Hi,
Yes, I am trying to use skull stripping from another package, since -gcut option did not work on our data for appropriate skull stripping, and as a result there is too much pial matter included as white matter.
a) Is brainmask.mgz an appropriate input file for recon-all -all? for example, should I run "recon-all -all -i brainmask.mgz -s SB001" ? or, am I still using the original .dcm file as input, and merely putting a copy of my skull stripped brain into the SUB/mri directory that was created in the previous processing attempt?
b) I am not understanding why i will still run skull stripping in the script here, if it is already done. Is the brainmask.auto.mgz generated just another duplicate copy that will be ignored for the actual segmentations? Will this still perform intensity normalization and other auto-recon1 steps normally?
Thank you, Michelle
On Tue, Jul 18, 2017 at 12:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Michelle
can you cc the list so others can answers? I'm also no longer sure which thread this is - were you trying to use the skull stripping from another package? If so, convert that file to be named brainmask.mgz, then do *not* include the -noskullstrip in your command line. Let us do the skull strippping, which will create a brainmask.auto.mgz, but should preserve the brainmask.mgz (since it is different than the .auto file)
cheers Bruce
On Tue, 18 Jul 2017, Michelle VanTieghem wrote:
Hi Bruce,
Thanks for the information. Sorry I had changed my mail settings so I wasn’t seeing your responses until now. I had tried to run all, but just skip skull strip step, as well as the talaraich check step since we saw errors with that too.
The command I used is follows:
recon-all -all -3T -mprage -notal-check -noskullstrip -i/vega/psych/users/mrv2115/fsdata/ORIG_AFNI_SKULLSTRIP/SB00 1/mprage_deobliqu e_brain.nii -s SB001
However, I am getting the following error during the registration step (see below). It looks like the mask volume brainmask.mgz hasn't been generated, but i don't know why. You suggested to convert my afni skull stripped brain to brain mask.mgz and place in the MRI folder. but am I still going to run the steps of autorecon-1 ? (intensity normalization, etc)? Does recon-all take inputs of already existing mri/brainmask.mgz files? It seems like it just needs one file and then re-generates a new directory with mri, scripts, ect. I would appreciate more detail on how to implement this!
Thank you,
Michelle
ERROR:
======= NUMBER OF OPENMP THREADS = 1 =======
aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/vega/psych/app/freesurfer/average/RB_all_2008-03-26.gca'...
average std = 6.9 using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mghRead(/vega/psych/users/mrv2115/fsdata/processed/SB001/ mri/brainmask.mgz, -1): could not $
mri_em_register: could not open mask volume brainmask.mgz.
Linux bogota.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_$
recon-all -s SB001 exited with ERRORS at Tue Jul 18 11:50:24 EDT 2017
——
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.
no, you don't use brainmask as input, you just put it in the subject's mri dir. recon-all should then recognize that it is different than brainmask.auto.mgz, assume it has been manually edited, and preserve those edits On Tue, 18 Jul 2017, Michelle VanTieghem wrote:
Hi, Yes, I am trying to use skull stripping from another package, since -gcut option did not work on our data for appropriate skull stripping, and as a result there is too much pial matter included as white matter.
a) Is brainmask.mgz an appropriate input file for recon-all -all? for example, should I run "recon-all -all -i brainmask.mgz -s SB001" ? or, am I still using the original .dcm file as input, and merely putting a copy of my skull stripped brain into the SUB/mri directory that was created in the previous processing attempt?
b) I am not understanding why i will still run skull stripping in the script here, if it is already done. Is the brainmask.auto.mgz generated just another duplicate copy that will be ignored for the actual segmentations? Will this still perform intensity normalization and other auto-recon1 steps normally?
