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] mri_convert PD
The files have been dropped.
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267b417faa9da6f7cff3c36228a
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
if you file drop these volumes we'll take a look
Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match the slice size and
thickness of T2 and PD images to the Freesurfer T1 images, after
converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
--like
${SUBJECT}/mri/norm.nii.gz ${**SUBJECT}/T2/T2_like_norm.nii.**gz
And having no problems. However, using the same code for the PD images I'm
arriving at a bus error each time (output below). Is there any possible
work
around for this?
(freesurfer-Darwin-leopard-**i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl
${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.**nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_**
norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.**gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
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Re: [Freesurfer] mri_convert PD
just took a look. Why is your PD.nii.gz two frames? The problem is
reslicing a 2-frame volume but specifying a volume as a template that
only has 1 frame. We shouldn't be core dumping, but that's the unusual
situation that is causing it.
cheers
Bruce
On Thu, 23 Jun 2011, G. William Chapman IV
wrote:
The files have been
dropped.https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267b417faa9da6f7cff3c36228a
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
if you file drop these volumes we'll take a look
Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match the slice size and
thickness of T2 and PD images to the Freesurfer T1 images, after
converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
--like
${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz
And having no problems. However, using the same code for the PD images I'm
arriving at a bus error each time (output below). Is there any possible
work
around for this?
(freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl
${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz
003_S_0907_M00/PD/PD_like_norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
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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
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Re: [Freesurfer] mri_convert PD
p.s. also, why are you specifying --like and -rl?
On Thu, 23 Jun 2011, G.
William Chapman IV wrote:
The files have been
dropped.https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267b417faa9da6f7cff3c36228a
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
if you file drop these volumes we'll take a look
Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match the slice size and
thickness of T2 and PD images to the Freesurfer T1 images, after
converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
--like
${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz
And having no problems. However, using the same code for the PD images I'm
arriving at a bus error each time (output below). Is there any possible
work
around for this?
(freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl
${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz
003_S_0907_M00/PD/PD_like_norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
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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
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dispose of the e-mail.
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Re: [Freesurfer] mri_convert PD
I'm not sure why the PD would be two frames -- the files were downloaded as
dcm from the ADNI database. After looking through them though, there was a
repeat of the slices, so I removed the second frame. Seems to have solved
the problem, as the reslice is working now.
On Thu, Jun 23, 2011 at 09:28, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
p.s. also, why are you specifying --like and -rl?
On Thu, 23 Jun 2011, G. William Chapman IV wrote:
The files have been dropped.https://www.nmr.mgh.**
harvard.edu/facility/filedrop/**showgroup/24787/1/**
d2a16267b417faa9da6f7cff3c3622**8ahttps://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267b417faa9da6f7cff3c36228a
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
if you file drop these volumes we'll take a look
Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match the slice size
and
thickness of T2 and PD images to the Freesurfer T1 images, after
converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
--like
${SUBJECT}/mri/norm.nii.gz ${**SUBJECT}/T2/T2_like_norm.nii.**gz
And having no problems. However, using the same code for the PD
images I'm
arriving at a bus error each time (output below). Is there any
possible work
around for this?
(freesurfer-Darwin-leopard-**i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl
${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.**
nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl
003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_**
norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.**
gz...
INFO: transform src into the like-volume:
003_S_0907_M00/mri/norm.nii.gz
Bus error
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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
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If the e-mail was sent to you in error
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Re: [Freesurfer] mri_convert PD
glad to hear it
Bruce
On Thu, 23 Jun 2011, G. William Chapman IV wrote:
I'm not sure why the PD would be two frames -- the files were downloaded as
dcm from the ADNI database. After looking through them though, there was a
repeat of the slices, so I removed the second frame. Seems to have solved
the problem, as the reslice is working now.
On Thu, Jun 23, 2011 at 09:28, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
p.s. also, why are you specifying --like and -rl?
On Thu, 23 Jun 2011, G. William Chapman IV wrote:
The files have
beendropped.https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1
/d2a16267b417faa9da6f7cff3c36228a
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
if you file drop these volumes we'll take a look
Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match
the slice size and
thickness of T2 and PD images to the Freesurfer T1
images, after converting
the norm.mgz and the T2/PD images to .nii.gz. For the
T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl
${SUBJECT}/mri/norm.nii.gz --like
${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz
And having no problems. However, using the same code
for the PD images I'm
arriving at a bus error each time (output below). Is
there any possible work
around for this?
(freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl
${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz
${SUBJECT}/PD/PD_like_norm.nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl
003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz
003_S_0907_M00/PD/PD_like_norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50
greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume
003_S_0907_M00/mri/norm.nii.gz...
INFO: transform src into the like-volume:
003_S_0907_M00/mri/norm.nii.gz
Bus error
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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] How to obtain volume of specific structure
You also might want to look at the command asegstats2table to generate a table of all results. Best Martin On Jun 22, 2011, at 10:08 PM, ZhiLiangLong lagosslong1...@163.com wrote: Hi all: After all recon-all -all processing has been completed for all subjects ,I want to obtain volume of specific structure of each subject(e.g., the volume of Caudate Nucleus). But i have no idea about it,Are there some tools or commands that can help? I hope you can give me some suggestions . Thanks! ___ 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.
[Freesurfer] long_mris_slopes
Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán ___ 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] long_mris_slopes
Hi Sean, I think the --out... names need to be without the ending (mgh) so for example --out-avg=long23.thickness-avg Maybe that'll fix it. Best, Martin On Thu, 2011-06-23 at 09:12 -0700, Seán Froudist Walsh wrote: Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán ___ 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] (no subject)
Hi Leo, you will need a T1-weighted image that is about 1mm isotropic cheers Bruce On Thu, 23 Jun 2011, leonardo kay wrote: Hi all Do anyone have experience doing parcellations using AXIAL T2 FLAIR acquisitions? What sequence do you recomend most for parcellation/labelling under freesurfer? Best regards, -- Leo Kay. ___ 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] (no subject)
Hi all Do anyone have experience doing parcellations using AXIAL T2 FLAIR acquisitions? What sequence do you recomend most for parcellation/labelling under freesurfer? Best regards, -- Leo Kay. ___ 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] Does the order of subjects need to match in .fsgd and isxconcat?
Dear freesurfer experts, I have a simple question about the use of isxconcat-sess. I plan to conduct a between-groups analysis later (using mri_glmfit), but as I am creating my osgm using isxconcat-sess, is it is necessary for the text file list of subjects (indicated by -sf) to match the order of subjects in my .fsgd file? Of course the .fsgd file will contain information about the group membership, but I wasn't sure if the order of subj had to line up in both files, nevertheless. Many thanks! ___ 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] Difference in hippocampal volume between scanners
Hi everyone! I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks! Jessica Liu ___ 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] Difference in hippocampal volume between scanners
This is not normal. Maybe you should check the aseg volume for improper segmentation. On Thu, Jun 23, 2011 at 19:27, Jessica Liu jessicali...@gmail.com wrote: Hi everyone! I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks! Jessica Liu ___ 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 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] Difference in hippocampal volume between scanners
Hi Jessica, what were the coils? Certainly you will find substantial differences comparing across both field strength and receive coil. Did the segmentations look reasonable? Was it the same sequence? Bruce On Thu, 23 Jun 2011, Jessica Liu wrote: Hi everyone! I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks! Jessica Liu ___ 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] Difference in hippocampal volume between scanners
Hi Jessica, the 1.5t scan looks kind of washed out and low contrast, but of course it's hard to tell from an image. The 3T looks much crisper. Were the sequence parameters matched? I'm not sure what you're trying to show with this. The 3T multi-channel scan will have a much, much higher SNR than the 1.5T single channel, so the results will not at all be comparable. Bruce On Thu, 23 Jun 2011, Jessica Liu wrote: Looking at the scans (attached, 3T on the left and 1.5T on the right, yellow hippocampus), I think you've made a good point. More comments are much appreciated, thanks! Jessica Liu 2011/6/23 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br This is not normal. Maybe you should check the aseg volume for improper segmentation. On Thu, Jun 23, 2011 at 19:27, Jessica Liu jessicali...@gmail.com wrote: Hi everyone! I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks! Jessica Liu ___ 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 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] Does the order of subjects need to match in .fsgd and isxconcat?
Hi John, they should line up. Technically, if you're just doing an OSGM (one-sample group mean), then the order is not important. But it you want to compare across groups, you need to make sure that the group memberships are properly assigned. doug On 6/23/11 5:05 PM, John Richey wrote: Dear freesurfer experts, I have a simple question about the use of isxconcat-sess. I plan to conduct a between-groups analysis later (using mri_glmfit), but as I am creating my osgm using isxconcat-sess, is it is necessary for the text file list of subjects (indicated by -sf) to match the order of subjects in my .fsgd file? Of course the .fsgd file will contain information about the group membership, but I wasn't sure if the order of subj had to line up in both files, nevertheless. Many thanks! ___ 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.
