Dear Dr. Fischl,
Thank you for offering to look at our data.
I have used the FTP server to upload a zip archive, based on the website instructions (http://freesurfer.net/fswiki/FtpFileExchange)
The file is in:
transfer/incoming/1353.zip (using anonymous and my email address for the user/password)
Please let us know if you have any thoughts on how we can improve our temporal lobe pial reconstruction.
Sincerely,
Las
2014-07-18 18:00 GMT+02:00 freesurfer-request@nmr.mgh.harvard.edu:
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Today's Topics:
- Re: mni152reg error (JacobML@nmr.mgh.harvard.edu)
- template replacement (Ilwoo Lyu)
- unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim (wang kangcheng)
- Re: unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim (Douglas Greve)
- Re: mni152reg error (Douglas Greve)
- Re: unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim (wang kangcheng)
- Re: unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim (Douglas Greve)
- Spatial smoothing in Matlab (Reza Rajimehr)
- Re: unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim (wang kangcheng)
- Re: Anterior Temporal Lobe / Pial Reconstruc?tion Troubles - part 1 (Las Blawimo)
- Re: selxavg3-sess error in ==> fast_selxavg3 at 434 (pfannmoelj@uni-greifswald.de)
- Errors in Mapping of Brodmann Areas (pfannmoelj@uni-greifswald.de)
- Re: mni152reg error (JacobML@nmr.mgh.harvard.edu)
- Re: Errors in Mapping of Brodmann Areas (Bruce Fischl)
- Re: Errors in Mapping of Brodmann Areas (pfannmoelj@uni-greifswald.de)
- Re: Anterior Temporal Lobe / Pial Reconstruc?tion Troubles - part 1 (Bruce Fischl)
- Thickness measurements on longitudinal data set (Bastian Cheng)
Message: 1 Date: Thu, 17 Jul 2014 13:14:43 -0400 (EDT) From: "JacobML@nmr.mgh.harvard.edu" jacobml@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mni152reg error To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Message-ID: 44065.172.20.147.36.1405617283.squirrel@mail.nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
Hello again Doug,
Thank you for sending the updated version of mri152reg. It ran without error and generated the reg.mni152.2mm.dat registration matrix.
Unfortunately though, when I tried to apply the transformation to the same subject's t_000.bfloat, the registration is not correct (command below).
mri_vol2vol --inv --targ /.../t_000.bfloat --mov $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
On a positive note, I was able to load the output image and MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be shifted too far anterior.
With my next attempt, I used mri_convert to make the t_000.bfloat into a .mgz and than ran mri_vol2vol, but the same misalignment occurred (see attached photo).
Using tkmedit, I have confirmed that this file aligns properly on this subject's native structural image, so I am not quite sure why the registration matrix may be off. Given that the reg.mni152.2mm.dat file reflects the transformation of the native struc to MNI, I wonder if I need to account for the reg file between the func data and the native struc?
Can you please let me know what I may be doing incorrectly?
As always, your help is very appreciated.
Jacob
Yea, i fixed this problem. I've attached a new version with the fix. doug
On 07/17/2014 10:35 AM, JacobML@nmr.mgh.harvard.edu wrote:
Hello Freesurfer Experts, I am trying to view stats generated with FsFast in fslview/MNIspace,
and
in doing so I have run mni152reg to generate the registration matrix.
That said, mni152reg did not complete correctly and below I have pasted the terminal output:
Thu Jul 17 09:58:10 EDT 2014 setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
/usr/local/freesurfer/stable5_3_0/bin/mni152reg --s
CD_cerv_pat4_sess1_recon Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
UTC
2014 x86_64 x86_64 x86_64 GNU/Linux fslregister --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
--s CD_cerv_pat4_sess1_recon --reg
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat --dof 12
mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833':
Permission denied
Log file is
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log Thu Jul 17 09:58:11 EDT 2014
--mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
--s CD_cerv_pat4_sess1_recon --reg
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat --dof 12
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ purkinje Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
UTC
2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1
/autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons mri_convert
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii mri_convert
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii niiWrite(): error opening file
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from
/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00
i_ras = (-1, 0, 0) j_ras = (-0, -0, -1) k_ras = (0, 1, 0) writing to
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... ERROR: failure writing
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii I tried to run the fslregister command from within the subject's directory
(in hopes to possible correct what may be a permissions issue), but
this
produces the same final error, "ERROR: failure writing
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." Lastly, probably to no surprise, the
/.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any
ideas how I may be able to correct these errors?
Thank you for the help! Jacob _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-
Las Blawimo