Thank you, Michelle
On Tue, Jul 18, 2017 at 12:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Michelle
can you cc the list so others can answers? I'm also no longer sure which thread this is - were you trying to use the skull stripping from another package? If so, convert that file to be named brainmask.mgz, then do *not* include the -noskullstrip in your command line. Let us do the skull strippping, which will create a brainmask.auto.mgz, but should preserve the brainmask.mgz (since it is different than the .auto file) cheers Bruce On Tue, 18 Jul 2017, Michelle VanTieghem wrote: Hi Bruce, Thanks for the information. Sorry I had changed my mail settings so I wasn’t seeing your responses until now. I had tried to run all, but just skip skull strip step, as well as the talaraich check step since we saw errors with that too. The command I used is follows: recon-all -all -3T -mprage -notal-check -noskullstrip-i/vega/psych/users/mrv2115/fsdata/ORIG_AFNI_SKULLSTRIP/SB001/mprage_deobli qu e_brain.nii -s SB001 However, I am getting the following error during the registration step (see below). It looks like the mask volume brainmask.mgz hasn't been generated, but i don't know why. You suggested to convert my afni skull stripped brain to brain mask.mgz and place in the MRI folder. but am I still going to run the steps of autorecon-1 ? (intensity normalization, etc)? Does recon-all take inputs of already existing mri/brainmask.mgz files? It seems like it just needs one file and then re-generates a new directory with mri, scripts, ect. I would appreciate more detail on how to implement this! Thank you, Michelle ERROR: ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/vega/psych/app/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'...mghRead(/vega/psych/users/mrv2115/fsdata/processed/SB001/mri/brainmask.mgz,
-1): could not $ mri_em_register: could not open mask volume brainmask.mgz. Linux bogota.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_$ recon-all -s SB001 exited with ERRORS at Tue Jul 18 11:50:24 EDT 2017 ——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.
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
Hi Bruce,
Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command:
recon-all -all -3T -mprage -s processed/Subnum
I get the following error: --------------------------------------------------
#@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask -------------------------------------------------
Can you please advise?
Hi,
After checking the images in the viewer, it appears that 001.mgz and brainmask.mgz are in the correct orientation, but brain.mgz (created by freesurfer) is rotated 90 degrees. The dimensions of the images don't match either.
001.mgz and brainmask.mgz are: dim1 219 dim2 268 dim3 265 dim4 1
brain.mgz is : dim1 256 dim2 256 dim3 256
On Mon, Aug 7, 2017 at 2:04 PM, Michelle VanTieghem < michelle.vantieghem@gmail.com> wrote:
Hi Bruce,
Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command:
recon-all -all -3T -mprage -s processed/Subnum
I get the following error:
#@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask
Can you please advise?
what viewer did you check in? If not freeview, look at it in freeview On Mon, 7 Aug 2017, Michelle VanTieghem wrote:
Hi, After checking the images in the viewer, it appears that 001.mgz and brainmask.mgz are in the correct orientation, but brain.mgz (created by freesurfer) is rotated 90 degrees. The dimensions of the images don't match either.
001.mgz and brainmask.mgz are: dim1 219 dim2 268 dim3 265 dim4 1
brain.mgz is : dim1 256 dim2 256 dim3 256
On Mon, Aug 7, 2017 at 2:04 PM, Michelle VanTieghem michelle.vantieghem@gmail.com wrote: Hi Bruce,
Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command:
recon-all -all -3T -mprage -s processed/Subnum
I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask
Can you please advise?
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
what was your mri_convert command line? It should be something like
mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz
cheers Bruce
On Mon, 7 Aug 2017, Michelle VanTieghem wrote:
Hi Bruce,
Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command:
recon-all -all -3T -mprage -s processed/Subnum
I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask
Can you please advise?
Hi,
I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz
and I re-did it using the -rl flag as you recommended.
it did not influence anything, same problem.
I'd appreciate any trouble shooting tips.
Thanks, M
On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what was your mri_convert command line? It should be something like
mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz
cheers Bruce
On Mon, 7 Aug 2017, Michelle VanTieghem wrote:
Hi Bruce,
Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command:
recon-all -all -3T -mprage -s processed/Subnum
I get the following error:
#@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask
Can you please advise?
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.
can you send us the output of mri_info on orig.mgz and brainmask.mgz created with the -rl flag? And also send us the full screen output of the command that fails?
thanks Bruce On Wed, 9 Aug 2017, Michelle VanTieghem wrote:
Hi, I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz
and I re-did it using the -rl flag as you recommended.
it did not influence anything, same problem.
I'd appreciate any trouble shooting tips.
Thanks, M
On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what was your mri_convert command line? It should be something like
mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz cheers Bruce On Mon, 7 Aug 2017, Michelle VanTieghem wrote: Hi Bruce, Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command: recon-all -all -3T -mprage -s processed/Subnum I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask ------------------------------------------------- Can you please advise?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.
