Re: [Freesurfer] bad freesurfer segmentation

2014-07-23 Thread Doety Prins
Just for the record, I accidentally e-mailed you that the slice thickness was 2 
mm, I now found out that the slice thickness is just 1 mm.

Doety
___
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] bad freesurfer segmentation

2014-07-17 Thread Doety Prins
Thanks Bruce! Now it's working, and the wm.mgz looks good!

Doety
___
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] bad freesurfer segmentation

2014-07-17 Thread Bruce Fischl
glad to hear it
Bruce
On Thu, 17 Jul 2014, Doety Prins wrote:

 Thanks Bruce! Now it's working, and the wm.mgz looks good!

 Doety
 ___
 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.



Re: [Freesurfer] bad freesurfer segmentation

2014-07-16 Thread Doety Prins
Hi Bruce,

Thanks for your answer. I was trying to use the fsl segment in freesurfer 
indeed. But since I couldn't get that working, I am now trying to do the trick 
with mri_segment. Sorry to ask you again, but I still have troubles with 
mri_segment. So I am trying to use the -wm_low flag to make the program do a 
different segmentation than the default. But it looks like mri_segment is still 
using the default settings? And the wm.new.mgz I get out of it looks completely 
the same as my previous wm.mgz

So my command is: mri_segment brain.mgz wm.new.mgz -wlo 110

This is what comes out:

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 105.4 +- 4.8 [80.0 -- 125.0]
GM (70.0) : 68.4 +- 10.3 [30.0 -- 96.0]
setting bottom of white matter range to 78.6
setting top of gray matter range to 88.9
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
3683 sparsely connected voxels removed...
thickening thin strands
20 segments, 2500 filled
8702 bright non-wm voxels segmented.
4341 diagonally connected voxels added...
white matter segmentation took 1.5 minutes
writing output to wm.new.mgz...

I put the output in bold which (I think) could be causing troubles(?) It looks 
like mri_segment is still using the default limits for wm and gm. I tried the 
same adding the flag -noauto, but it didn't make any difference.

Do you know what I am doing wrong here? How should I use mri_segment in order 
to really set different ranges of wm and gm intensities?

Again, thanks for your help!!

Doety___
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] bad freesurfer segmentation

2014-07-16 Thread Bruce Fischl

Hi Doety

for mri_segment the options have to come before the required arguments 
not at the end of the command line.


cheers
Bruce
On Wed, 16 Jul 2014, Doety Prins wrote:


Hi Bruce,
Thanks for your answer. I was trying to use the fsl segment in freesurfer
indeed. But since I couldn't get that working, I am now trying to do the
trick with mri_segment. Sorry to ask you again, but I still have troubles
with mri_segment. So I am trying to use the -wm_low flag to make the program
do a different segmentation than the default. But it looks like mri_segment
is still using the default settings? And the wm.new.mgz I get out of it
looks completely the same as my previous wm.mgz

So my command is: mri_segment brain.mgz wm.new.mgz -wlo 110

This is what comes out:

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 105.4 +- 4.8 [80.0 -- 125.0]
GM (70.0) : 68.4 +- 10.3 [30.0 -- 96.0]
setting bottom of white matter range to 78.6
setting top of gray matter range to 88.9
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
3683 sparsely connected voxels removed...
thickening thin strands
20 segments, 2500 filled
8702 bright non-wm voxels segmented.
4341 diagonally connected voxels added...
white matter segmentation took 1.5 minutes
writing output to wm.new.mgz...

I put the output in bold which (I think) could be causing troubles(?) It
looks like mri_segment is still using the default limits for wm and gm. I
tried the same adding the flag -noauto, but it didn't make any difference.

Do you know what I am doing wrong here? How should I use mri_segment in
order to really set different ranges of wm and gm intensities?

Again, thanks for your help!!

Doety

___
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] bad freesurfer segmentation

2014-07-15 Thread Doety Prins
Hi Bruce,

Thanks for your reply. Yes I realize now that this is causing me the
troubles. But since fsl is able to do a good segmentation, I think
Freesurfer should also be able to do this?

I am now using MRI_segment, in which I want to set new limits for the white
matter, but it doesn't seem to work yet. I use wm.mgz as input volume and
output volume something like wm.new.mgz, and -wm_low and -wm_hi with
different values as optional arguments. But what file should be included as
'classifier file'? I couldn't find that anywhere in the description.

