daniel, How did you send your scans to Bruce? Thanks, Fatima From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu [mailto: mailto:freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu]On Behalf Of Daniel Ferreira Padilla Sent: 14 September 2011 09:19 To: 'Khoa Nguyen' Cc: mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all Error: _FindFacePath Hello Khoa, Thank you very much for your suggestion. I checked both brainmask.mgz and wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope something can be done. Cheers! Daniel Ferreira - Ocultar texto citado - 2011/9/13 Khoa Nguyen mailto:k...@nmr.mgh.harvard.edu k...@nmr.mgh.harvard.edu Hi Daniel, Usually when I get the FindFacePath error, the wm.mgz is very bad. You can try placing control points on the wm and rerun -autorecon2 and -autorecon3. That worked for me. -Khoa On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote: Dear Bruce and experts, I would really appreciate if you can help me with my scans. I have successfully processed all my sample but got this same FindFacePath error with 2 subjects. I checked the brainmask and wm files and for me they look ok. So I do not know how can I fix this error. Thank you very much in advance ERROR: _FindFacePath: could not find path! Linux neuroimagen 2.6.35-30-generic #54-Ubuntu SMP Tue Jun 7 18:41:54 UTC 2011 x86_64 GNU/Linux recon-all -s GJ169_3D exited with ERRORS at Sat Aug 20 07:53:56 WEST 2011 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 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 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.
Re: [Freesurfer] Recon-all Error: _FindFacePath
Dear Bruce and experts, I would really appreciate if you can help me with my scans. I have successfully processed all my sample but got this same FindFacePath error with 2 subjects. I checked the brainmask and wm files and for me they look ok. So I do not know how can I fix this error. Thank you very much in advance ERROR: _FindFacePath: could not find path! Linux neuroimagen 2.6.35-30-generic #54-Ubuntu SMP Tue Jun 7 18:41:54 UTC 2011 x86_64 GNU/Linux recon-all -s GJ169_3D exited with ERRORS at Sat Aug 20 07:53:56 WEST 2011 ___ 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.
Re: [Freesurfer] error while loading shared libraries:libtiff.so.3
Thanks Jordi, thanks Krish, The problem goes on. I have checked my libtiff files ($ sudo apt-cache search libtiff) and have got exactly the same as you, Jordi. The problem is that libtiff.so.3 is not between them. I also managed to do the symbolic link with sudo ln -sf usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3. So, as I have 6 different lib folders I have created this libtiff.so.3 link in each one of them, cause I do not know where recon-all is pointing to. So, these are my lib folders: /lib /lib32 /lib64 /usr//lib /usr//lib32 /usr/ /lib64 Only in those three folders inside /usr/ have got the following files: pngtools - series of tools for PNG (Portable Network Graphics) images libtiff-doc - TIFF manipulation and conversion documentation libtiff-tools - TIFF manipulation and conversion tools libtiff4 - Tag Image File Format (TIFF) library libtiff4-dev - Tag Image File Format library (TIFF), development files libtiffxx0c2 - Tag Image File Format (TIFF) library -- C++ interface libtiff-opengl - TIFF manipulation and conversion tools So, perhaps recon-all is pointing to libs outside /usr/, where I do not have these files. Should I paste them on it? And how can I do it by command line? Please, any other idea? Thank you very much Daniel 2011/6/20 Krish Subramaniam mailto:kr...@nmr.mgh.harvard.edu kr...@nmr.mgh.harvard.edu Hi Daniel You get permission denied because you need write permissions for /usr/lib ( wherever libtiff.so.3 is ). If you think you have the permissions, prefix your ln command with a sudo and it'll ask for your password, and that should work successfully. If you don't have permissions, you need to ask your system administrator to do so. -Krish On Jun 20, 2011, at 5:44 AM, Daniel Ferreira Padilla wrote: Dear all, I'm using Ubuntu 10.10 and have the same problem only when working with 4.5 version (I also use 5.1 version without any problem). I have followed previous suggestions making a symbolic link named libtiff.so.3, but it gives me back the message denied permission. Also tried to install it with sudo aptitude install ia32-libs but it did not recognize aptitude command. So I tried with sudo apt-get install ia32-libs instead and it was ok, but I am still having the same problem. So, what could I do? Can I download libtiff.so.3 from somewhere? How can I avoid that denied permission? Thank you very much for your help. Daniel Ferreira # #@# Cortical ribbon mask Sat Jun 18 17:57:36 WEST 2011 /home/neuroimagen/DANI/subjects/uu0148_36_1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance uu0148_36_1 mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux neuroimagen 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jun 18 17:57:36 WEST 2011 ___ Freesurfer mailing list mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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.