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
-bash-4.1$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 3.0505 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.9364
talairach xfm : /vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 122.7709 0.0000 0.0000 1.0000 -124.9495 0.0000 -1.0000 0.0000 127.0636 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 122.7709 -0.0000 -0.0000 -1.0000 127.0636 -0.0000 1.0000 -0.0000 124.9495 0.0000 0.0000 0.0000 1.0000 ---------------------------------------------------------------------------------------- -bash-4.1$ mri_info brainmask.mgz Volume information for brainmask.mgz type: MGH dimensions: 221 x 274 x 261 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 274.000 dof: 0 xstart: -110.5, xend: 110.5 ystart: -137.0, yend: 137.0 zstart: -130.5, zend: 130.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 3.0505 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.9364
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 0.0000 0.0000 1.0000 -131.4364 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 -0.0000 -0.0000 1.0000 131.4364 0.0000 0.0000 0.0000 1.0000 --------------------------------------------------------------------------------------------------------- Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 0 (-1) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 83 (83), valley at 0 (-1) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 23 seconds. #-------------------------------------------- #@# Mask BFS Wed Aug 9 02:03:44 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux reno.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SB020_fu1 exited with ERRORS at Wed Aug 9 02:03:46 EDT 2017
On Wed, Aug 9, 2017 at 4:11 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the output of mri_info on orig.mgz and brainmask.mgz created with the -rl flag? And also send us the full screen output of the command that fails?
thanks Bruce
On Wed, 9 Aug 2017, Michelle VanTieghem wrote:
Hi,
I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz
and I re-did it using the -rl flag as you recommended.
it did not influence anything, same problem.
I'd appreciate any trouble shooting tips.
Thanks, M
On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what was your mri_convert command line? It should be something like
mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz cheers Bruce On Mon, 7 Aug 2017, Michelle VanTieghem wrote: Hi Bruce, Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command: recon-all -all -3T -mprage -s processed/Subnum I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask ------------------------------------------------- Can you please advise?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.
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
are you sure you created the brainmask with -rl orig.mgz? It should have the same dimensions afterwards.
On Wed, 9 Aug 2017, Michelle VanTieghem wrote:
-bash-4.1$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 3.0505 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.9364
talairach xfm :/vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri/transforms/talaira ch.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 122.7709 0.0000 0.0000 1.0000 -124.9495 0.0000 -1.0000 0.0000 127.0636 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 122.7709 -0.0000 -0.0000 -1.0000 127.0636 -0.0000 1.0000 -0.0000 124.9495 0.0000 0.0000 0.0000 1.0000
-bash-4.1$ mri_info brainmask.mgz Volume information for brainmask.mgz type: MGH dimensions: 221 x 274 x 261 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 274.000 dof: 0 xstart: -110.5, xend: 110.5 ystart: -137.0, yend: 137.0 zstart: -130.5, zend: 130.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 3.0505 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.9364
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 0.0000 0.0000 1.0000 -131.4364 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 -0.0000 -0.0000 1.0000 131.4364 0.0000 0.0000 0.0000 1.0000
Iterating 2 times
3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 0 (-1) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 83 (83), valley at 0 (-1) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 23 seconds. #-------------------------------------------- #@# Mask BFS Wed Aug 9 02:03:44 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux reno.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SB020_fu1 exited with ERRORS at Wed Aug 9 02:03:46 EDT 2017
On Wed, Aug 9, 2017 at 4:11 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send us the output of mri_info on orig.mgz and brainmask.mgz created with the -rl flag? And also send us the full screen output of the command that fails?
thanks Bruce On Wed, 9 Aug 2017, Michelle VanTieghem wrote: Hi, I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz and I re-did it using the -rl flag as you recommended. it did not influence anything, same problem. I'd appreciate any trouble shooting tips. Thanks, M On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what was your mri_convert command line? It should be something like mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz cheers Bruce On Mon, 7 Aug 2017, Michelle VanTieghem wrote: Hi Bruce, Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command: recon-all -all -3T -mprage -s processed/Subnum I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask ------------------------------------------------- Can you please advise? 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. -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
Hi Bruce,
I got this to work, but we are still having the same problem wth over-inclusion of pial matter in the white matter segmentations even when using skullstrip from other packages (AFNI , FSL, ANTs).
I am mainly interested in the subcortical volumes, and I want to do a longitudinal analysis of the subcortical volumes. Does the longitudinal freesurfer pipeline depend on good quality segmentation across whole brain? or can I use it to obtain longitudinal subcortical volumes and ignore the fact that the white matter segmentation is less than perfect for many subjects? Is it a problem that the whole-brain volume measures will be off due to the over-inclusion of skull in WM?
I would appreciate any advice or insights you may have!