Thanks in advance for your help again!

Doety


Op vrijdag 11 juli 2014 heeft Bruce Fischl fis...@nmr.mgh.harvard.edu het
volgende geschreven:
 the 2mm slice thickness is going to be problematic and is probably why you
 lose so much cortical constrast. Typically we don't recommend using
 anything more than 1.5 and really no reason these days not to get closer
to
 1mm (for example, you can get a very nice 1.25mmx1.25x1mm mprage in a bit
 over 2 minutes)

 cheers
 Bruce


 On
 Fri, 11 Jul 2014, Doety Prins wrote:

 slice thickness: 2 mm
 Repetition time: 25 ms (I think this might have caused the low contrast)
 flip angle: 30 degrees
 I'm sorry, can't find any data on acceleration

 Doety

 On 11 jul. 2014, at 15:10, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 Hi Doety

 that is a very low contrast-to-noise image. Can you give us more details
 on the acquisition? The matrix was 256x256, what is the slice thickness?
 And the other parameter (sequence name? TR/TR/flip angle? acceleration?)

 cheers
 Bruce


 On
 Thu, 10 Jul 2014, Doety Prins wrote:

 Hi Bruce,

 Thanks for your reply. In my previous e-mail I already tried to attach
 one of my subjects, but got the response that the message was too big,
and
 therefore it was rejected. So how should I upload the image? The images
are
 T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.

 I discovered that FSL does a proper segmentation on this subjects, so
I was looking for a way to import these segments from FSL into the
Freesurfer pipeline, but I didn't succeed so far. I used the white matter
segment from FSL as wm.mgz (in a subject in which I already ran recon-all),
I used mri_vol2vol to get this segment in the right space, and normalized
with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it
gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1
depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't
have the right size. Do you have any experience with this? Or any ideas
about this?

 Best regards,

 Doety

 On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:

 Hi Doety

 yes, that looks pretty bad. Can you tell us about the acquisition?
What
 resolution/field strength/scan type was it?

 If you upload the subject we will take a look

 cheers
 Bruce
 On Wed, 9 Jul 2014, Doety
 Prins
 wrote:

 Dear freesurfer experts,

 I experienced some problems with the segmentation of my T1 scans,
as both the white surface and the pial surface are placed incorrectly (see
attached images). This seems to me to be a too big difference with what it
should look like, that I think could not be fixed with the standard
troubleshooting strategies.

 Do you have any solutions for this? Is it for instance possible to
make changes to the recon-all script to shift the surfaces?

 Thanks in advance,

 Doety


 ___
 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 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


 ___
 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

___
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 

Re: [Freesurfer] bad freesurfer segmentation

2014-07-15 Thread Bruce Fischl
Hi Doety

our segmentation assumes we can resolve cortex as it used an adaptive 
filtering that estimates the orientation of the gray/white boundary in 
spatial neighborhoods. It may be more sensitive to low resolution than FSL. 
Not sure if anyone has a script for importing FSL segmentations into our 
processing pipeline, but someone might.

cheers
Bruce



On Tue, 15 Jul 2014, Doety Prins wrote:

 Hi Bruce,
 
 Thanks for your reply. Yes I realize now that this is causing me the
 troubles. But since fsl is able to do a good segmentation, I think
 Freesurfer should also be able to do this?
 
 I am now using MRI_segment, in which I want to set new limits for the white
 matter, but it doesn't seem to work yet. I use wm.mgz as input volume and
 output volume something like wm.new.mgz, and -wm_low and -wm_hi with
 different values as optional arguments. But what file should be included as
 'classifier file'? I couldn't find that anywhere in the description.
 
 Thanks in advance for your help again!
 
 Doety
 
 
 Op vrijdag 11 juli 2014 heeft Bruce Fischl fis...@nmr.mgh.harvard.edu het
 volgende geschreven:
  the 2mm slice thickness is going to be problematic and is probably why you
  lose so much cortical constrast. Typically we don't recommend using
  anything more than 1.5 and really no reason these days not to get closer
 to
  1mm (for example, you can get a very nice 1.25mmx1.25x1mm mprage in a bit
  over 2 minutes)
 
  cheers
  Bruce
 
 
  On
  Fri, 11 Jul 2014, Doety Prins wrote:
 
  slice thickness: 2 mm
  Repetition time: 25 ms (I think this might have caused the low contrast)
  flip angle: 30 degrees
  I'm sorry, can't find any data on acceleration
 