Re: [Freesurfer] error while loading shared libraries:libtiff.so.3
Dear all, I'm using Ubuntu 10.10 and have the same problem only when working with 4.5 version (I also use 5.1 version without any problem). I have followed previous suggestions making a symbolic link named libtiff.so.3, but it gives me back the message denied permission. Also tried to install it with sudo aptitude install ia32-libs but it did not recognize aptitude command. So I tried with sudo apt-get install ia32-libs instead and it was ok, but I am still having the same problem. So, what could I do? Can I download libtiff.so.3 from somewhere? How can I avoid that denied permission? Thank you very much for your help. Daniel Ferreira # #@# Cortical ribbon mask Sat Jun 18 17:57:36 WEST 2011 /home/neuroimagen/DANI/subjects/uu0148_36_1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance uu0148_36_1 mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux neuroimagen 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jun 18 17:57:36 WEST 2011 ___ 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] issues about pial and wm edit
Dear all, I will really appreciate if you can help me with some issues about editing the pial surface. I have carefully followed the information on the web and looked up the mailing list but I still have the same doubts: 1) I have noticed that pial surface usually includes more than GM (dura, vessels...). My first question is if should we edit this kind of error. Sometimes I am completely sure what I need to correct, but I don't want to put human error in it. Moreover, we will spend to much time with big samples. 2) I have tried to edit the pial surface following the tutorial. After re-running -autorecon2-pial nothing seems to change. The voxels I deleted before are still there and the pial surface looks the same. What could be happening? 3) I have had the same problem with WM edit. After -autorecon2-wm everything remain as before edit. 4) I have read about regenerate the new pial surface with make_final_surfaces or from inside recon-all with -finalsurfs. The command could be something like this? recon-all -s mysubjectname -finalsurfs 5) If I need to fix pial and wm lesions in the same subject, do I need to run autorecon2-pial and -autorecon2-wm separately? Can I do it at the same time? And if I could, what command do I have to use? I hope these are not too much questions. Thank you very much in advance. Daniel Ferreira ___ 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.
Re: [Freesurfer] tksurfer error
Yes, I click over the redraw button but it doesnt work. It is strange but despite tksurfer window is empty, when I click on it, labels and values appear in tksurfer tools window. Any other idea? Thank you very much in advance -Mensaje original- De: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Enviado el: miércoles, 10 de febrero de 2010 15:49 Para: Daniel Ferreira Padilla CC: freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] tksurfer error have you tried clicking the redraw button? On Wed, 10 Feb 2010, Daniel Ferreira Padilla wrote: Dear Freesurfer users, I hope you could help me with that problem. I do the recon-all preprocessing step and then I try tksurfer. But the following error comes up. Moreover tksurfer window open up but it looks like 'empty'. Please find it attached. Thank you very much! Daniel Ferreira freesurfer-Linux-centos4-stable-pub-v4.5.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/Neuropsicologia/freesurfer FSFAST_HOME /home/Neuropsicologia/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/Neuropsicologia/DANI/subjects MNI_DIR /home/Neuropsicologia/freesurfer/mni FSL_DIR /home/Neuropsicologia/fsl neuropsicolo...@linux-tand:~ cd DANI/subjects neuropsicolo...@linux-tand:~/DANI/subjects tksurfer GJ25_3D lh inflated -aparc -gray surfer: current subjects dir: /home/Neuropsicologia/DANI/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/Neuropsicologia/DANI/subjects surfer: Reading header info from /home/Neuropsicologia/DANI/subjects/GJ25_3D/mri/T1.mgz surfer: vertices=123902, faces=247800 surfer: curvature read: min=-1.349975 max=2.259740 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fin al.txt) Found embedded color table in annotation. surfer: single buffered window surfer: tkoInitWindow(GJ25_3D) surfer: using interface /home/Neuropsicologia/freesurfer/lib/tcl/tksurfer.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_common.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/Neuropsicologia/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