Thanks, Michelle
On Wed, Aug 9, 2017 at 6:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
are you sure you created the brainmask with -rl orig.mgz? It should have the same dimensions afterwards.
On Wed, 9 Aug 2017, Michelle VanTieghem wrote:
-bash-4.1$ mri_info orig.mgz
Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 3.0505 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.9364
talairach xfm :/vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri/ transforms/talaira ch.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 122.7709 0.0000 0.0000 1.0000 -124.9495 0.0000 -1.0000 0.0000 127.0636 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 122.7709 -0.0000 -0.0000 -1.0000 127.0636 -0.0000 1.0000 -0.0000 124.9495 0.0000 0.0000 0.0000 1.0000
-bash-4.1$ mri_info brainmask.mgz Volume information for brainmask.mgz type: MGH dimensions: 221 x 274 x 261 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 274.000 dof: 0 xstart: -110.5, xend: 110.5 ystart: -137.0, yend: 137.0 zstart: -130.5, zend: 130.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 3.0505 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.9364
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 0.0000 0.0000 1.0000 -131.4364 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 -0.0000 -0.0000 1.0000 131.4364 0.0000 0.0000 0.0000 1.0000
Iterating 2 times
3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 0 (-1) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 83 (83), valley at 0 (-1) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 23 seconds. #-------------------------------------------- #@# Mask BFS Wed Aug 9 02:03:44 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux reno.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SB020_fu1 exited with ERRORS at Wed Aug 9 02:03:46 EDT 2017
On Wed, Aug 9, 2017 at 4:11 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send us the output of mri_info on orig.mgz and brainmask.mgz created with the -rl flag? And also send us the full screen output of the command that fails?
thanks Bruce On Wed, 9 Aug 2017, Michelle VanTieghem wrote: Hi, I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz and I re-did it using the -rl flag as you recommended. it did not influence anything, same problem. I'd appreciate any trouble shooting tips. Thanks, M On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what was your mri_convert command line? It should be something like mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz cheers Bruce On Mon, 7 Aug 2017, Michelle VanTieghem wrote: Hi Bruce, Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command: recon-all -all -3T -mprage -s processed/Subnum I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask ------------------------------------------------- Can you please advise? 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. -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
Hi,
As a related question, we have been using FSL 5.3. I would like to use LME methods. I noticed that FSL 5.3 "Allows processing of subjects with single time point through the longitudinal stream to include them without bias into statistical analysis (LME)." but the Matlabs LME tools are only mentioned for FSL 6.0.
Does FSL 5.3 allow for LME, but not through matlab tools? Is it possible to use the matlab LME with data processed on 5.3?
Thanks, Michelle
On Fri, Aug 25, 2017 at 5:25 PM, Michelle VanTieghem < michelle.vantieghem@gmail.com> wrote:
Hi Bruce,
I got this to work, but we are still having the same problem wth over-inclusion of pial matter in the white matter segmentations even when using skullstrip from other packages (AFNI , FSL, ANTs).
I am mainly interested in the subcortical volumes, and I want to do a longitudinal analysis of the subcortical volumes. Does the longitudinal freesurfer pipeline depend on good quality segmentation across whole brain? or can I use it to obtain longitudinal subcortical volumes and ignore the fact that the white matter segmentation is less than perfect for many subjects? Is it a problem that the whole-brain volume measures will be off due to the over-inclusion of skull in WM?
I would appreciate any advice or insights you may have!
Thanks, Michelle
On Wed, Aug 9, 2017 at 6:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
are you sure you created the brainmask with -rl orig.mgz? It should have the same dimensions afterwards.
On Wed, 9 Aug 2017, Michelle VanTieghem wrote:
-bash-4.1$ mri_info orig.mgz
Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 3.0505 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.9364
talairach xfm :/vega/psych/users/mrv2115/fsd ata/processed/SB020_fu1/mri/transforms/talaira ch.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 122.7709 0.0000 0.0000 1.0000 -124.9495 0.0000 -1.0000 0.0000 127.0636 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 122.7709 -0.0000 -0.0000 -1.0000 127.0636 -0.0000 1.0000 -0.0000 124.9495 0.0000 0.0000 0.0000 1.0000
-bash-4.1$ mri_info brainmask.mgz Volume information for brainmask.mgz type: MGH dimensions: 221 x 274 x 261 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 274.000 dof: 0 xstart: -110.5, xend: 110.5 ystart: -137.0, yend: 137.0 zstart: -130.5, zend: 130.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 3.0505 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.9364
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 0.0000 0.0000 1.0000 -131.4364 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 -0.0000 -0.0000 1.0000 131.4364 0.0000 0.0000 0.0000 1.0000
Iterating 2 times
3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 0 (-1) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 83 (83), valley at 0 (-1) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 23 seconds. #-------------------------------------------- #@# Mask BFS Wed Aug 9 02:03:44 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux reno.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SB020_fu1 exited with ERRORS at Wed Aug 9 02:03:46 EDT 2017
On Wed, Aug 9, 2017 at 4:11 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: can you send us the output of mri_info on orig.mgz and brainmask.mgz created with the -rl flag? And also send us the full screen output of the command that fails?