  Doety
 
  On 11 jul. 2014, at 15:10, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
 
  Hi Doety
 
  that is a very low contrast-to-noise image. Can you give us more details
  on the acquisition? The matrix was 256x256, what is the slice thickness?
  And the other parameter (sequence name? TR/TR/flip angle? acceleration?)
 
  cheers
  Bruce
 
 
  On
  Thu, 10 Jul 2014, Doety Prins wrote:
 
  Hi Bruce,
 
  Thanks for your reply. In my previous e-mail I already tried to attach
  one of my subjects, but got the response that the message was too big,
 and
  therefore it was rejected. So how should I upload the image? The images
 are
  T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.
 
  I discovered that FSL does a proper segmentation on this subjects, so I
 was looking for a way to import these segments from FSL into the Freesurfer
 pipeline, but I didn't succeed so far. I used the white matter segment from
 FSL as wm.mgz (in a subject in which I already ran recon-all), I used
 mri_vol2vol to get this segment in the right space, and normalized with
 mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me
 the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 !=
 volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right
 size. Do you have any experience with this? Or any ideas about this?
 
  Best regards,
 
  Doety
 
  On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
 
  Hi Doety
 
  yes, that looks pretty bad. Can you tell us about the acquisition?
 What
  resolution/field strength/scan type was it?
 
  If you upload the subject we will take a look
 
  cheers
  Bruce
  On Wed, 9 Jul 2014, Doety
  Prins
  wrote:
 
  Dear freesurfer experts,
 
  I experienced some problems with the segmentation of my T1 scans, as
 both the white surface and the pial surface are placed incorrectly (see
 attached images). This seems to me to be a too big difference with what it
 should look like, that I think could not be fixed with the standard
 troubleshooting strategies.
 
  Do you have any solutions for this? Is it for instance possible to
 make changes to the recon-all script to shift the surfaces?
 
  Thanks in advance,
 
  Doety
 
 
  ___
  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 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
 
 
  ___
  Freesurfer mailing list
  

Re: [Freesurfer] bad freesurfer segmentation

2014-07-11 Thread Bruce Fischl
Hi Doety

that is a very low contrast-to-noise image. Can you give us more details 
on the acquisition? The matrix was 256x256, what is the slice thickness? 
And the other parameter (sequence name? TR/TR/flip angle? acceleration?)

cheers
Bruce


On 
Thu, 10 Jul 2014, Doety Prins wrote:

 Hi Bruce,

 Thanks for your reply. In my previous e-mail I already tried to attach 
one of my subjects, but got the response that the message was too big, and 
therefore it was rejected. So how should I upload the image? The images are 
T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.

 I discovered that FSL does a proper segmentation on this subjects, so I was 
 looking for a way to import these segments from FSL into the Freesurfer 
 pipeline, but I didn't succeed so far. I used the white matter segment from 
 FSL as wm.mgz (in a subject in which I already ran recon-all), I used 
 mri_vol2vol to get this segment in the right space, and normalized with 
 mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me 
 the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != 
 volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right 
 size. Do you have any experience with this? Or any ideas about this?

 Best regards,

 Doety

 On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Doety

 yes, that looks pretty bad. Can you tell us about the acquisition? What
 resolution/field strength/scan type was it?

 If you upload the subject we will take a look

 cheers
 Bruce
 On Wed, 9 Jul 2014, Doety
 Prins
 wrote:

 Dear freesurfer experts,

 I experienced some problems with the segmentation of my T1 scans, as both 
 the white surface and the pial surface are placed incorrectly (see 
 attached images). This seems to me to be a too big difference with what it 
 should look like, that I think could not be fixed with the standard 
 troubleshooting strategies.

 Do you have any solutions for this? Is it for instance possible to make 
 changes to the recon-all script to shift the surfaces?

 Thanks in advance,

 Doety


 ___
 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 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


Re: [Freesurfer] bad freesurfer segmentation

2014-07-11 Thread Bruce Fischl
the 2mm slice thickness is going to be problematic and is probably why you 
lose so much cortical constrast. Typically we don't recommend using 
anything more than 1.5 and really no reason these days not to get closer to 
1mm (for example, you can get a very nice 1.25mmx1.25x1mm mprage in a bit 
over 2 minutes)

cheers
Bruce


On 
Fri, 11 Jul 2014, Doety Prins wrote:

 slice thickness: 2 mm
 Repetition time: 25 ms (I think this might have caused the low contrast)
 flip angle: 30 degrees
 I'm sorry, can't find any data on acceleration

 Doety

 On 11 jul. 2014, at 15:10, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Doety

 that is a very low contrast-to-noise image. Can you give us more details
 on the acquisition? The matrix was 256x256, what is the slice thickness?
 And the other parameter (sequence name? TR/TR/flip angle? acceleration?)

 cheers
 Bruce


 On
 Thu, 10 Jul 2014, Doety Prins wrote:

 Hi Bruce,

 Thanks for your reply. In my previous e-mail I already tried to attach
 one of my subjects, but got the response that the message was too big, and
 therefore it was rejected. So how should I upload the image? The images are
 T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.

 I discovered that FSL does a proper segmentation on this subjects, so I was 
 looking for a way to import these segments from FSL into the Freesurfer 
 pipeline, but I didn't succeed so far. I used the white matter segment from 
 FSL as wm.mgz (in a subject in which I already ran recon-all), I used 
 mri_vol2vol to get this segment in the right space, and normalized with 
 mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me 
 the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 
 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the 
 right size. Do you have any experience with this? Or any ideas about this?

 Best regards,

 Doety

 On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Doety

 yes, that looks pretty bad. Can you tell us about the acquisition? What
 resolution/field strength/scan type was it?

 If you upload the subject we will take a look

 cheers
 Bruce
 On Wed, 9 Jul 2014, Doety
 Prins
 wrote:

 Dear freesurfer experts,

 I experienced some problems with the segmentation of my T1 scans, as 
 both the white surface and the pial surface are placed incorrectly (see 
 attached images). This seems to me to be a too big difference with what 
 it should look like, that I think could not be fixed with the standard 
 troubleshooting strategies.

 Do you have any solutions for this? Is it for instance possible to make 
 changes to the recon-all script to shift the surfaces?

 Thanks in advance,

 Doety


 ___
 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 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


 ___
 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


Re: [Freesurfer] bad freesurfer segmentation

2014-07-11 Thread Doety Prins
slice thickness: 2 mm
Repetition time: 25 ms (I think this might have caused the low contrast)
flip angle: 30 degrees
I'm sorry, can't find any data on acceleration

Doety

On 11 jul. 2014, at 15:10, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Doety
 
 that is a very low contrast-to-noise image. Can you give us more details 
 on the acquisition? The matrix was 256x256, what is the slice thickness? 
 And the other parameter (sequence name? TR/TR/flip angle? acceleration?)
 
 cheers
 Bruce
 
 
 On 
 Thu, 10 Jul 2014, Doety Prins wrote:
 
 Hi Bruce,
 
 Thanks for your reply. In my previous e-mail I already tried to attach 
 one of my subjects, but got the response that the message was too big, and 
 therefore it was rejected. So how should I upload the image? The images are 
 T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.
 
 I discovered that FSL does a proper segmentation on this subjects, so I was 
 looking for a way to import these segments from FSL into the Freesurfer 
 pipeline, but I didn't succeed so far. I used the white matter segment from 
 FSL as wm.mgz (in a subject in which I already ran recon-all), I used 
 mri_vol2vol to get this segment in the right space, and normalized with 
 mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me 
 the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != 
 volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right 
 size. Do you have any experience with this? Or any ideas about this?
 
 Best regards,
 
 Doety
 
 On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 Hi Doety
 
 yes, that looks pretty bad. Can you tell us about the acquisition? What
 resolution/field strength/scan type was it?
 
 If you upload the subject we will take a look
 
 cheers
 Bruce
 On Wed, 9 Jul 2014, Doety
 Prins
 wrote:
 
 Dear freesurfer experts,
 
 I experienced some problems with the segmentation of my T1 scans, as both 
 the white surface and the pial surface are placed incorrectly (see 
 attached images). This seems to me to be a too big difference with what 
 it should look like, that I think could not be fixed with the standard 
 troubleshooting strategies.
 
 Do you have any solutions for this? Is it for instance possible to make 
 changes to the recon-all script to shift the surfaces?
 