thanks Bruce On Wed, 9 Aug 2017, Michelle VanTieghem wrote: Hi, I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz and I re-did it using the -rl flag as you recommended. it did not influence anything, same problem. I'd appreciate any trouble shooting tips. Thanks, M On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what was your mri_convert command line? It should be something like mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz cheers Bruce On Mon, 7 Aug 2017, Michelle VanTieghem wrote: Hi Bruce, Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command: recon-all -all -3T -mprage -s processed/Subnum I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask ------------------------------------------------- Can you please advise? 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. -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
Hi Michelle
the wm segmentation is kind of irrelevant - it's the ?h.white surfaces that matter (and maybe not even those if you only care about subcortical things)
cheers Bruce On Fri, 25 Aug 2017, Michelle VanTieghem wrote:
Hi Bruce, I got this to work, but we are still having the same problem wth over-inclusion of pial matter in the white matter segmentations even when using skullstrip from other packages (AFNI , FSL, ANTs).
I am mainly interested in the subcortical volumes, and I want to do a longitudinal analysis of the subcortical volumes. Does the longitudinal freesurfer pipeline depend on good quality segmentation across whole brain? or can I use it to obtain longitudinal subcortical volumes and ignore the fact that the white matter segmentation is less than perfect for many subjects? Is it a problem that the whole-brain volume measures will be off due to the over-inclusion of skull in WM?
I would appreciate any advice or insights you may have!
Thanks, Michelle
On Wed, Aug 9, 2017 at 6:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: are you sure you created the brainmask with -rl orig.mgz? It should have the same dimensions afterwards.
On Wed, 9 Aug 2017, Michelle VanTieghem wrote: -bash-4.1$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 3.0505 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.9364 talairach xfm :/vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri/transforms/talaira ch.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 122.7709 0.0000 0.0000 1.0000 -124.9495 0.0000 -1.0000 0.0000 127.0636 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 122.7709 -0.0000 -0.0000 -1.0000 127.0636 -0.0000 1.0000 -0.0000 124.9495 0.0000 0.0000 0.0000 1.0000 --------------------------------------------------------------------------- ------------- -bash-4.1$ mri_info brainmask.mgz Volume information for brainmask.mgz type: MGH dimensions: 221 x 274 x 261 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 274.000 dof: 0 xstart: -110.5, xend: 110.5 ystart: -137.0, yend: 137.0 zstart: -130.5, zend: 130.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 3.0505 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.9364 talairach xfm : Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 0.0000 0.0000 1.0000 -131.4364 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 -0.0000 -0.0000 1.0000 131.4364 0.0000 0.0000 0.0000 1.0000 --------------------------------------------------------------------------- ------------------------------ Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 0 (-1) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 83 (83), valley at 0 (-1) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 23 seconds. #-------------------------------------------- #@# Mask BFS Wed Aug 9 02:03:44 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux reno.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SB020_fu1 exited with ERRORS at Wed Aug 9 02:03:46 EDT 2017 On Wed, Aug 9, 2017 at 4:11 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: can you send us the output of mri_info on orig.mgz and brainmask.mgz created with the -rl flag? And also send us the full screen output of the command that fails? thanks Bruce On Wed, 9 Aug 2017, Michelle VanTieghem wrote: Hi, I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz and I re-did it using the -rl flag as you recommended. it did not influence anything, same problem. I'd appreciate any trouble shooting tips. Thanks, M On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what was your mri_convert command line? It should be something like mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz cheers Bruce On Mon, 7 Aug 2017, Michelle VanTieghem wrote: Hi Bruce, Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command: recon-all -all -3T -mprage -s processed/Subnum I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask ------------------------------------------------- Can you please advise? 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. -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Michelle VanTieghem