 Thanks in advance,
 
 Doety
 
 
 ___
 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 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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


Re: [Freesurfer] bad freesurfer segmentation

2014-07-10 Thread Doety Prins
Hi Bruce,

Thanks for your reply. In my previous e-mail I already tried to attach one of 
my subjects, but got the response that the message was too big, and therefore 
it was rejected. So how should I upload the image? The images are T1-weighted, 
3D, acquired with a 3T scanner, resolution 256 256.

I discovered that FSL does a proper segmentation on this subjects, so I was 
looking for a way to import these segments from FSL into the Freesurfer 
pipeline, but I didn't succeed so far. I used the white matter segment from FSL 
as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol 
to get this segment in the right space, and normalized with mri_normalize. Then 
I rerun recon-all with -autorecon2-wm. But it gives me the error message: 
'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' 
So apparently, the wm.mgz still doesn't have the right size. Do you have any 
experience with this? Or any ideas about this?

Best regards,

Doety

On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Doety
 
 yes, that looks pretty bad. Can you tell us about the acquisition? What 
 resolution/field strength/scan type was it?
 
 If you upload the subject we will take a look
 
 cheers
 Bruce
 On Wed, 9 Jul 2014, Doety 
 Prins 
 wrote:
 
 Dear freesurfer experts,
 
 I experienced some problems with the segmentation of my T1 scans, as both 
 the white surface and the pial surface are placed incorrectly (see attached 
 images). This seems to me to be a too big difference with what it should 
 look like, that I think could not be fixed with the standard 
 troubleshooting strategies.
 
 Do you have any solutions for this? Is it for instance possible to make 
 changes to the recon-all script to shift the surfaces?
 
 Thanks in advance,
 
 Doety
 
 
 ___
 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


Re: [Freesurfer] bad freesurfer segmentation

2014-07-10 Thread Louis Nicholas Vinke
Hi Doety,
Consider these options for uploading data:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

I think recon-all is expecting your wm.mgz to be conformed or 256^3. 
Something like: mri_convert wm.mgz wm.conform.mgz --conform

You would need to rename wm.conform.mgz to wm.mgz, after renaming or 
saving a copy of the current non-conformed wm mask you got from FSL.
-Louis

On Thu, 10 Jul 2014, Doety Prins wrote:

 Hi Bruce,

 Thanks for your reply. In my previous e-mail I already tried to attach one of 
 my subjects, but got the response that the message was too big, and therefore 
 it was rejected. So how should I upload the image? The images are 
 T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256.

 I discovered that FSL does a proper segmentation on this subjects, so I was 
 looking for a way to import these segments from FSL into the Freesurfer 
 pipeline, but I didn't succeed so far. I used the white matter segment from 
 FSL as wm.mgz (in a subject in which I already ran recon-all), I used 
 mri_vol2vol to get this segment in the right space, and normalized with 
 mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me 
 the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != 
 volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right 
 size. Do you have any experience with this? Or any ideas about this?

 Best regards,

 Doety

 On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Doety

 yes, that looks pretty bad. Can you tell us about the acquisition? What
 resolution/field strength/scan type was it?

 If you upload the subject we will take a look

 cheers
 Bruce
 On Wed, 9 Jul 2014, Doety
 Prins
 wrote:

 Dear freesurfer experts,

 I experienced some problems with the segmentation of my T1 scans, as both 
 the white surface and the pial surface are placed incorrectly (see 
 attached images). This seems to me to be a too big difference with what it 
 should look like, that I think could not be fixed with the standard 
 troubleshooting strategies.

 Do you have any solutions for this? Is it for instance possible to make 
 changes to the recon-all script to shift the surfaces?

 Thanks in advance,

 Doety


 ___
 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 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


Re: [Freesurfer] bad freesurfer segmentation

2014-07-09 Thread Bruce Fischl
Hi Doety

yes, that looks pretty bad. Can you tell us about the acquisition? What 
resolution/field strength/scan type was it?

If you upload the subject we will take a look

cheers
Bruce
On Wed, 9 Jul 2014, Doety 
Prins 
wrote:

 Dear freesurfer experts,

 I experienced some problems with the segmentation of my T1 scans, as both 
 the white surface and the pial surface are placed incorrectly (see attached 
 images). This seems to me to be a too big difference with what it should 
 look like, that I think could not be fixed with the standard troubleshooting 
 strategies.

 Do you have any solutions for this? Is it for instance possible to make 
 changes to the recon-all script to shift the surfaces?

 Thanks in advance,

 Doety


___
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.